Low ds/dn Does Not Correlate With High Variation of Amino Acid Sequences Along the gp120 Protein Structure
|
|
|
- Noah Price
- 5 years ago
- Views:
Transcription
1 Low ds/dn Does Not Correlate With High Variation of Amino Acid Sequences Along the gp120 Protein Structure Zach Goldstein & Jordan Detamore BIOL 368: Bioinformatics Laboratory Department of Biology Loyola Marymount University November 15, 2016
2 Outline Low ds/dn ratios may correlate with high amino acid variations along the V3 loop of the gp120 protein Subjects selected from Markham et al. (1998) demonstrated high or low ds/dn values Amino acid sequence alignment using ClustalW and BoxShade showed conflicting results 6 Non-consensus segments along gp120 are found along the V3 loop and on the exterior surface of the protein Further research would examine the impact of variations in these 6 non-consensus sites
3 Outline Low ds/dn ratios may correlate with high amino acid variations along the V3 loop of the gp120 protein Subjects selected from Markham et al. (1998) demonstrated high or low ds/dn values Amino acid sequence alignment using ClustalW and BoxShade showed conflicting results 6 Non-consensus segments along gp120 are found along the V3 loop and on the exterior surface of the protein Further research would examine the impact of variations in these 6 non-consensus sites
4 HIV is a Retrovirus With Many Different Structures gp120: Facilitates HIV entry into host cell by binding to CD4 gp41: Responsible for fusion of viral and target cell membranes V3 Region: Highly variable region of gp120 that facilitates coreceptor binding
5 Non-Synonymous Mutation Rates May Demonstrate Significant Changes in Amino Acid Sequence Non synonymous mutations (dn) are nucleotide changes that lead to the coding of a different amino acid. Synonymous mutations (ds) are nucleotide changes that do not lead to the coding of a different amino acid. These ratios were formed for each consensus strain for all subjects. The smaller the ratio, the larger amount of non synonymous mutations, the more potential for differences in amino acid sequences
6 20 Standard Amino Acids Vary in Structure and Properties 4 Groups of Amino Acids Acidic Basic Uncharged Polar Nonpolar Position affects function Size affects function
7 Do Mutation Rates Affect Variation in Amino Acid Sequences? Questions: Does a low ds/dn ratio value result in high amino acid variation? Do subjects with low ds/dn ratios vary from each other? Do the sites of variation have nonconservative mutations? Hypotheses: Low ds/dn ratio values will result in high amino acid variation. Subjects with low ds/dn ratios will vary greatly from each other. The sites of high variation will result in nonconservative mutations.
8 Outline Low ds/dn ratios may correlate with high amino acid variations along the V3 loop of the gp120 protein Subjects selected from Markham et al. (1998) demonstrated high or low ds/dn values Amino acid sequence alignment using ClustalW and BoxShade showed conflicting results 6 Non-consensus segments along gp120 are found along the V3 loop and on the exterior surface of the protein Further research would examine the impact of variations in these 6 non-consensus sites
9 Subjects Selected Based on Differences in ds/dn Ratios Four subjects with highest ds/dn ratio and four subjects with lowest ds/dn ratio were chosen Three random clones were selected from the first and last visit Subjects had different numbers of visits spread over the four years Unable to chose subjects from same visit date
10 New Groups Formed Based on Highest and Lowest ds/dn Ratios Rapid Progressor (Subject #) Moderate Progresso r (Subject #) Nonprogressor (Subject #) Subjects demonstrating highest ds/dn ratios Subjects demonstrating lowest ds/dn ratios
11 Outline Low ds/dn ratios may correlate with high amino acid variations along the V3 loop of the gp120 protein Subjects selected from Markham et al. (1998) demonstrated high or low ds/dn values Amino acid sequence alignment using ClustalW and BoxShade showed conflicting results 6 Non-consensus segments along gp120 are found along the V3 loop and on the exterior surface of the protein Further research would examine the impact of variations in these 6 non-consensus sites
12 Phylogenetic Trees Show No Clear Difference in Variation Between Low ds/dn Subjects and High ds/dn Subjects High ds/dn ratio subjects Low ds/dn ratio subjects Biology Workbench: ClustalW
13 BoxShade and ClustalW Were Used to Analyze Amino Acid Sequences
14 Low Ratio Subjects Had More Non-Consensus Sites than High Ratio Subjects
15 BoxShade Highlights a Higher Frequency of Non-Consensus Sites in Subjects From the High ds/dn Group High ds/dn Subjects Low ds/dn Subjects
16 Outline Low ds/dn ratios may correlate with high amino acid variations along the V3 loop of the gp120 protein Subjects selected from Markham et al. (1998) demonstrated high or low ds/dn values Amino acid sequence alignment using ClustalW and BoxShade showed conflicting results 6 Non-consensus segments along gp120 are found along the V3 loop and on the exterior surface of the protein Further research would examine the impact of variations in these 6 non-consensus sites
17 Comparison of all Subjects Show 6 Sites With no Amino Acid Consensus
18 The V3 Region Sticks Out of gp120 Facing the Antibody Antibody gp120 CD4 Huang et al. (2005)
19 Three Sites Along the V3 Region Show Variability Along the Outside of the Protein Key Lysine (B) Glycine (NP), Arginine (B), Isoleucine (NP), Asparagine (P), Tyrosine ( P), Glutamic Acid (A), Threonine (P), Alanine (NP) Asparagine (P) Glycine (NP), Arginine (B), Lysine (B), Glutamic Acid (A), Proline (NP) Lysine (B) Leucine (NP), Asparagine (P), Insertion Cn3D macromolecular structure viewer A: Acidic B: Basic P: Polar NP: Nonpolar
20 Three Sites Along the immunogenetic tip of the V3 Region Show High Variability Lysine (B) Glutamine (P) or insertion Isoleucine (NP) Asparagine (P), Proline (NP), Serine (P), Histidine (B), Leucine (NP) Threonine (P) Alanine (NP) Cn3D macromolecular structure viewer Key A: Acidic B: Basic P: Polar NP: Nonpolar
21 Non-Consensus Regions of gp120 Match Variable Segments Studied by Andrianov & Anishchenko (2012) A 35-residue-long segment of the V3 loop shows high structure variability 3 segments along the same V3 region found to be highly variable Conservation of amino acid composition found at pinch sites are targets for anti-aids medication
22 Low ds/dn Ratios Demonstrate no Clear Relationship to Higher Rates of Non-Consensus Segments Along the V3 Loop The sites of high variation result in nonconservative mutations, causing changes in protein structure and function Interactions and functions of protein may be affected by variations in primary sequence Non-Consensus segments found along V3 loop and on the outside region of gp120 using BoxShade were not consistent with ClustalW
23 Outline Low ds/dn ratios may correlate with high amino acid variations along the V3 loop of the gp120 protein Subjects selected from Markham et al. (1998) demonstrated high or low ds/dn values Amino acid sequence alignment using ClustalW and BoxShade showed conflicting results 6 Non-consensus segments along gp120 are found along the V3 loop and on the exterior surface of the protein Further research would examine the impact of variations in these 6 non-consensus sites
24 Functions of Amino Acid Variations Must be Studied to Observe the Effect of Non-Consensus Sites Low ds/dn ratio subjects show trend towards significant rates of mutations causing variable amino acid structure using BoxShade Specific functions of amino acid substitutions along the V3 loop should be studied V3 region should be targeted for anti-aids medications due to rigidity in structure, studying variations in structure may prove helpful Data can be used to identify HIV-1 immune system evasion
25 Summary Low ds/dn ratios may correlate with high amino acid variations along the V3 loop of the gp120 protein Subjects selected from Markham et al. (1998) demonstrated high or low ds/dn values Amino acid sequence alignment using ClustalW and BoxShade showed conflicting results 6 Non-consensus segments along gp120 are found along the V3 loop and on the exterior surface of the protein Further research would examine the impact of variations in these 6 non-consensus sites
26 Acknowledgements Dr. Kam Dahlquist Department of Biology at Loyola Marymount University Bioinformatics Lab Fall 2016
27 References Andrianov, A. M., & Anishchenko, I. V. (2009). Computational model of the HIV-1 subtype A V3 loop: Study on the conformational mobility for structure-based anti-aids drug design. Journal of Biomolecular Structure and Dynamics, 27(2), DOI: / Huang CC et al. Science (2005) 310 p Structure of a v3-containing hiv-1 gp120 core. Kwong, P. D., Wyatt, R., Robinson, J., Sweet, R. W., Sodroski, J., & Hendrickson, W. A. (1998). Structure of an HIV gp120 envelope glycoprotein in complex with the CD4 receptor and a neutralizing human antibody. Nature, 393(6686), DOI: /31405 Markham, R.B., Wang, W.C., Weisstein, A.E., Wang, Z., Munoz, A., Templeton, A., Margolick, J., Vlahov, D., Quinn, T., Farzadegan, H., & Yu, X.F. (1998). Patterns of HIV-1 evolution in individuals with differing rates of CD4 T cell decline. Proc Natl Acad Sci U S A. 95, doi: /pnas Cn3D macromolecular structure viewer Biology Workbench
Nonsynonymous Amino Acid Mutations in gp120 Binding Sites are Related to Progression of HIV-1
Nonsynonymous Amino Acid Mutations in gp120 Binding Sites are Related to Progression of HIV-1 Matthew Allegretti and Anindita Varshneya BIOL 368: Bioinformatics Laboratory Loyola Marymount University November
Does A Significant Change in CD4 Cell Count Affect The Number of Amino Acid Mutations In A Subject s Corresponding DNA Sequence
Does A Significant Change in CD4 Cell Count Affect The Number of Amino Acid Mutations In A Subject s Corresponding DNA Sequence Courtney Merriam and Shivum Desai Biology 368: Bioinformatics Loyola Marymount
Subtyping Sequences from Patterns of HIV-1 evolution in individuals with differing rates of CD4 T cell decline by Markham et al.
Subtyping Sequences from Patterns of HIV-1 evolution in individuals with differing rates of CD4 T cell decline by Markham et al. By: Matthew Oki & Jordan Detamore Loyola Marymount University 11 October
ds/dn Ratios Do Not Provide A More Consistent Means of Comparison Between HIV-1 Progressor Groups
ds/dn Ratios Do Not Provide A More Consistent Means of Comparison Between HIV-1 Progressor Groups Zach Goldstein and Shivum Desai October 11, 2016 Department of Biology Loyola Marymount University Outline
Correlation analysis between CD4 T Cell counts and genetic diversity indicate no relationship Mia Huddleston and Anindita Varshneya
Correlation analysis between CD4 T Cell counts and genetic diversity indicate no relationship Mia Huddleston and Anindita Varshneya Department of Biology Loyola Marymount University October 11, 2016 Outline
CD4 T Cell Decline Is Not Associated With Amino Acid Changes in HIV-1 gp120
CD4 T Cell Decline Is Not Associated With Amino Acid Changes in HIV-1 gp120 Colin Wikholm and Isai Lopez BIOL 368: Bioinformatics Laboratory Department of Biology Loyola Marymount University November 15,
Loyola Marymount University Department of Biology October 25, Zach, Matt, Mia, Will
Alexander M. Andrianov & Ivan V. Anishchenko (2009) Computational Model of the HIV-1 Subtype A V3 Loop: Study on the Conformational Mobility for Structure Based Anti-AIDS Drug Design, Journal of Biomolecular
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
Lecture 3: 8/24. CHAPTER 3 Amino Acids
Lecture 3: 8/24 CHAPTER 3 Amino Acids 1 Chapter 3 Outline 2 Amino Acid Are Biomolecules and their Atoms Can Be Visualized by Two Different Ways 1) Fischer projections: Two dimensional representation of
Protein Folding LARP
Protein Folding LARP Version: 1.0 Release: April 2018 Amplyus 2018 minipcr TM Protein Folding LARP (Live Action Role Play) Summary Materials In this activity, students will role play to make a folded protein
Amino acids. (Foundation Block) Dr. Essa Sabi
Amino acids (Foundation Block) Dr. Essa Sabi Learning outcomes What are the amino acids? General structure. Classification of amino acids. Optical properties. Amino acid configuration. Non-standard amino
Proteins consist in whole or large part of amino acids. Simple proteins consist only of amino acids.
Today we begin our discussion of the structure and properties of proteins. Proteins consist in whole or large part of amino acids. Simple proteins consist only of amino acids. Conjugated proteins contain
PHAR3316 Pharmacy biochemistry Exam #2 Fall 2010 KEY
1. How many protons is(are) lost when the amino acid Asparagine is titrated from its fully protonated state to a fully deprotonated state? A. 0 B. 1 * C. 2 D. 3 E. none Correct Answer: C (this question
Page 8/6: The cell. Where to start: Proteins (control a cell) (start/end products)
Page 8/6: The cell Where to start: Proteins (control a cell) (start/end products) Page 11/10: Structural hierarchy Proteins Phenotype of organism 3 Dimensional structure Function by interaction THE PROTEIN
1. Describe the relationship of dietary protein and the health of major body systems.
Food Explorations Lab I: The Building Blocks STUDENT LAB INVESTIGATIONS Name: Lab Overview In this investigation, you will be constructing animal and plant proteins using beads to represent the amino acids.
So where were we? But what does the order mean? OK, so what's a protein? 4/1/11
So where were we? We know that DNA is responsible for heredity Chromosomes are long pieces of DNA DNA turned out to be the transforming principle We know that DNA is shaped like a long double helix, with
Protein sequence alignment using binary string
Available online at www.scholarsresearchlibrary.com Scholars Research Library Der Pharmacia Lettre, 2015, 7 (5):220-225 (http://scholarsresearchlibrary.com/archive.html) ISSN 0975-5071 USA CODEN: DPLEB4
If you like us, please share us on social media. The latest UCD Hyperlibrary newsletter is now complete, check it out.
Sign In Forgot Password Register username username password password Sign In If you like us, please share us on social media. The latest UCD Hyperlibrary newsletter is now complete, check it out. ChemWiki
CHAPTER 29 HW: AMINO ACIDS + PROTEINS
CAPTER 29 W: AMI ACIDS + PRTEIS For all problems, consult the table of 20 Amino Acids provided in lecture if an amino acid structure is needed; these will be given on exams. Use natural amino acids (L)
PROTEINS. Amino acids are the building blocks of proteins. Acid L-form * * Lecture 6 Macromolecules #2 O = N -C -C-O.
Proteins: Linear polymers of amino acids workhorses of the cell tools, machines & scaffolds Lecture 6 Macromolecules #2 PRTEINS 1 Enzymes catalysts that mediate reactions, increase reaction rate Structural
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
Amino acids. Dr. Mamoun Ahram Summer semester,
Amino acids Dr. Mamoun Ahram Summer semester, 2017-2018 Resources This lecture Campbell and Farrell s Biochemistry, Chapters 3 (pp.66-76) General structure (Chiral carbon) The amino acids that occur in
9/6/2011. Amino Acids. C α. Nonpolar, aliphatic R groups
Amino Acids Side chains (R groups) vary in: size shape charge hydrogen-bonding capacity hydrophobic character chemical reactivity C α Nonpolar, aliphatic R groups Glycine (Gly, G) Alanine (Ala, A) Valine
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
Amino Acids. Amino Acids. Fundamentals. While their name implies that amino acids are compounds that contain an NH. 3 and CO NH 3
Fundamentals While their name implies that amino acids are compounds that contain an 2 group and a 2 group, these groups are actually present as 3 and 2 respectively. They are classified as α, β, γ, etc..
1-To know what is protein 2-To identify Types of protein 3- To Know amino acids 4- To be differentiate between essential and nonessential amino acids
Amino acids 1-To know what is protein 2-To identify Types of protein 3- To Know amino acids 4- To be differentiate between essential and nonessential amino acids 5-To understand amino acids synthesis Amino
LAB#23: Biochemical Evidence of Evolution Name: Period Date :
LAB#23: Biochemical Evidence of Name: Period Date : Laboratory Experience #23 Bridge Worth 80 Lab Minutes If two organisms have similar portions of DNA (genes), these organisms will probably make similar
Gentilucci, Amino Acids, Peptides, and Proteins. Peptides and proteins are polymers of amino acids linked together by amide bonds CH 3
Amino Acids Peptides and proteins are polymers of amino acids linked together by amide bonds Aliphatic Side-Chain Amino Acids - - H CH glycine alanine 3 proline valine CH CH 3 - leucine - isoleucine CH
0010 Amino Acids 40 Profile - Plasma
Accession #: Order #: G1234567 Date Collected: Date Received: 01/22/2013 Reference #: Patient: Date of Birth: 02/05/1962 Date of Report: Telephone: 7704464583 Ordering Physician: 1234 Main St. Anywhere,
Objective: You will be able to explain how the subcomponents of
Objective: You will be able to explain how the subcomponents of nucleic acids determine the properties of that polymer. Do Now: Read the first two paragraphs from enduring understanding 4.A Essential knowledge:
PROTEIN. By: Shamsul Azahari Zainal Badari Department of Resource Management and Consumer Studies Faculty of Human Ecology UPM
PROTEIN By: Shamsul Azahari Zainal Badari Department of Resource Management and Consumer Studies Faculty of Human Ecology UPM OBJECTIVES OF THE LECTURE By the end of this lecture, student can: Define
M1 - Renal, Fall 2007
University of Michigan Deep Blue deepblue.lib.umich.edu 2007-09 M1 - Renal, Fall 2007 Lyons, R.; Burney, R. Lyons, R., Burney, R. (2008, August 07). Renal. Retrieved from Open.Michigan - Educational Resources
Age-related reference ranges
Authoriser: Peter Beresford Page 1 of 6 Age-related reference ranges Alkaline Phosphatase (ALP) IU/L Both less than 14 days 90 273 Both 14 days
Section 1 Proteins and Proteomics
Section 1 Proteins and Proteomics Learning Objectives At the end of this assignment, you should be able to: 1. Draw the chemical structure of an amino acid and small peptide. 2. Describe the difference
Mutations and Disease Mutations in the Myosin Gene
Biological Sciences Initiative HHMI Mutations and Disease Mutations in the Myosin Gene Goals Explore how mutations can lead to disease using the myosin gene as a model system. Explore how changes in the
Macromolecules of Life -3 Amino Acids & Proteins
Macromolecules of Life -3 Amino Acids & Proteins Shu-Ping Lin, Ph.D. Institute of Biomedical Engineering E-mail: splin@dragon.nchu.edu.tw Website: http://web.nchu.edu.tw/pweb/users/splin/ Amino Acids Proteins
Fatty acids and phospholipids
PYS 4xx Intro 2 1 PYS 4xx Intro 2 - Molecular building blocks We now describe in more detail the nomenclature and composition of several classes of compounds of relevance to the cell, including: membrane
Biological systems interact, and these systems and their interactions possess complex properties. STOP at enduring understanding 4A
Biological systems interact, and these systems and their interactions possess complex properties. STOP at enduring understanding 4A Homework Watch the Bozeman video called, Biological Molecules Objective:
Activities for the α-helix / β-sheet Construction Kit
Activities for the α-helix / β-sheet Construction Kit The primary sequence of a protein, composed of amino acids, determines the organization of the sequence into the secondary structure. There are two
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
بسم هللا الرحمن الرحيم
بسم هللا الرحمن الرحيم Biochemistry Lec #1 Dr. Nafith AbuTarboush- (30.6.2014) Amino Acids 1 Campbell and Farrell s Biochemistry, Chapter 3 (pp.66-76) Introduction: Biochemistry is two courses; one is
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
Chapter 3: Amino Acids and Peptides
Chapter 3: Amino Acids and Peptides BINF 6101/8101, Spring 2018 Outline 1. Overall amino acid structure 2. Amino acid stereochemistry 3. Amino acid sidechain structure & classification 4. Non-standard
Properties of amino acids in proteins
Properties of amino acids in proteins one of the primary roles of DNA (but far from the only one!!!) is to code for proteins A typical bacterium builds thousands types of proteins, all from ~20 amino acids
0010 Amino Acid Analysis - 40 Plasma
770.446.5483 770.441.2237 This report contains reference range adjustments from routine revalidation procedures. It also contains the following three upgrades: 1) The amino acids have been reorganized
Biomolecules: amino acids
Biomolecules: amino acids Amino acids Amino acids are the building blocks of proteins They are also part of hormones, neurotransmitters and metabolic intermediates There are 20 different amino acids in
Molecular Biology. general transfer: occurs normally in cells. special transfer: occurs only in the laboratory in specific conditions.
Chapter 9: Proteins Molecular Biology replication general transfer: occurs normally in cells transcription special transfer: occurs only in the laboratory in specific conditions translation unknown transfer:
Amino Acid Analyzer AAA400
Amino Acid Analyzer AAA400 Determination of amino acid of hydrolyzates (food and feed) Column: LG ANB OSTION 3.6x340 12μm Eluents: sodium-citrate buffers, 0.2 M NaOH Aspartic Acid, Threonine, Serine, Glutamic
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,
Analysis of Cancer Proteins: Pattern Identification on Escherichia coli Species
Research Article imedpub Journals http://www.imedpub.com Colorectal Cancer: Open Access DOI: 10.21767/2471-9943.100005 Abstract Analysis of Cancer Proteins: Pattern Identification on Escherichia coli Species
Amino acids. Dr. Mamoun Ahram and Dr. Diala Abu-Hassan Summer semester,
Amino acids Dr. Mamoun Ahram and Dr. Diala Abu-Hassan Summer semester, 2017-2018 dr.abuhassand@gmail.com Resources This lecture Campbell and Farrell s Biochemistry, Chapters 3 (pp.66-76) General structure
THE UNIVERSITY OF MANITOBA. DATE: Oct. 22, 2002 Midterm EXAMINATION. PAPER NO.: PAGE NO.: 1of 6 DEPARTMENT & COURSE NO.: 2.277/60.
PAPER NO.: PAGE NO.: 1of 6 GENERAL INSTRUCTIONS You must mark the answer sheet with pencil (not pen). Put your name and enter your student number on the answer sheet. The examination consists of multiple
I) Choose the best answer: 1- All of the following amino acids are neutral except: a) glycine. b) threonine. c) lysine. d) proline. e) leucine.
1- All of the following amino acids are neutral except: a) glycine. b) threonine. c) lysine. d) proline. e) leucine. 2- The egg white protein, ovalbumin, is denatured in a hard-boiled egg. Which of the
Review II: The Molecules of Life
Review II: The Molecules of Life Judy Wieber BBSI @ Pitt 2007 Department of Computational Biology University of Pittsburgh School of Medicine May 24, 2007 Outline Introduction Proteins Carbohydrates Lipids
Chemistry 121 Winter 17
Chemistry 121 Winter 17 Introduction to Organic Chemistry and Biochemistry Instructor Dr. Upali Siriwardane (Ph.D. Ohio State) E-mail: upali@latech.edu Office: 311 Carson Taylor Hall ; Phone: 318-257-4941;
DETECTION OF LOW FREQUENCY CXCR4-USING HIV-1 WITH ULTRA-DEEP PYROSEQUENCING. John Archer. Faculty of Life Sciences University of Manchester
DETECTION OF LOW FREQUENCY CXCR4-USING HIV-1 WITH ULTRA-DEEP PYROSEQUENCING John Archer Faculty of Life Sciences University of Manchester HIV Dynamics and Evolution, 2008, Santa Fe, New Mexico. Overview
Amino acids-incorporated nanoflowers with an
Amino acids-incorporated nanoflowers with an intrinsic peroxidase-like activity Zhuo-Fu Wu 1,2,+, Zhi Wang 1,+, Ye Zhang 3, Ya-Li Ma 3, Cheng-Yan He 4, Heng Li 1, Lei Chen 1, Qi-Sheng Huo 3, Lei Wang 1,*
Introduction to Proteomics Dr. Sanjeeva Srivastava Department of Biosciences and Bioengineering Indian Institute of Technology - Bombay
Introduction to Proteomics Dr. Sanjeeva Srivastava Department of Biosciences and Bioengineering Indian Institute of Technology - Bombay Lecture 01 Introduction to Amino Acids Welcome to the proteomic course.
Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Concept 5.4: Proteins have many structures, resulting in a wide range of functions Proteins account for more than 50% of the dry mass of most cells Protein functions include structural support, storage,
Amino acids. You are required to know and identify the 20 amino acids : their names, 3 letter abbreviations and their structures.
Amino acids You are required to know and identify the 20 amino acids : their names, 3 letter abbreviations and their structures. If you wanna make any classification in the world, you have to find what
Different levels of protein structure
Dr. Sanjeeva Srivastava Proteins and its function Amino acids: building blocks Different levels of protein structure Primary, Secondary, Tertiary, Quaternary 2 Proteomics ourse PTEL 1 Derived from Greek
Lecture 11 AMINO ACIDS AND PROTEINS
Lecture 11 AMINO ACIDS AND PROTEINS The word "Protein" was coined by J.J. Berzelius in 1838 and was derived from the Greek word "Proteios" meaning the first rank. Proteins are macromolecular polymers composed
Methionine (Met or M)
Fig. 5-17 Nonpolar Fig. 5-17a Nonpolar Glycine (Gly or G) Alanine (Ala or A) Valine (Val or V) Leucine (Leu or L) Isoleucine (Ile or I) Methionine (Met or M) Phenylalanine (Phe or F) Polar Trypotphan (Trp
AMINO ACIDS STRUCTURE, CLASSIFICATION, PROPERTIES. PRIMARY STRUCTURE OF PROTEINS
AMINO ACIDS STRUCTURE, CLASSIFICATION, PROPERTIES. PRIMARY STRUCTURE OF PROTEINS Elena Rivneac PhD, Associate Professor Department of Biochemistry and Clinical Biochemistry State University of Medicine
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.
Identification of Mutation(s) in. Associated with Neutralization Resistance. Miah Blomquist
Identification of Mutation(s) in the HIV 1 gp41 Subunit Associated with Neutralization Resistance Miah Blomquist What is HIV 1? HIV-1 is an epidemic that affects over 34 million people worldwide. HIV-1
CHAPTER FIVE: COMMERCIAL APPLICATIONS TABLE 12 COMMERCIAL AMINO ACIDS BY USE... 35
CHAPTER ONE: INTRODUCTION... 1 STUDY GOALS AND OBJECTIVES... 1 REASONS FOR DOING THIS STUDY... 1 INTENDED AUDIENCE... 1 SCOPE OF REPORT... 2 METHODOLOGY AND INFORMATION SOURCES... 2 ANALYST CREDENTIALS...
Judy Wieber. Department of Computational Biology. May 27, 2008
Review II: The Molecules of Life Judy Wieber BBSI @ Pitt 2008 Department of Computational Biology University it of Pittsburgh School of Medicine i May 27, 2008 Outline Introduction Proteins Carbohydrates
Annual Report ERNDIM-EQAS Quantitative Amino Acids 2004
Annual Report ERNDIM-EQAS Quantitative Amino Acids 2004 1. Purpose The purpose of the ERNDIM External Quality Assurance Scheme for Quantitative Organic Acids is the monitoring of the analytical quality
Biology. Lectures winter term st year of Pharmacy study
Biology Lectures winter term 2008 1 st year of Pharmacy study 3 rd Lecture Chemical composition of living matter chemical basis of life. Atoms, molecules, organic compounds carbohydrates, lipids, proteins,
Biomolecular Mass Spectrometry
Lipids ot different than other organic small molecules Carbohydrates Polymers of monosaccharides linked via glycosidic bonds (acetals/ ketals) many different combinationsvery interesting no time ucleic
2018/9/24 AMINO ACIDS. Important. 436 Notes Original slides. 438 notes Extra information
2018/9/24 AMINO ACIDS Important. 436 Notes Original slides. 438 notes Extra information Objectives: What are the amino acids? General structure. Classification of amino acids. Optical properties. Amino
Number of Differences from Species 1
Molecular Evidence for Evolution Name: Pre Lab Activity: Genes code for amino acids, amino acids code for proteins and proteins build body structures. Therefore, one way to observe the relatedness of species
Q1: Circle the best correct answer: (15 marks)
Q1: Circle the best correct answer: (15 marks) 1. Which one of the following incorrectly pairs an amino acid with a valid chemical characteristic a. Glycine, is chiral b. Tyrosine and tryptophan; at neutral
Chapter 4: Information and Knowledge in the Protein Insulin
Chapter 4: Information and Knowledge in the Protein Insulin This chapter will calculate the information and molecular knowledge in a real protein. The techniques discussed in this chapter to calculate
Annual Report ERNDIM-EQAS Quantitative Amino Acids 2002
Annual Report ERNDIM-EQAS Quantitative Amino Acids 2002 1. Purpose The purpose of the ERNDIM External Quality Assurance Scheme for Quantitative Organic Acids is the monitoring of the analytical quality
COMPUTATIONAL ANALYSIS OF CONSERVED AND MUTATED AMINO ACIDS IN GP160 PROTEIN OF HIV TYPE-1
Journal of Cell and Tissue Research Vol. 10(3) 2359-2364 (2010) ISSN: 0973-0028 (Available online at www.tcrjournals.com) Original Article COMPUTATIONAL ANALYSIS OF CONSERVED AND MUTATED AMINO ACIDS IN
Biochemistry Prof. S. Dasgupta Department of Chemistry Indian Institute of Technology Kharagpur. Lecture -02 Amino Acids II
Biochemistry Prof. S. Dasgupta Department of Chemistry Indian Institute of Technology Kharagpur Lecture -02 Amino Acids II Ok, we start off with the discussion on amino acids. (Refer Slide Time: 00:48)
Controlled biomimetic crystallization of ZIF-8 particles by amino acids
Electronic Supplementary Material (ESI) for CrystEngComm. This journal is The Royal Society of Chemistry 2016 Supporting information for Controlled biomimetic crystallization of ZIF-8 particles by amino
Midterm 1 Last, First
Midterm 1 BIS 105 Prof. T. Murphy April 23, 2014 There should be 6 pages in this exam. Exam instructions (1) Please write your name on the top of every page of the exam (2) Show all work for full credit
Lecture 4. Grouping Amino Acid 7/1/10. Proteins. Amino Acids. Where Are Proteins Located. Nonpolar Amino Acids
Proteins Lecture 4 Proteins - Composition of Proteins (Amino Acids) Chapter 21 ection 1-6! Proteins are compounds of high molar mass consisting almost entirely of amino acid chain(s)! Molar masses range
Lipids: diverse group of hydrophobic molecules
Lipids: diverse group of hydrophobic molecules Lipids only macromolecules that do not form polymers li3le or no affinity for water hydrophobic consist mostly of hydrocarbons nonpolar covalent bonds fats
Proteins are sometimes only produced in one cell type or cell compartment (brain has 15,000 expressed proteins, gut has 2,000).
Lecture 2: Principles of Protein Structure: Amino Acids Why study proteins? Proteins underpin every aspect of biological activity and therefore are targets for drug design and medicinal therapy, and in
(a) (i) Describe how the production and action of interferon differs from the production and action of lysozyme. (3)
1 Histamine and the proteins interferon and lysozyme are involved in the non-specific responses to infection. (a) (i) escribe how the production and action of interferon differs from the production and
Thin-Layer Chromatography of Amino Acids HASPI Medical Biology Lab 15b Background Macromolecules
Thin-Layer Chromatography of s HASPI Medical Biology Lab 15b Background Macromolecules Name: Period: Date: There are four major types of biological macromolecules that make up the human body: nucleic acids
Identification of a Single Amino Acid Required for APOBEC3 Antiretroviral Cytidine Deaminase Activity
JOURNAL OF VIROLOGY, June 2011, p. 5691 5695 Vol. 85, No. 11 0022-538X/11/$12.00 doi:10.1128/jvi.00243-11 Copyright 2011, American Society for Microbiology. All Rights Reserved. Identification of a Single
CHEM-342 Introduction to Biochemistry Your Name Final Examination - Individual (Part I) Friday, 26 May :30 12:15 PM H. B. White - Instructor
HEM-342 Introduction to Biochemistry Final Examination - Individual (Part I) Friday, 26 May 2006 10:30 12:15 PM H. B. White - Instructor Range 28-72(2) out of 85, Average 53.5 Important - Please read this
CHM333 LECTURE 6: 1/25/12 SPRING 2012 Professor Christine Hrycyna AMINO ACIDS II: CLASSIFICATION AND CHEMICAL CHARACTERISTICS OF EACH AMINO ACID:
AMINO ACIDS II: CLASSIFICATION AND CHEMICAL CHARACTERISTICS OF EACH AMINO ACID: - The R group side chains on amino acids are VERY important. o Determine the properties of the amino acid itself o Determine
AMINO ACIDS NON-ESSENTIAL ESSENTIAL
Edith Frederika Introduction A major component of food is PROTEIN The protein ingested as part of our diet are not the same protein required by the body Only 40 to 50 gr of protein is required by a normal
YUMI YAMAGUCHI-KABATA AND TAKASHI GOJOBORI* Center for Information Biology, National Institute of Genetics, Mishima , Japan
JOURNAL OF VIROLOGY, May 2000, p. 4335 4350 Vol. 74, No. 9 0022-538X/00/$04.00 0 Copyright 2000, American Society for Microbiology. All Rights Reserved. Reevaluation of Amino Acid Variability of the Human
Distribution of the amino acids in Nature Frequency in proteins (%)
Distribution of the amino acids in ature Amino Acid Frequency in proteins (%) Leucine Alanine Glycine erine Valine Glutamic acid Threonine Arginine Lysine Aspartic acid Isoleucine Proline Asparagine Glutamine
Protein Modeling Event
Protein Modeling Event School Name: School Number: Team Member 1: Team Member 2: : Pre-Build Score: On-Site Build Score: Test Score: Tie Breaker: Total: Final Rank: Part I: Pre-Build (40% of total score)
استاذ الكيمياءالحيوية
قسم الكيمياء الحيوية د.دولت على سالمه استاذ الكيمياءالحيوية ٢٠١٥-٢٠١٤ الرمز الكودي : ٥١٢ المحاضرة األولى ١ Content : Definition of proteins Definition of amino acids Definition of peptide bond General
History (August 2010) Therapy for Experienced Patients. History (September 2010) History (November 2010) 12/2/11
(August 2010) Therapy for Experienced Patients Hiroyu Hatano, MD, MHS Assistant Professor of Medicine University of California San Francisco Medical Management of AIDS December 2011 42M HIV (CD4=450, VL=6250,
Introduction to proteins and protein structure
Introduction to proteins and protein structure The questions and answers below constitute an introduction to the fundamental principles of protein structure. They are all available at [link]. What are
AP Bio. Protiens Chapter 5 1
Concept.4: Proteins have many structures, resulting in a wide range of functions Proteins account for more than 0% of the dry mass of most cells Protein functions include structural support, storage, transport,
1. (38 pts.) 2. (25 pts.) 3. (15 pts.) 4. (12 pts.) 5. (10 pts.) Bonus (12 pts.) TOTAL (100 points)
Moorpark College Chemistry 11 Spring 2010 Instructor: Professor Torres Examination #5: Section Five May 4, 2010 ame: (print) ame: (sign) Directions: Make sure your examination contains TWELVE total pages
Biomolecules Amino Acids & Protein Chemistry
Biochemistry Department Date: 17/9/ 2017 Biomolecules Amino Acids & Protein Chemistry Prof.Dr./ FAYDA Elazazy Professor of Biochemistry and Molecular Biology Intended Learning Outcomes ILOs By the end
Bioinformation Volume 5
Identification of sequence mutations affecting hemagglutinin specificity to sialic acid receptor in influenza A virus subtypes Usman Sumo Friend Tambunan*, Ramdhan Department of Chemistry, Faculty of Mathematics