Biochemistry Online: An Approach Based on Chemical Logic

CHAPTER 2 - PROTEIN STRUCTURE

G: PREDICTING PROTEIN PROPERTIES FROM SEQUENCES

BIOCHEMISTRY - DR. JAKUBOWSKI

Last Update: 3/9/16

Learning Goals/Objectives for Chapter 2G: After class and this reading, students will be able to:

find web based proteomics protein to analyze protein sequences and structures
describe the basis for methods used to predict the secondary structure and hydrophobic structures of proteins
analyze secondary structure and hydropathy plots from web-based proteomics programs.
describe differences between integral and peripheral membranes proteins, and how each could be purified.
explain how hydropathy and secondary structure plots can be used to predict membrane spanning sequences of proteins
describe in general the theoretical and empirically based methods to predict protein tertiary structure from a primary sequence
describe possible early intermediates in protein folding as determined by theoretical methods

G3. Prediction of Hydrophobicity

In a completely analogous fashion, a hydrophobic propensity or hydopathy can be calculated. In this system, empirical measures of the hydrophobic nature of the side chains are used to assign a number to a given amino acid. Many hydropathy scales are used. Several are based on the Dmo transfer of the side chains from water to a nonpolar solvent. Two commonly used scales are the Kyte-Doolittle Hydropathy and Hopp-Woods scales (used more like a hydrophilicity index to predict surface or water accessible structures that might be recognized by the immune system)

Hydrophobicity Indices for Amino Acids

Amino Acid	Kyte-Doolittle	Hopp-Woods
Alanine	1.8	-0.5
Arginine	-4.5	3.0
Asparagine	-3.5	0.2
Aspartic acid	-3.5	3.0
Cysteine	2.5	-1.0
Glutamine	-3.5	0.2
Glutamic acid	-3.5	3.0
Glycine	-0.4	0.0
Histidine	-3.2	-0.5
Isoleucine	4.5	-1.8
Leucine	3.8	-1.8
Lysine	-3.9	3.0
Methionine	1.9	-1.3
Phenylalanine	2.8	-2.5
Proline	-1.6	0.0
Serine	-0.8	0.3
Threonine	-0.7	-0.4
Tryptophan	-0.9	-3.4
Tyrosine	-1.3	-2.3
Valine	4.2	-1.5

For a water-soluble protein, a continuous stretch of amino acids found to have a high average hydropathy is probably buried in the interior of the protein. Consider the example of bovine a-chymotrypsinogen, a 245 amino acid protein, whose sequence is shown below in single letter code.

1 CGVPAIQPVLSGLSRIVNGEEAVPGSWPWQVSLQDKTGFHFCGGSLINENWVVTAAHCGV
61 TTSDVVVAGEFDQGSSSEKIQKLKIAKVFKNSKYNSLTINNDITLLKLSTAASFSQTVSA
121 VCLPSASDDFAAGTTCVTTGWGLTRYTNANTPDRLQQASLPLLSNTNCKKYWGTKIKDAM
181 ICAGASGVSSCMGDSGGPLVCKKNGAWTLVGIVSWGSSTCSTSTPGVYARVTALVNWVQQ
241 TLAAN

A hydrophathy plot for chymotrypsinogen (sum of hydropathies of seven consecutive residues) shows many stretches that are presumably buried in the interior of the protein.

Figure: hydrophathy plot for chymotrypsinogen

back Navigation

Return to Chapter 2G: Predicting Protein Properties from Sequences

Return to Biochemistry Online Table of Contents

Archived version of full Chapter 2G: Predicting Protein Property from Sequences

Biochemistry Online by Henry Jakubowski is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.