Workshop on Analysis and prediction of contacts in proteins

Size: px
Start display at page:

Download "Workshop on Analysis and prediction of contacts in proteins"

Transcription

1 Workshop on Analysis and prediction of contacts in proteins Eran Eyal 1, Vladimir Potapov 2, Ronen Levy 3, Vladimir Sobolev 3 and Marvin Edelman 3 1 Sheba Medical Center, Ramat Gan, Israel; Departments of Biochemistry 2 and Plant Sciences 3, Weizmann Institute of Science, Rehovot, Israel I II III IV Analysis of ligand-protein contacts using LPC and PDBsum Analysis of inter-atomic contacts in proteins and protein-protein interfaces using CSU and CMA Metal binding site prediction using CHED and seqched Predicting side chain conformations using SCCOMP and analysis of equilibrium dynamics (for advanced users) 1

2 I. Analysis of ligand-protein contacts using LPC and PDBsum During this session we will be working with the following software for analysis of interactions in PDB structures: LPC - Ligand-Protein Contacts (Sobolev et al. Bioinformatics, 1999, 15, ) PDBsum: a database of the known 3D structures of proteins and nucleic acids (Laskowski et al., Trends Biochem. Sci., 1997, 22, 488) 1. Enter and click Servers-->LPC/CSU: At the first line choose LPC; at the second line choose JMOL; at the third line type 2fxe in the field "PDB ID code" (HIV-1 protease Crm complexed with the antiretroviral drug Atazanavir); at the fifth line click "run" You should get a list of all the ligands in the structure you chose. 2. Choose size of picture Large ; ligand No 3 (DR7, i.e. Atazanavir, a substituted canedioic acid dimethyl ester) and Click RUN The program gives several options to consider: - Using option CONTACTS GROUPED BY Ligand atoms, find (in the table and picture the most solvent accessible atoms in the protein-ligand complex ( Compl column) and in the protein free of ligand ( Uncompl column); Note, the first atom, called in PDB as CAA, has a large solvent accessible surface in the free ligand, but a relatively high buried surface in the complex. On the other hand, atom CAO has almost the same solvent accessibility in both the free and complexed ligand. - Using option CONTACTS GROUPED BY Residues, find which residues forming the binding pocket have the largest contacts with the ligand. Which of the four mutations M46I, V82F, I84V, L90M, and in which chain, directly influence ligand binding? - Using option CONTACTS SORTED BY - Contact types, find the largest distance for a putative hydrogen bonds (denoted Hb) in the file. What could the distance 5.3 A, between the OBJ atom of the ligand and the N atom of Gly48 chain B signify in this case? Note, the OBJ atom has, in addition, a strong H-bond to a water molecule (HOH 115B). - Using option CONTACTS SORTED BY- residues, find which type of contacts do Asp25, ILE47 and VAL82 form; Note, definition and number of different contact type is provided under the link "Contacts grouped by contact type - Using option DERIVED DATA Complementarity, find the probable results of atom-type substitution for atoms OAI or CAA) in the ligands. Note, in the table obtained, you may see changes in ligand complementarity upon atom replacement. Red and green colours indicates "considerable" decrease and increase in normalized complementarity, respectively. 3. Open: 4. Enter PDB ID 2fxe and click Find 5. At the left side, where it says DR7, click link to "Ligands" 6. The accessed page enables to view the ligand molecule in details and shows the contact distances. 2

3 II Analysis of inter-atomic contacts in proteins and proteinprotein interfaces using CSU and CMA The goal of this exercise is to get acquainted with tools for analysis of interatomic contacts within proteins and in protein-protein interfaces. You will work with two servers: Contacts of Structural Units (CSU) and Contact Map Analysis (CMA). The CSU server (Sobolev et al. Bioinformatics, 1999, 15, ) identifies all atom-atom contacts of any single residue in a particular PDB structure. The CMA server (Sobolev et al. NAR, 2005, 33, W39-W43) identifies all residue-residue contacts in particular PDB structure, represents them in a graphical way (contact map) and provides detailed information on atom contacts between any two chosen residues. Server URLs: CSU (with visualization) CSU (text version) CMA Contacts of Structural Units 1. Load PDB file of HIV protease from by typing 2FXD in the PDB ID field. Press Search and in the resulting page click the link Save to disk. 2. Navigate to the CSU server (with visualization), choose CSU option, load the structure that you locally saved on your computer and press Run. (NOTE: if your structure is deposited in the PDB, you can enter PDB ID and run the analysis. In this exercise you will load locally saved file to get acquainted with this option). 3. The server analyzes content of the PDB file and displays a page where you have to choose ChainID, Residue No and Insertion code of the residue of interest. In this exercise you will analyze contacts of Phe residue in position 82 of chain A. Enter necessary information (leave the field Insertion code blank) and start the analysis by pressing on the Submit. 4. In the displayed page you will see three areas: Navigation menu, Visualization area and Contacts area. Navigation menu is used to choose a preferred way to list atomatom contacts. (NOTE: You can set the size of visualization area in the previous page by choosing Large or Small option). 5. Phe82 is a mutation that may affect the binding of the inhibitor. Does this mutation have a contact with the drug (ligand DR7)? Choose the link CONTACTS GROUPED BY: Residue atoms and examine contacts of atoms in aromatic ring of Phe82. (How many atoms in Phe82? How many contacts for each atom? Is a particular atom buried or exposed in protein structure?) 6. Choose the link CONTACTS GROUPED BY: Residues and examine what residues make contacts with Phe82. (How many residues are in contact with Phe82? What is the minimal distance between two contacting residues? What is a contact surface area between two residues? How many atom-atom contacts between two residues?) 3

4 7. Choose the link CONTACTS GROUPED BY: Contact types and examine different types of contacts (hydrogen bonds, hydrophobic contacts, etc.) formed by Phe82. (How many hydrogen bonds are formed with Phe82? How many aromataromat contacts, etc.?) 8. The menu CONTACTS SORTED BY gives detailed information about all atom-atom contacts between Phe82 and neighboring residues. There three different options to sort list of atoms (Residue atoms/residues/contact types). Try them. 9. You can choose a different residue or a PDB file for analysis by clicking on appropriate link in GO TO menu. A short description of CSU approach is given under Help menu. 10. Analyze H bonds formed by HOH 115B in the PDB entry 2FXE from the first exercise. 11. A text version of the CSU server is also available (see URL above). It essentially provides the same information but in a printer-friendly way. Contact Map Analysis 1. Navigate to the CMA server. Choose the locally saved PDB file in the appropriate field of the web form. Enter A in the field Chain #1 and enter B in the field Chain #2 and run the analysis by pressing Submit. 2. In the displayed page (Contact Map screen), all contacts in the interface between chain A and chain B of the submitted structure are represented as a contact map. 3. Take a look at the left side of the contact map. You will see all residues in chain A that make contacts with residues in chain B. At the top of the contact map you will see all residues in chain B. (NOTE: you can find detailed information on all atomatom and residue-residue contacts at the bottom of the page. Explore links to Full list of atom-atom contacts and to List of displayed residue-residue contacts), 4. Each residue-residue contact in the interface between chains A and B is represented as a blue square. When you click on any blue square you get detailed information on all atom-atom contacts between two selected residues. You can display any atomatom contact in the visualization area by clicking on appropriate check-box. 5. Analyze which contacts are formed with Phe82 (chain A) across the interface? 6. Links to a more detailed CSU analysis are provided for two residues at the bottom of the screen. 7. The CMA server can analyze contacts not only between two chains but also within a chain. To do this, enter the same chain identifier in the fields Chain #1 and Chain #2. Enter 2FXD in the PDB ID field, enter A in Chain #1 and Chain #2 fields and press Submit button. You will get all contacts within chain A in HIV protease. 4

5 8. Note, that you can change the size of the contact map by choosing different Scale parameter of the main page of the CMA server. You can also display only contacts that have contact area above chosen threshold. 9. You can compare contact maps for the wild type (2FXE) and the mutant (2FXD) structures of HIV protease by opening them in two browser windows. 5

6 III Metal binding site prediction using CHED and seqched Often proteins bind metal ions at the catalytic site or at regions important for structure. To predict these regions in the protein, two alternative procedures can be applied depending on your available input data. Structure-based Prediction (CHED) (Babor et al., Proteins, 2008, 70, ) 1. Access the CHED website at: The approach uses a PDB protein as an input. Therefore, it should be applied only in case the protein was resolved structurally. 2. Check whether the crystal structure of the human P53 core domain is predicted to bind a metal: Scroll down to the box where you are asked to insert a PDB ID code, and type "1UOL". At the box on the right add the chain id A. Click on the Run. 3. The procedure offers two types of predictions, with different degrees of confidence: Mild filtration and Stringent filtration. The mild filter eliminates some of the false predictions keeping almost all correct predictions. In contrast, the stringent filter eliminates most false predictions at the expense of loosing some true predictions. Click on the link Stringent filtration. How many residues were predicted? Now click on the link Mild filtration How many residues were predicted? Among the predicted residues by mild, which residues are more probable to bind metal? 4. In the java applet you can view the protein structure. The predicted residues are colored in green. Right click on the applet, and select zoom and increase to 200% in case you would like to have a better view of the predicted metal site. Sequence-based Prediction (SeqCHED) (Levy et al, Proteins, 2009, 76, ) 1.Access the SeqCHED website at: The approach uses a protein sequence as an input. Therefore, it can be applied in case the protein was not resolved structurally. 2. Scroll down to the first part of the instructions where it says "1) Click on button to select option". Here you are offered to choose whether you would like to give a protein sequence as an input for analysis, or give the Uniprot/Swissprot protein sequence ID. Mark the option where it says "Insert UniProt sequence ID" and type "Q4A7M9" in the associated box. The relevant sequence of mannose-6-phosphate isomerase will be downloaded automatically when you will activate the procedure. 3. The results will be sent to your address. Therefore, type an address where it says "2) Results will be sent to your address". Click on the Submit. 4. The application will check for homology of your target sequence to PDB templates. Open the mail sent to you, and access the associated link. 5. Scroll down to the table below. How many templates did you get? The procedure will model in 3D the side-chains of your sequence on the backbone of the template you select. Which template is probable to give a better prediction (compare the sequence identity, structural resolution, and existence of metal in the template)? 6. Click on the template you prefer where it says, "prediction using ". 7. How many metal binding sites are predicted by the stringent filter? How many are predicted by the mild filter? Which of them is more probable to be a true one? 6

7 IV Predicting side chain conformations using SCCOMP and analysis of equilibrium dinamics (for advanced users). Modeling of side chain conformations 1. Placing of side chains on a fixed backbone is an important final step for building a complete structural model of proteins. It is also needed in order to model point mutations and to complete missing structural information in experiments. 2. In this exercise we will know a tool for structural modeling of side chains, get to feel the quality of the prediction of such tools and use it to model mutations. 3. During the exercise we will work with HIV-1 protease, a major target for HIV drugs. This protein cleaves the pre-mature viral peptides and allows the formation of mature proteins needed to complete the viral cell cycle. HIV-1 protease is a homodimer with two identical subunits of 99 amino-acids each. Most of the FDA approved drugs against HIV are targeted to block the enzymatic activity of this protein. We will work with X-ray crystallographic structures of HIV-1 protease resolved with the inhibitor 4. Download from one of the PDB browsers such as OCA (HYPERLINK the structures of two structures of HIVprotease with the inhibitor Atazanavir. The PDB codes are 2fxd and 2aqu. 5. Open the SCCOMP server foe side chain modeling at: HYPERLINK ignmtest.ccbb.pitt.edu/sccomp.html. This is a web interface for the program SCCOMP (Eyal et al., J. Comput Chem, 2004, 25: ) which makes on line modeling of side chain conformations. The scoring function of this program is based on contact surface areas. 6. We will first get a general impression for the quality of the prediction by placing all side chains on the backbone and compare to the real positions of the side chains (known in this case). 7. Enter PDB code 2fxd under "Enter PDB id". In the pull down titled "Output PDB file" choose "Input coordinates and model". You will get back a file which includes both the prediction and the original side chains deposited in the file. Enter an internet-based account (such as gmail or hotmail) and submit. The calculation takes less than a minute and after that you will receive an with the resulting model attached. 8. Open the and save the model. Open the file in a molecular graphics program such as Rasmol and color it according by models. 9. Which residues are predicted more accurately buried or exposed? Which residues are predicted better, those with aromatic rings or linear side chains? 10. Select residue 82. Note that the Phenylalanine in this position is a mutation which is a well known drug-resistance mutation rapidly evolved against several drugs. Does the program successfully model the side chain of this Phenylalanine? Which type of interaction is formed between the Phenylalanine and the inhibitor? 7

8 11. Do you think that this mutation will be affective as a drug resistant mutation against Atazanavir? 12. We will now mutate the protein in this position in silico back to the wild type residue which is Valine in this case. Go back to the SCCOMP web site. Enter again "2fxd". Now go to the "To model a residue" form and enter in positions 82 of chains A and B the residue VAL. Under the "Output PDB file" pull down choose now "Model only". Only coordinates of the model will be retrieved. Open the model that you get. Is there still an interaction between the Valine and the Atazanavir? You can use LPC to check the interactions between position 82 and the inhibitor. Note, SCCOMP can be downloaded locally to unix/linux platforms. This can be useful when we want to run the program by automatically for many structures/mutations. Equilibrium dynamics It is now clear that in many cases understanding the motion of molecular machines is crucial to elucidating their function. In this exercise we will get to know a simple tool for analysis of the basic cooperative motions of a molecule in equilibrium state, the Anisotropic Network Model (ANM). This tool performs a simple type of normal mode analysis. During the exercise we will work with HIV-1 protease, the major target for HIV drugs. This protein cleaves the pre-mature viral peptides and allows the formation of mature proteins needed to complete the viral cell cycle. 1. Open the ANM server (Eyal E, Bioinformatics. 2006, 22: ) at: This web interface takes as input PDB coordinates and performs the calculations to determine the dynamics of the system in this state. 2. In the "Enter the PDB id of your protein" form, enter the PDB code 2fxd. Leave the "*" symbol for the chain ID such that the calculations will include both subunits of this dimer. Also leave the other parameters unchanged. Submit. 3. The calculation will take several seconds, after which you will be looking at the motion of this molecule, which is displayed as a network of interacting residues. Red colors indicate more mobile regions and blue colors indicate static regions. 4. Select the "chain connectivity" bottom in order to see the molecule as a backbone trace and colored according to its subunits. You may watch more easily the direction of the motion by checking on the "vectors" box. 5. The region between residues is known as the "flap" region of HIV protease. This is a highly mobile region which controls the access of soluble molecules into the active site. Use the "Labels" pull-down to label some of the residues in the flap region. 8

9 6. The basic motion of the molecule is decomposed to normal modes. As a default, you are watching the mode which exhibits the most cooperative and slow motion. You can watch other modes (the 20 slowest modes) by changing the current visible mode in the "Modes" pull down. 7. Determine in which modes the flap region is more mobile among the slowest 10 modes. These modes are assumed to be functionally relevant for the purpose of accessibility to the binding site. 8. The simplest way to evaluate the prediction of the ANM model is to compare the magnitude of fluctuations of each residue to that found experimentally in the X-ray crystallography the B-factors profile. Open the "B-factors/mode fluctuations" link at the bottom of the page. Compare the theoretical fluctuations predicted by the model (which are summed over all normal modes) and the experimental B-factors. The correlation coefficient between the two curves is The residues involved in the catalytic reaction are located at positions Residues crucial for many inhibitors binding sites are located also around residue 50. Check in the graphs: are these regions relatively mobile or static? Can you think why? 10. You can try the ANM server on your own favorite PDB structure. 9

Term Definition Example Amino Acids

Term Definition Example Amino Acids Name 1. What are some of the functions that proteins have in a living organism. 2. Define the following and list two amino acids that fit each description. Term Definition Example Amino Acids Hydrophobic

More information

Lecture 10 More about proteins

Lecture 10 More about proteins Lecture 10 More about proteins Today we're going to extend our discussion of protein structure. This may seem far-removed from gene cloning, but it is the path to understanding the genes that we are cloning.

More information

Project Manual Bio3055. Cholesterol Homeostasis: HMG-CoA Reductase

Project Manual Bio3055. Cholesterol Homeostasis: HMG-CoA Reductase Project Manual Bio3055 Cholesterol Homeostasis: HMG-CoA Reductase Bednarski 2003 Funded by HHMI Cholesterol Homeostasis: HMG-CoA Reductase Introduction: HMG-CoA Reductase is an enzyme in the cholesterol

More information

HOMEWORK II and Swiss-PDB Viewer Tutorial DUE 9/26/03 62 points total. The ph at which a peptide has no net charge is its isoelectric point.

HOMEWORK II and Swiss-PDB Viewer Tutorial DUE 9/26/03 62 points total. The ph at which a peptide has no net charge is its isoelectric point. BIOCHEMISTRY I HOMEWORK II and Swiss-PDB Viewer Tutorial DUE 9/26/03 62 points total 1). 8 points total T or F (2 points each; if false, briefly state why it is false) The ph at which a peptide has no

More information

BIOCHEMISTRY I HOMEWORK III DUE 10/15/03 66 points total + 2 bonus points = 68 points possible Swiss-PDB Viewer Exercise Attached

BIOCHEMISTRY I HOMEWORK III DUE 10/15/03 66 points total + 2 bonus points = 68 points possible Swiss-PDB Viewer Exercise Attached BIOCHEMISTRY I HOMEWORK III DUE 10/15/03 66 points total + 2 bonus points = 68 points possible Swiss-PDB Viewer Exercise Attached 1). 20 points total T or F (2 points each; if false, briefly state why

More information

The Hospital Anxiety and Depression Scale Guidance and Information

The Hospital Anxiety and Depression Scale Guidance and Information The Hospital Anxiety and Depression Scale Guidance and Information About Testwise Testwise is the powerful online testing platform developed by GL Assessment to host its digital tests. Many of GL Assessment

More information

SMPD 287 Spring 2015 Bioinformatics in Medical Product Development. Final Examination

SMPD 287 Spring 2015 Bioinformatics in Medical Product Development. Final Examination Final Examination You have a choice between A, B, or C. Please email your solutions, as a pdf attachment, by May 13, 2015. In the subject of the email, please use the following format: firstname_lastname_x

More information

TMWSuite. DAT Interactive interface

TMWSuite. DAT Interactive interface TMWSuite DAT Interactive interface DAT Interactive interface Using the DAT Interactive interface Using the DAT Interactive interface... 1 Setting up the system to use the DAT Interactive interface... 1

More information

Structural Analysis of TCRpMHC Complexes Using Computational Tools. Feroze Mohideen Briarcliff High School

Structural Analysis of TCRpMHC Complexes Using Computational Tools. Feroze Mohideen Briarcliff High School Structural Analysis of TCRpMHC Complexes Using Computational Tools Feroze Mohideen Briarcliff High School TCR-pMHC Complexes Peptide Structure of TCR-pMHC complex PDB AO7 Crossreactivity is the ability

More information

IMPaLA tutorial.

IMPaLA tutorial. IMPaLA tutorial http://impala.molgen.mpg.de/ 1. Introduction IMPaLA is a web tool, developed for integrated pathway analysis of metabolomics data alongside gene expression or protein abundance data. It

More information

User Guide. Protein Clpper. Statistical scoring of protease cleavage sites. 1. Introduction Protein Clpper Analysis Procedure...

User Guide. Protein Clpper. Statistical scoring of protease cleavage sites. 1. Introduction Protein Clpper Analysis Procedure... User Guide Protein Clpper Statistical scoring of protease cleavage sites Content 1. Introduction... 2 2. Protein Clpper Analysis Procedure... 3 3. Input and Output Files... 9 4. Contact Information...

More information

OneTouch Reveal Web Application. User Manual for Healthcare Professionals Instructions for Use

OneTouch Reveal Web Application. User Manual for Healthcare Professionals Instructions for Use OneTouch Reveal Web Application User Manual for Healthcare Professionals Instructions for Use Contents 2 Contents Chapter 1: Introduction...4 Product Overview...4 Intended Use...4 System Requirements...

More information

Amino Acids. Review I: Protein Structure. Amino Acids: Structures. Amino Acids (contd.) Rajan Munshi

Amino Acids. Review I: Protein Structure. Amino Acids: Structures. Amino Acids (contd.) Rajan Munshi Review I: Protein Structure Rajan Munshi BBSI @ Pitt 2005 Department of Computational Biology University of Pittsburgh School of Medicine May 24, 2005 Amino Acids Building blocks of proteins 20 amino acids

More information

Hands-On Ten The BRCA1 Gene and Protein

Hands-On Ten The BRCA1 Gene and Protein Hands-On Ten The BRCA1 Gene and Protein Objective: To review transcription, translation, reading frames, mutations, and reading files from GenBank, and to review some of the bioinformatics tools, such

More information

Molecular Dynamics of HIV-1 Reverse Transcriptase

Molecular Dynamics of HIV-1 Reverse Transcriptase Molecular Dynamics of HIV-1 Reverse Transcriptase Abderrahmane Benghanem Rensselaer Polytechnic Institute,Troy, NY Mentor: Dr. Maria Kurnikova Carnegie Mellon, Pittsburgh PA Outline HIV-1 Reverse Transcriptase

More information

Phenylketonuria (PKU) Structure of Phenylalanine Hydroxylase. Biol 405 Molecular Medicine

Phenylketonuria (PKU) Structure of Phenylalanine Hydroxylase. Biol 405 Molecular Medicine Phenylketonuria (PKU) Structure of Phenylalanine Hydroxylase Biol 405 Molecular Medicine 1998 Crystal structure of phenylalanine hydroxylase solved. The polypeptide consists of three regions: Regulatory

More information

User Instruction Guide

User Instruction Guide User Instruction Guide Table of Contents Logging In and Logging Out of MMSx 1 Creating a TPN (Terminal Profile Number) 2 Single Merchant 2 From Navigation Bar 2 From Home Page Link 4 Multiple Merchants

More information

Excerpt from J. Mol. Biol. (2002) 320, :

Excerpt from J. Mol. Biol. (2002) 320, : Excerpt from J. Mol. Biol. (2002) 320, 1095 1108: Crystal Structure of the Ternary Complex of the Catalytic Domain of Human Phenylalanine Hydroxylase with Tetrahydrobiopterin and 3-(2-Thienyl)-L-alanine,

More information

Detergent solubilised 5 TMD binds pregnanolone at the Q245 neurosteroid potentiation site.

Detergent solubilised 5 TMD binds pregnanolone at the Q245 neurosteroid potentiation site. Supplementary Figure 1 Detergent solubilised 5 TMD binds pregnanolone at the Q245 neurosteroid potentiation site. (a) Gel filtration profiles of purified 5 TMD samples at 100 nm, heated beforehand for

More information

Lionbridge Connector for Hybris. User Guide

Lionbridge Connector for Hybris. User Guide Lionbridge Connector for Hybris User Guide Version 2.1.0 November 24, 2017 Copyright Copyright 2017 Lionbridge Technologies, Inc. All rights reserved. Published in the USA. March, 2016. Lionbridge and

More information

Project Manual Bio3055. Apoptosis: Superoxide Dismutase I

Project Manual Bio3055. Apoptosis: Superoxide Dismutase I Project Manual Bio3055 Apoptosis: Superoxide Dismutase I Bednarski 2003 Funded by HHMI Apoptosis: Superoxide Dismutase I Introduction: Apoptosis is another name for programmed cell death. It is a series

More information

USER GUIDE: NEW CIR APP. Technician User Guide

USER GUIDE: NEW CIR APP. Technician User Guide USER GUIDE: NEW CIR APP. Technician User Guide 0 Table of Contents 1 A New CIR User Interface Why?... 3 2 How to get started?... 3 3 Navigating the new CIR app. user interface... 6 3.1 Introduction...

More information

Arginine side chain interactions and the role of arginine as a mobile charge carrier in voltage sensitive ion channels. Supplementary Information

Arginine side chain interactions and the role of arginine as a mobile charge carrier in voltage sensitive ion channels. Supplementary Information Arginine side chain interactions and the role of arginine as a mobile charge carrier in voltage sensitive ion channels Craig T. Armstrong, Philip E. Mason, J. L. Ross Anderson and Christopher E. Dempsey

More information

List of Figures. List of Tables

List of Figures. List of Tables Supporting Information for: Signaling Domain of Sonic Hedgehog as Cannibalistic Calcium-Regulated Zinc-Peptidase Rocio Rebollido-Rios 1, Shyam Bandari 3, Christoph Wilms 1, Stanislav Jakuschev 1, Andrea

More information

Trilateral Project WM4

Trilateral Project WM4 ANNEX 2: Comments of the JPO Trilateral Project WM4 Comparative studies in new technologies Theme: Comparative study on protein 3-dimensional (3-D) structure related claims 1. Introduction As more 3-D

More information

May 2003: Hemoglobin Red Blood, Blue Blood Use and Abuse of Hemoglobin

May 2003: Hemoglobin Red Blood, Blue Blood Use and Abuse of Hemoglobin Red Blood, Blue Blood Ever wondered why blood vessels appear blue? Oxygenated blood is bright red: when you are cut, the blood you see is brilliant red oxygenated blood. Deoxygenated blood is deep purple:

More information

Clay Tablet Connector for hybris. User Guide. Version 1.5.0

Clay Tablet Connector for hybris. User Guide. Version 1.5.0 Clay Tablet Connector for hybris User Guide Version 1.5.0 August 4, 2016 Copyright Copyright 2005-2016 Clay Tablet Technologies Inc. All rights reserved. All rights reserved. This document and its content

More information

Introduction to Protein Structure Collection

Introduction to Protein Structure Collection Introduction to Protein Structure Collection Teaching Points This collection is designed to introduce students to the concepts of protein structure and biochemistry. Different activities guide students

More information

Student Guide. Concluding module. Visualizing proteins

Student Guide. Concluding module. Visualizing proteins Student Guide Concluding module Visualizing proteins Developed by bioinformaticsatschool.eu (part of NBIC) Text Hienke Sminia Illustrations Bioinformaticsatschool.eu Yasara.org All the included material

More information

7.014 Problem Set 2 Solutions

7.014 Problem Set 2 Solutions 7.014 Problem Set 2 Solutions Please print out this problem set and record your answers on the printed copy. Answers to this problem set are to be turned in at the box outside 68-120 by 11:45 Friday, February

More information

Ras and Cell Signaling Exercise

Ras and Cell Signaling Exercise Ras and Cell Signaling Exercise Learning Objectives In this exercise, you will use, a protein 3D- viewer, to explore: the structure of the Ras protein the active and inactive state of Ras and the amino

More information

FIRM. Full Iterative Relaxation Matrix program

FIRM. Full Iterative Relaxation Matrix program FIRM Full Iterative Relaxation Matrix program FIRM is a flexible program for calculating NOEs and back-calculated distance constraints using the full relaxation matrix approach. FIRM is an interactive

More information

Data mining with Ensembl Biomart. Stéphanie Le Gras

Data mining with Ensembl Biomart. Stéphanie Le Gras Data mining with Ensembl Biomart Stéphanie Le Gras (slegras@igbmc.fr) Guidelines Genome data Genome browsers Getting access to genomic data: Ensembl/BioMart 2 Genome Sequencing Example: Human genome 2000:

More information

Instructor Guide to EHR Go

Instructor Guide to EHR Go Instructor Guide to EHR Go Introduction... 1 Quick Facts... 1 Creating your Account... 1 Logging in to EHR Go... 5 Adding Faculty Users to EHR Go... 6 Adding Student Users to EHR Go... 8 Library... 9 Patients

More information

ProScript User Guide. Pharmacy Access Medicines Manager

ProScript User Guide. Pharmacy Access Medicines Manager User Guide Pharmacy Access Medicines Manager Version 3.0.0 Release Date 01/03/2014 Last Reviewed 11/04/2014 Author Rx Systems Service Desk (T): 01923 474 600 Service Desk (E): servicedesk@rxsystems.co.uk

More information

Entering HIV Testing Data into EvaluationWeb

Entering HIV Testing Data into EvaluationWeb Entering HIV Testing Data into EvaluationWeb User Guide Luther Consulting, LLC July, 2014/v2.2 All rights reserved. Table of Contents Introduction... 3 Accessing the CTR Form... 4 Overview of the CTR Form...

More information

About REACH: Machine Captioning for Video

About REACH: Machine Captioning for Video About REACH: Machine Captioning for Video REACH is a machine captioning service provided as a part of Kaltura. Starting July 1, 2018, REACH automatically captions and tags all new videos created with Kaltura

More information

BlueBayCT - Warfarin User Guide

BlueBayCT - Warfarin User Guide BlueBayCT - Warfarin User Guide December 2012 Help Desk 0845 5211241 Contents Getting Started... 1 Before you start... 1 About this guide... 1 Conventions... 1 Notes... 1 Warfarin Management... 2 New INR/Warfarin

More information

Anders Hansson. A closer look at proteins! The compact version

Anders Hansson. A closer look at proteins! The compact version Anders Hansson A closer look at proteins! The compact version The first lesson Introduction ----------------------------------------- 1 Download -------------------------------------------- 2 RasWin-----------------------------------------------

More information

Chemical Mechanism of Enzymes

Chemical Mechanism of Enzymes Chemical Mechanism of Enzymes Enzyme Engineering 5.2 Definition of the mechanism 1. The sequence from substrate(s) to product(s) : Reaction steps 2. The rates at which the complex are interconverted 3.

More information

Catalysis & specificity: Proteins at work

Catalysis & specificity: Proteins at work Catalysis & specificity: Proteins at work Introduction Having spent some time looking at the elements of structure of proteins and DNA, as well as their ability to form intermolecular interactions, it

More information

Diabetes Management Software V1.3 USER S MANUAL

Diabetes Management Software V1.3 USER S MANUAL Diabetes Management Software V1.3 Manufacturer: BIONIME CORPORATION No. 100, Sec. 2, Daqing St., South Dist., Taichung City 40242, Taiwan http: //www.bionime.com E-mail: info@bionime.com Made in Taiwan

More information

Table of Contents Morning Set-up (GSI equipment, only)... 2 Opening AudBase... 3 Choosing a patient... 3 Performing Pure-Tone Air & Bone

Table of Contents Morning Set-up (GSI equipment, only)... 2 Opening AudBase... 3 Choosing a patient... 3 Performing Pure-Tone Air & Bone AudBase Guidebook Table of Contents Morning Set-up (GSI equipment, only)... 2 Opening AudBase... 3 Choosing a patient... 3 Performing Pure-Tone Air & Bone Conduction... 6 Testing using a GSI-61 Audiometer:...

More information

Protein Investigator. Protein Investigator - 3

Protein Investigator. Protein Investigator - 3 Protein Investigator Objectives To learn more about the interactions that govern protein structure. To test hypotheses regarding protein structure and function. To design proteins with specific shapes.

More information

OncoPPi Portal A Cancer Protein Interaction Network to Inform Therapeutic Strategies

OncoPPi Portal A Cancer Protein Interaction Network to Inform Therapeutic Strategies OncoPPi Portal A Cancer Protein Interaction Network to Inform Therapeutic Strategies 2017 Contents Datasets... 2 Protein-protein interaction dataset... 2 Set of known PPIs... 3 Domain-domain interactions...

More information

Module 3: Pathway and Drug Development

Module 3: Pathway and Drug Development Module 3: Pathway and Drug Development Table of Contents 1.1 Getting Started... 6 1.2 Identifying a Dasatinib sensitive cancer signature... 7 1.2.1 Identifying and validating a Dasatinib Signature... 7

More information

Walkthrough

Walkthrough 0 8. Walkthrough Simulate Product. Product selection: Same look as estore. Filter Options: Technology levels listed by descriptor words. Simulate: Once product is selected, shows info and feature set Order

More information

Chapter 1: Managing workbooks

Chapter 1: Managing workbooks Chapter 1: Managing workbooks Module A: Managing worksheets You use the Insert tab on the ribbon to insert new worksheets. True or False? Which of the following are options for moving or copying a worksheet?

More information

Hemoglobin & Sickle Cell Anemia Exercise

Hemoglobin & Sickle Cell Anemia Exercise Name StarBiochem Hemoglobin & Sickle Cell Anemia Exercise Learning Objectives In this exercise, you will use StarBiochem, a protein 3D viewer, to explore the structure of the normal hemoglobin protein

More information

Agile Product Lifecycle Management for Process

Agile Product Lifecycle Management for Process Nutrition Surveillance Management User Guide Release 5.2.1 Part No. E13901-01 September 2008 Copyrights and Trademarks Copyright 1995, 2008, Oracle Corporation and/or its affiliates. All rights reserved.

More information

HOW TO USE THE BENCHMARK CALENDAR SYSTEM

HOW TO USE THE BENCHMARK CALENDAR SYSTEM HOW TO USE THE BENCHMARK CALENDAR SYSTEM 1. Go to Website http://doris.clk.co.st-johns.fl.us/benchmarkweb 2. You can use Firefox or Internet Explorer 11 to login to Benchmark. Compatibility mode is no

More information

Cancer Rates and Cement Plants 1

Cancer Rates and Cement Plants 1 Cancer Rates and Cement Plants 1 Introduction: I designed this lesson because I am concerned with the waste produced from Lafarge Corporation in Alpena, MI. Lafarge is a cement plant that incinerates toxic

More information

Biological Mass Spectrometry. April 30, 2014

Biological Mass Spectrometry. April 30, 2014 Biological Mass Spectrometry April 30, 2014 Mass Spectrometry Has become the method of choice for precise protein and nucleic acid mass determination in a very wide mass range peptide and nucleotide sequencing

More information

Elemental Kinection. Requirements. 2 May Version Texas Christian University, Computer Science Department

Elemental Kinection. Requirements. 2 May Version Texas Christian University, Computer Science Department Elemental Kinection Requirements Version 2.1 2 May 2016 Elemental Kinection Requirements i Revision History All revision history listed below. Version Change Summary Date 1.0 Initial Draft 10 November

More information

Chemical Nature of the Amino Acids. Table of a-amino Acids Found in Proteins

Chemical Nature of the Amino Acids. Table of a-amino Acids Found in Proteins Chemical Nature of the Amino Acids All peptides and polypeptides are polymers of alpha-amino acids. There are 20 a- amino acids that are relevant to the make-up of mammalian proteins (see below). Several

More information

CS612 - Algorithms in Bioinformatics

CS612 - Algorithms in Bioinformatics Spring 2016 Protein Structure February 7, 2016 Introduction to Protein Structure A protein is a linear chain of organic molecular building blocks called amino acids. Introduction to Protein Structure Amine

More information

Biochemistry 15 Doctor /7/2012

Biochemistry 15 Doctor /7/2012 Heme The Heme is a chemical structure that diffracts by light to give a red color. This chemical structure is introduced to more than one protein. So, a protein containing this heme will appear red in

More information

User Manual. RaySafe i2 dose viewer

User Manual. RaySafe i2 dose viewer User Manual RaySafe i2 dose viewer 2012.03 Unfors RaySafe 5001048-A All rights are reserved. Reproduction or transmission in whole or in part, in any form or by any means, electronic, mechanical or otherwise,

More information

Automated process to create snapshot reports based on the 2016 Murray Community-based Groups Capacity Survey: User Guide Report No.

Automated process to create snapshot reports based on the 2016 Murray Community-based Groups Capacity Survey: User Guide Report No. research for a sustainable future Automated process to create snapshot reports based on the 2016 Murray Community-based Groups Capacity Survey: User Guide Report No. 116 Steven Vella Gail Fuller Michael

More information

SAM Teacher s Guide Four Levels of Protein Structure

SAM Teacher s Guide Four Levels of Protein Structure SAM Teacher s Guide Four Levels of Protein Structure Overview Students explore how protein folding creates distinct, functional proteins by examining each of the four different levels of protein structure.

More information

CEU MASS MEDIATOR USER'S MANUAL Version 2.0, 31 st July 2017

CEU MASS MEDIATOR USER'S MANUAL Version 2.0, 31 st July 2017 CEU MASS MEDIATOR USER'S MANUAL Version 2.0, 31 st July 2017 1. Introduction... 2 1.1. System Requirements... 2 2. Peak search... 3 2.1. Simple Search... 3 2.2. Advanced Search... 5 2.3. Batch Search...

More information

Q: How do I get the protein concentration in mg/ml from the standard curve if the X-axis is in units of µg.

Q: How do I get the protein concentration in mg/ml from the standard curve if the X-axis is in units of µg. Photometry Frequently Asked Questions Q: How do I get the protein concentration in mg/ml from the standard curve if the X-axis is in units of µg. Protein standard curves are traditionally presented as

More information

BIOL 458 BIOMETRY Lab 7 Multi-Factor ANOVA

BIOL 458 BIOMETRY Lab 7 Multi-Factor ANOVA BIOL 458 BIOMETRY Lab 7 Multi-Factor ANOVA PART 1: Introduction to Factorial ANOVA ingle factor or One - Way Analysis of Variance can be used to test the null hypothesis that k or more treatment or group

More information

Hemoglobin & Sickle Cell Anemia Exercise

Hemoglobin & Sickle Cell Anemia Exercise Name StarBiochem Hemoglobin & Sickle Cell Anemia Exercise Background Hemoglobin is the protein in red blood cells responsible for carrying oxygen from the lungs to the rest of the body and for returning

More information

Molecular Graphics Perspective of Protein Structure and Function

Molecular Graphics Perspective of Protein Structure and Function Molecular Graphics Perspective of Protein Structure and Function VMD Highlights > 20,000 registered Users Platforms: Unix (16 builds) Windows MacOS X Display of large biomolecules and simulation trajectories

More information

We are going to talk about two classifications of proteins: fibrous & globular.

We are going to talk about two classifications of proteins: fibrous & globular. Slide # 13 (fibrous proteins) : We are going to talk about two classifications of proteins: fibrous & globular. *fibrous proteins: (dense fibers) *Their structures are mainly formed of the secondary structure

More information

Supplementary Figure 1 (previous page). EM analysis of full-length GCGR. (a) Exemplary tilt pair images of the GCGR mab23 complex acquired for Random

Supplementary Figure 1 (previous page). EM analysis of full-length GCGR. (a) Exemplary tilt pair images of the GCGR mab23 complex acquired for Random S1 Supplementary Figure 1 (previous page). EM analysis of full-length GCGR. (a) Exemplary tilt pair images of the GCGR mab23 complex acquired for Random Conical Tilt (RCT) reconstruction (left: -50,right:

More information

Pathway Exercises Metabolism and Pathways

Pathway Exercises Metabolism and Pathways 1. Find the metabolic pathway for glycolysis. For this exercise use PlasmoDB.org Pathway Exercises Metabolism and Pathways a. Navigate to the search page for Identify Metabolic Pathways based on Pathway

More information

Biochemistry - I. Prof. S. Dasgupta Department of Chemistry Indian Institute of Technology, Kharagpur Lecture 1 Amino Acids I

Biochemistry - I. Prof. S. Dasgupta Department of Chemistry Indian Institute of Technology, Kharagpur Lecture 1 Amino Acids I Biochemistry - I Prof. S. Dasgupta Department of Chemistry Indian Institute of Technology, Kharagpur Lecture 1 Amino Acids I Hello, welcome to the course Biochemistry 1 conducted by me Dr. S Dasgupta,

More information

ARV Mode of Action. Mode of Action. Mode of Action NRTI. Immunopaedia.org.za

ARV Mode of Action. Mode of Action. Mode of Action NRTI. Immunopaedia.org.za ARV Mode of Action Mode of Action Mode of Action - NRTI Mode of Action - NNRTI Mode of Action - Protease Inhibitors Mode of Action - Integrase inhibitor Mode of Action - Entry Inhibitors Mode of Action

More information

Cbl ubiquitin ligase: Lord of the RINGs

Cbl ubiquitin ligase: Lord of the RINGs Cbl ubiquitin ligase: Lord of the RINGs Not just quite interesting - really interesting! A cell must be able to degrade proteins when their activity is no longer required. Many eukaryotic proteins are

More information

CoCoLysis: A Web-Accessible Coiled-Coil Protein Database with Analysis Tools

CoCoLysis: A Web-Accessible Coiled-Coil Protein Database with Analysis Tools CoCoLysis: A Web-Accessible Coiled-Coil Protein Database with Analysis Tools David Brinkmann, Sai Nandoor, Jugal Kalita, Brian Tripet AND Robert Hodges sainandoor@hotmail.com, david.brinkmann@hp.com, kalita@pikespeak.uccs.edu

More information

Contour Diabetes app User Guide

Contour Diabetes app User Guide Contour Diabetes app User Guide Contents iii Contents Chapter 1: Introduction...5 About the CONTOUR DIABETES app...6 System and Device Requirements...6 Intended Use...6 Chapter 2: Getting Started...7

More information

Getting Started.

Getting Started. Getting Started www.scientificbraintrainingpro.com Summary 1. First steps... 2 2. Log in... 2 3. Create an account for a patient... 3 4. Access an exercise with this patient... 4 5. Viewing the results

More information

GST: Step by step Build Diary page

GST: Step by step Build Diary page GST: At A Glance The home page has a brief overview of the GST app. Navigate through the app using either the buttons on the left side of the screen, or the forward/back arrows at the bottom right. There

More information

Study on Different types of Structure based Properties in Human Membrane Proteins

Study on Different types of Structure based Properties in Human Membrane Proteins 2017 IJSRST Volume 3 Issue 7 Print ISSN: 2395-6011 Online ISSN: 2395-602X Themed Section: Science and Technology Study on Different types of Structure based Properties in Human Membrane Proteins S. C.

More information

Data Management System (DMS) User Guide

Data Management System (DMS) User Guide Data Management System (DMS) User Guide Eversense and the Eversense logo are trademarks of Senseonics, Incorporated. Other brands and their products are trademarks or registered trademarks of their respective

More information

Table of Contents. Contour Diabetes App User Guide

Table of Contents. Contour Diabetes App User Guide Table of Contents Introduction... 3 About the CONTOUR Diabetes App... 3 System and Device Requirements... 3 Intended Use... 3 Getting Started... 3 Downloading CONTOUR... 3 Apple... 3 Android... 4 Quick

More information

Spectrum. Quick Start Tutorial

Spectrum. Quick Start Tutorial Spectrum Quick Start Tutorial March 2005 Table of Contents Introduction... 2 What you will learn... 4 Basic Steps in Using Spectrum... 4 Step 1. Installing Spectrum... 4 Step 2. Changing the language in

More information

Exploring HIV Evolution: An Opportunity for Research Sam Donovan and Anton E. Weisstein

Exploring HIV Evolution: An Opportunity for Research Sam Donovan and Anton E. Weisstein Microbes Count! 137 Video IV: Reading the Code of Life Human Immunodeficiency Virus (HIV), like other retroviruses, has a much higher mutation rate than is typically found in organisms that do not go through

More information

Chymotrypsin Lecture. Aims: to understand (1) the catalytic strategies used by enzymes and (2) the mechanism of chymotrypsin

Chymotrypsin Lecture. Aims: to understand (1) the catalytic strategies used by enzymes and (2) the mechanism of chymotrypsin Chymotrypsin Lecture Aims: to understand (1) the catalytic strategies used by enzymes and (2) the mechanism of chymotrypsin What s so great about enzymes? They accomplish large rate accelerations (10 10-10

More information

Sleep Apnea Therapy Software User Manual

Sleep Apnea Therapy Software User Manual Sleep Apnea Therapy Software User Manual Page ii Notices Revised Notice Trademark Copyright 103392 Rev B Published February 8, 2013 and supersedes all previous versions. The information contained in this

More information

Jmol and Crystal. Bob Hanson St. Olaf College, Northfield, MN

Jmol and Crystal. Bob Hanson St. Olaf College, Northfield, MN Jmol and Crystal Bob Hanson St. Olaf College, Northfield, MN http://www.stolaf.edu/people/hansonr Crystal Workshop MSSC2018 l'università di Torino, Italia 4 Sep 2018 Bob Hanson St. Olaf College Jmol Topics

More information

Mechanisms of Enzymes

Mechanisms of Enzymes Mechanisms of Enzymes Presented by Dr. Mohammad Saadeh The requirements for the Pharmaceutical Biochemistry I Philadelphia University Faculty of pharmacy How enzymes work * Chemical reactions have an energy

More information

Online hearing test Lullenstyd Audiology :

Online hearing test Lullenstyd Audiology : Online hearing test Lullenstyd Audiology : http://www.lullenstyd.com Éva Keresztessy ELTE Bárczi Gusztáv Faculty of Special Education Department of Hearing Impairment, H-1093 Budapest, Ecseri út 3, Hungary,

More information

The North Carolina Health Data Explorer

The North Carolina Health Data Explorer The North Carolina Health Data Explorer The Health Data Explorer provides access to health data for North Carolina counties in an interactive, user-friendly atlas of maps, tables, and charts. It allows

More information

RESULTS REPORTING MANUAL. Hospital Births Newborn Screening Program June 2016

RESULTS REPORTING MANUAL. Hospital Births Newborn Screening Program June 2016 RESULTS REPORTING MANUAL Hospital Births Newborn Screening Program June 2016 CONTENTS GETTING STARTED... 1 Summary... 1 Logging In... 1 Access For New Hires... 2 Reporting Parental Refusals... 3 Adding

More information

EasyComp. The TPN Compatibility Software. Clinical Nutrition

EasyComp. The TPN Compatibility Software. Clinical Nutrition EasyComp The TPN Compatibility Software Clinical Nutrition Content 1. General Information 5 1.1 What is EasyComp? 4 1.2 Features and functions of EasyComp 5 1.3 IT requirements 5 t2. Starting EasyComp

More information

East Stroudsburg University Athletic Training Medical Forms Information and Directions

East Stroudsburg University Athletic Training Medical Forms Information and Directions East Stroudsburg University Athletic Training Medical Forms Information and Directions 2013 2014 All student athletes must complete all medical information forms on the ATS Webportal by July 27 th, 2013.

More information

Data Management, Data Management PLUS User Guide

Data Management, Data Management PLUS User Guide Data Management, Data Management PLUS User Guide Table of Contents Introduction 3 SHOEBOX Data Management and Data Management PLUS (DM+) for Individual Users 4 Portal Login 4 Working With Your Data 5 Manually

More information

smk72+ Handbook Prof. Dr. Andreas Frey Dr. Lars Balzer Stephan Spuhler smk72+ Handbook Page 1

smk72+ Handbook Prof. Dr. Andreas Frey Dr. Lars Balzer Stephan Spuhler smk72+ Handbook Page 1 smk72+ Handbook Prof. Dr. Andreas Frey Dr. Lars Balzer Stephan Spuhler Email: support@kompetenzscreening.de Page 1 Table of Contents HOME... 3 BASIC INFORMATION ON LOGGING IN... 4 LOGIN PROCESS FOR PARTICIPANTS...

More information

Web Feature Services Tutorial

Web Feature Services Tutorial Southeast Alaska GIS Library Web Feature Services Tutorial Prepared By Mike Plivelich Version 0.2 Status Draft Updates Continual Release Date June 2010 1 TABLE OF CONTENTS Page # INTRODUCTION...3 PURPOSE:...

More information

Table S1: Kinetic parameters of drug and substrate binding to wild type and HIV-1 protease variants. Data adapted from Ref. 6 in main text.

Table S1: Kinetic parameters of drug and substrate binding to wild type and HIV-1 protease variants. Data adapted from Ref. 6 in main text. Dynamical Network of HIV-1 Protease Mutants Reveals the Mechanism of Drug Resistance and Unhindered Activity Rajeswari Appadurai and Sanjib Senapati* BJM School of Biosciences and Department of Biotechnology,

More information

General Single Ion Calibration. Pete 14-May-09

General Single Ion Calibration. Pete 14-May-09 General Single Ion Calibration Pete 14-May-09 Purpose of SI calibration Measure the instrument response of a single ion. Necessary for understanding of error in instrument (counting statistics) Calculation

More information

University of Alaska Connected! FAQs

University of Alaska Connected! FAQs University of Alaska Connected! FAQs 1. What is Connected? Connected! allows employees and spouses/fips to connect a fitness device or app to Healthyroads.com. This will allow additional tracking options

More information

3.2 Ligand-Binding at Nicotinic Acid Receptor Subtypes GPR109A/B

3.2 Ligand-Binding at Nicotinic Acid Receptor Subtypes GPR109A/B 3.2 Ligand-Binding at Nicotinic Acid Receptor Subtypes GPR109A/B 3.2.1 Characterization of the Ligand Binding Site at GPR109A Receptor Ligands of GPR109A Receptor are Carboxylic Acids Nicotinic acid (pyridine-3-carboxylic

More information

GridMAT-MD: A Grid-based Membrane Analysis Tool for use with Molecular Dynamics

GridMAT-MD: A Grid-based Membrane Analysis Tool for use with Molecular Dynamics GridMAT-MD: A Grid-based Membrane Analysis Tool for use with Molecular Dynamics William J. Allen, Justin A. Lemkul, and David R. Bevan Department of Biochemistry, Virginia Tech User s Guide Version 1.0.2

More information

Chapter 10. Regulatory Strategy

Chapter 10. Regulatory Strategy Chapter 10 Regulatory Strategy Regulation of enzymatic activity: 1. Allosteric Control. Allosteric proteins have a regulatory site(s) and multiple functional sites Activity of proteins is regulated by

More information