2004 - Protein Structure & Function - From Sequence to Consequence - G. Petsko & D. Ringe.pdf

1
From Sequence to Structure
The genomics revolution is providing gene sequences in exponentially increasing
numbers. Converting this sequence information into functional information for the gene
products coded by these sequences is the challenge for post-genomic biology. The first step
in this process will often be the interpretation of a protein sequence in terms of the three-
dimensional structure into which it folds. This chapter summarizes the basic concepts that
underlie the relationship between sequence and structure and provides an overview of the
architecture of proteins.
1-0 Overview: Protein Function and Architecture
1-1 Amino Acids
1-2 Genes and Proteins
1-3 The Peptide Bond
1-4 Bonds that Stabilize Folded Proteins
1-5 Importance and Determinants of Secondary Structure
1-6 Properties of the Alpha Helix
1-7 Properties of the Beta Sheet
1-8 Prediction of Secondary Structure
1-9 Folding
1-10 Tertiary Structure
1-11 Membrane Protein Structure
1-12 Protein Stability: Weak Interactions and Flexibility
1-13 Protein Stability: Post-Translational Modifications
1-14 The Protein Domain
1-15 The Universe of Protein Structures
1-16 Protein Motifs
1-17 Alpha Domains and Beta Domains
1-18 Alpha/Beta, Alpha+Beta and Cross-Linked Domains
1-19 Quaternary Structure: General Principles
1-20 Quaternary Structure: Intermolecular Interfaces
1-21 Quaternary Structure: Geometry
1-22 Protein Flexibility
1-0 Overview: Protein Function and Architecture
Binding TATA binding protein Myoglobin
Specific recognition of other molecules is
central to protein function. The molecule that is
bound (the ligand) can be as small as the
oxygen molecule that coordinates to the heme
group of myoglobin, or as large as the specific
DNA sequence (called the TATA box) that is
bound—and distorted—by the TATA binding
protein. Specific binding is governed by shape
complementarity and polar interactions such as
hydrogen bonding.
The TATA bi