CHAPTER 3 Amino Acids, Peptides, Proteins Learning goals: Structure and naming of amino acids Structure and properties of peptides Ionization behavior of amino acids and peptides Methods to characterize peptides and proteins
Proteins: Main Agents of Biological Function Catalysis enolase (in the glycolytic pathway) DNA polymerase (in DNA replication) Transport hemoglobin (transports O 2 in the blood) lactose permease (transports lactose across the cell membrane) Structure collagen (connective tissue) keratin (hair, nails, feathers, horns) Motion myosin (muscle tissue) actin (muscle tissue, cell motility)
Amino Acids: Building Blocks of Protein Proteins are linear heteropolymers of -amino acids Amino acids have properties that are well-suited to carry out a variety of biological functions Capacity to polymerize Useful acid-base properties Varied physical properties Varied chemical functionality
Amino acids share many features, differing only at the R substituent
Most -amino acids are chiral The -carbon always has four substituents and is tetrahedral All (except proline) have: an acidic carboxyl group a basic amino group an -hydrogen connected to the -carbon The fourth substituent (R) is unique In glycine, the fourth substituent is also hydrogen
Amino Acids: Atom Naming Organic nomenclature: start from one end Biochemical designation: start from -carbon and go down the R-group
All amino acids are chiral (except glycine) Proteins only contain L amino acids
Amino Acids: Classification Common amino acids can be placed in five basic groups depending on their R substituents: Nonpolar, aliphatic (7) Aromatic (3) Polar, uncharged (5) Positively charged (3) Negatively charged (2)
A number representing its hydrophilic or hydrophobic properties. The larger the number is, the more hydrophobic amino acid.
Hydrophobic A, V, L, I : cluster 형성경향 : Hydrophobic interaction G : the simplest one M : sulfur-containing P : a cyclic amino acid
These amino acid side chains absorb UV light at 270 280 nm
sulfhydryl group hydroxyl group amide group N Q These amino acids side chains can form hydrogen bonds. Cysteine can form disulfide bonds.
amino group imidazole group K R guanidinium group K, R : nuclear localization signal H : facilitate many enzyme-catalyzed reactions by serving as proton donor/acceptor
carboxyl group D E
Uncommon Amino Acids in Proteins Not incorporated by ribosomes except for Selenocysteine Arise by post-translational modifications of proteins Reversible modifications, especially phosphorylation, are important in regulation and signaling
Modified Amino Acids Found in Proteins a derivative of proline : plant cell wall protein, collagen fiber a derivative of 4 lysine : 섬유단백질 elastin a derivative of lysine : collagen fiber a derivative of lysine : myosin ( 근육수축단백질 ) a derivative of glutamate : prothrombin ( 혈액응고단백질 ) 합성중에형성 S 대신 selenium a derivative of serine
Reversible Modifications of Amino Acids
Ionization of Amino Acids At acidic ph, the carboxyl group is protonated and the amino acid is in the cationic form. At neutral ph, the carboxyl group is deprotonated but the amino group is protonated. The net charge is zero; such ions are called Zwitterions. At alkaline ph, the amino group is neutral NH 2 and the amino acid is in the anionic form.
Cation Zwitterion Anion
Chemical Environment Affects pk a Values -carboxy group is much more acidic than in carboxylic acids -amino group is slightly less basic than in amines
Amino acids can act as buffers Amino acids with uncharged side chains, such as glycine, have two pk a values: The pk a of the -carboxyl group is 2.34 The pk a of the -amino group is 9.6 It can act as a buffer in two ph regimes.
Buffer Regions
Amino acids carry a net charge of zero at a specific ph (the pi) Zwitterions predominate at ph values between the pk a values of the amino and carboxyl groups For amino acids without ionizable side chains, the Isoelectric Point (equivalence point, pi) is pk 1 pk pi 2 2 At this point, the net charge is zero AA is least soluble in water AA does not migrate in electric field
Ionizable side chains can show up in titration curves Ionizable side chains can be also titrated Titration curves are now more complex pk a values are discernable if two pk a values are more than two ph units apart Why is the side chain pk a so much higher?
How to Calculate the pi When the Side Chain is Ionizable Identify species that carries a net zero charge Identify pk a value that defines the acid strength of this zwitterion: (pk 2 ) Identify pk a value that defines the base strength of this zwitterion: (pk 1 ) Take the average of these two pk a values
Formation of Peptides Peptides are small condensation products of amino acids They are small compared to proteins (M w < 10 kda)
Peptide ends are not the same Numbering (and naming) starts from the amino terminus AA 1 AA 2 AA 3 AA 4 AA 5
Naming peptides: start at the N-terminus Using full amino acid names Serylglycyltyrosylalanylleucine Using the three-letter code abbreviation Ser-Gly-Tyr-Ala-Leu For longer peptides (like proteins) the oneletter code can be used SGYAL
Peptides: A Variety of Functions Hormones and pheromones insulin (think sugar) oxytocin (think childbirth) sex-peptide (think fruit fly mating) Neuropeptides substance P (pain mediator) Antibiotics polymyxin B (for Gram bacteria) bacitracin (for Gram + bacteria) Protection, e.g., toxins amanitin (mushrooms) conotoxin (cone snails) chlorotoxin (scorpions)
Proteins are: Polypeptides (covalently linked -amino acids) + possibly: cofactors functional non-amino acid component metal ions or organic molecules coenzymes organic cofactors NAD + in lactate dehydrogenase prosthetic groups covalently attached cofactors heme in myoglobin other modifications
Polypeptide size and number varies greatly in proteins
Classes of Conjugated Proteins
A mixture of proteins can be separated Separation relies on differences in physical and chemical properties Charge Size Affinity for a ligand Solubility Hydrophobicity Thermal stability Chromatography is commonly used for preparative separation
Column Chromatography
Separation by Charge
Separation by Size
Separation by Affinity
HPLC (high-performance liquid chromatography) : high pressure pump -> limit diffusional spreading -> improve resolution
Electrophoresis for Protein Analysis Separation in analytical scale is commonly done by electrophoresis Electric field pulls proteins according to their charge Gel matrix hinders mobility of proteins according to their size and shape
SDS PAGE: Molecular Weight SDS sodium dodecyl sulfate a detergent SDS micelles bind to and unfold all the proteins SDS gives all proteins an uniformly negative charge The native shape of proteins does not matter Rate of movement will only depend on size: small proteins will move faster
SDS-PAGE can be used to calculate the molecular weight of a protein
Isoelectric focusing can be used to determine the pi of a protein
Isoelectric focusing and SDS-PAGE are combined in 2D electrophoresis
(-) (+).
MALDI-TOF MS STR (PerSepive) MALDI TOF MS delayed extraction Reflector High current detector STR (PerSepive)
MALDI-TOF MS Matrix-Assisted Laser Desorption/Ionization Time Of Flight MS Sample plate Extraction grids Laser Timed ion selector Reflector detector Reflector Linear detector Pumping UV laser 337 nm Disorbed ions Pumping Matrix Sample
Specific activity (activity/total protein) can be used to assess protein purity
Protein Sequencing It is essential to further biochemical analysis that we know the sequence of the protein we are studying Actual sequence generally determined from DNA sequence Edman Degradation (Classical method) Successive rounds of N-terminal modification, cleavage, and identification Can be used to identify protein with known sequence Mass Spectrometry (Modern method) MALDI MS and ESI MS can precisely identify the mass of a peptide, and thus the amino acid sequence Can be used to determine post-translational modifications
Edman s Degradation
MS Procedures for Sequence IDs
MS-based proteomics experiments; In solution_lc/ms/ms 분석 세균분비물질추출 LC-MS/MS 분석 단백질동정
Representations of three consensus sequences P loop, an ATP-binding structure Protein families : share structural and functional features : identified based on a.a. sequence similalities Some families are defined by identities involving only a few a.a. critical to a certain proteins The functional information come from the consensus sequence EF hand, a Ca 2+ -binding structur
Representations of three consensus sequences Hsp70 proteins from two well-studied bacterial species, E. coli and Bacillus subtilis
Bioinformatics; a tool to elucidate the history of life on earth Bioinformatics : the application of computer science and information technology to the field of biology Example: www.pubmed.gov : http://signal.salk.edu/cgi-bin/tdnaexpress : http://www.ricearray.org/expression/expression.php (LOC_Os03g26870) : workbench.sdsc.edu EF-1α/EF-Tu The variation in the signature sequence reflects the significant evolutionary divergence that has occurred at this site since it first appeared in a common ancestor of both groups.
Protein Sequences as Clues to Evolutionary Relationships Sequences of homologous proteins from a wide range of species can be aligned and analyzed for differences Differences indicate evolutionary divergences Analysis of multiple protein families can indicate evolutionary relationships between organisms, ultimately the history of life on Earth