Fundamentals Of Protein Chemistry Prof. Swagata Dasgupta NPTEL .
N PT EL Fundamentals of Protein Chemistry Prof. Swagata Dasgupta Department of Chemistry Module 01: Amino Acids and the Peptide Bond Lecture 02: Amino Acids II
Amino Acid properties PT Hydrophobicity N Amino acid titration EL Isoelectric point Spectroscopic properties of Amino Acids
Amino Acids PT Hydrophobicity N Polar/ Non-Polar EL Chirality
Properties of Amino Acids R Size and shape Cα C O EL H OAt physiological pH Zwitterionic form PT Hydrophobicity Aromaticity N H3 Charge/Polarity N Conformation - usually determined by side chain Propensity to adopt a particular conformation Relative position in protein
Classification of Amino Acids Acidic N Aliphatic Aromatic PT Non-Polar/ Hydrophobic EL 20 standard amino acids classification based on properties Polar/Hydrophilic Neutral Basic
Polar Amino Acids Neutral: Cysteine Asparagine, Glutamine, Serine, Threonine PT EL Acidic: N Aspartic acid ( Asp, D) MW. 115.09 pKa 3.9 Glutamic acid ( Glu,E) MW. 129.12 pKa 4.07
Lysine ( Lys, K) MW. 128.17 pKa 10.79 N Histidine ( His, H) MW. 137.14 pKa 6.04 PT EL Basic Amino acids Arginine ( Arg, R) MW. 156.19 pKa 12.48
Nomenclature of side chains of amino acid Nonhydrogen atoms of the amino acid side chain are named in sequence with the Greek alphabet γ EL ε N PT δ β α
PT EL Acid-base properties of amino acids N Henderson-Hasselbalch Equation pH pKa log[A-]/[HA]
Isoelectric Point (pI) EL Definition: the pH at which a molecule carries no net electric charge N PT Using the Henderson-Hasselbalch equation pI ½(pK1 pK2) For amino acids pK1 pKa of carboxyl group pK2 pKa of amino group
The dissociation of first proton from the -carboxyl group The dissociation of the second proton from the -amino group Gly H2O Gly0 H2O 0][H O ] [Gly 3 K1 [Gly ] EL Gly0 H3O Gly- H3O N PT -][H O ] [Gly 3 K2 [Gly0] [Gly0] pH pK1 log [Gly ] [Gly-] pH pK2 log [Gly0]
Titration of Glycine COO- COOH H3N C H H3N pK1 pH 2.3 C H2N H pK2 pH 9.6 COOC N PT EL H H H Calculation of the the pI (isoelectric point) where the amino acid is neutral. pI average of (pK below neutral pK above neutral) pI of Glycine (pK1 pK2)/2 (2.3 9.6)/2 6 H
N PT EL Titration curve of Glycine pH H NCH COO- H NCH COO- H 3 2 2 2 12 10 8 COO Neutral form pI 6 C H3N H 4 H 2 H3 NCH2COOH H3 NCH2COO- H 0 0.5 1.0 1.5 2.0 0 H ions dissociated/molecule
Titration of amino acids with ionizable side chains N PT EL Acidic amino acids Basic amino acids Histidine
EL PT N
N PT EL Lysine titration
COON H C CH2 N NH2 pKa 9.3 H -1 COO N 2 H CH2 N NH3 H pKa 1.8 0 0 2 4 6 8 10 1214 pH 0 H COO- PT 1 C EL pKa 6.0 N Mols -OH added per mol histidine Histidine Titration 3 H N C CH2 NH3 N 1 H COOH H N H C NH3 CH2 N H 2
Amino acid on surface of enzyme O C H C N C H2 N EL 0 NH H PT pKa 6.0 O H 0 0 N Mols OH- added Histidine Titration 6 12 pH 1 C C NH H N C H2 N H
Amino acid in active site O C H C N C H2 EL pKa 6.0 PT pKa 6.0 O H pKa 6.0 0 0 2 4 6 8 10 12 14 pH N 0 NH N Mols OH- added Histidine Titration H C C NH H N C H2 N H 1 - - - -
The Acid-Base Chemistry of the Amino Acids EL pI 2.35 9.78 6.1 2 Lysine Lys PT Glutamic acid Glu N pI 9.18 10.79 10.0 2 pI 2.10 4.07 3.1 2 Glycine Gly
Hydrophobicity of amino acids EL Glycine, Alanine, Valine, Leucine, Isoleucine, Methionine, Proline, Phenylalanine, Tyrosine, Tryptophan: Hydrophobic Amino acids PT Phenylalanine, Tyrosine, Tryptophan: Aromatic amino acids N HYDROPATHY INDEX – measure of hydrophobicity
4.5 4.2 3.8 2.8 2.5 N PT Leucine Phenylalanine Cysteine Hydropathy index EL Kyte – Doolittle Amino acid hydropathy index Isoleucine Valine Methionine 1.9 Alanine 1.8
Glycine Threonine - 0.4 - 0.7 - 0.9 - 0.8 - 1.3 N PT Tryptophan Serine Tyrosine Hydropathy index EL Kyte – Doolittle Amino acid hydropathy index Proline - 1.6 Histidine - 3.2
Glutamic acid Lysine PT Glutamine Aspartic acid Asparagine Hydropathy index - 3.5 - 3.5 - 3.5 - 3.5 - 3.9 - 4.5 EL Amino acid N Kyte – Doolittle hydropathy index Arginine
Hydropathy plot To identify hydrophobic regions in proteins Commonly used to identify transmembrane regions PT EL Method: Sliding window approach Window size of 7, 9 or 11 residues considered The average hydropathy index value of the amino acid residues is calculated and plotted. N From the positive and negative region of this plot, the surface and core constructing regions for normal and transmembrane protein can be figured out.
Hydropathy Plot N Window size of 7 PT EL Method: Sliding window approach Window size of 7, 9 or 11 residues considered The average hydropathy index value of the amino acid residues is calculated and plotted. Ile Leu Ala Val Ser Asp Thr Met Gly
Sliding window approach Window of 7 residues PT EL Ile Leu Ala Val Ser Asp Thr Met Gly 4.5 3.8 1.8 4.2 -0.8 -3.5 -0.7 1.9 -0.4 9.3/7 1.33 N 6.7/7 0.95 2.5/7 0.357
EL Lysozyme PT 12 10 8 6 4 2 0 ATPase N % Composition Amino acid composition for the 20 amino acids in transmembrane and globular proteins A C D E F G H I K L MN P Q R S T VW Y Amino acids
Amino Acids PT Hydrophobicity N Polar/ Non-Polar EL Chirality
PT EL Voet, Voet and Pratt: Principles of Biochemistry. Fourth edition N Lehninger: Biochemistry
EL PT N
20 standard amino acids classification based on properties Non-Polar/ Hydrophobic Aromatic Polar/Hydrophilic Acidic . Titration of amino acids with ionizableside chains Acidic amino acids Basic amino acids Histidine NPTEL. NPTEL. Lysine titration NPTEL. Histidine Titration 3 2 1 0 0 2 4 6 8 10 1214 pK a 1.8 pK a
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protein:ligand, K eq [protein:ligand] [protein][ligand] (1) can be restated as, K eq 1 [ligand] p 1 p 0 (2) where p 0 is the fraction of free protein and p 1, the fraction of protein binding the ligand. Assuming low protein concentration, one can imagine an isolated protein in a solution of Nindistinguishable ligands. Under these premises .
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of protein assay for research applications. Protein assays based on these methods are divided into two categories: dye binding protein assays and protein a ssays based on alkaline copper. The dye binding protein assay s are based on the binding of protein molecules to Coomassie dye under acidic conditions.
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