Biochemistry Online: An Approach Based on Chemical Logic

CHAPTER 2 - PROTEIN STRUCTURE

C: UNDERSTANDING PROTEIN CONFORMATION

BIOCHEMISTRY - DR. JAKUBOWSKI

3/4/16

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

describe the differences between primary, secondary, supersecondary, tertiary, quaternary and domain protein structure
explain the basis of CD measurements for secondary structure
describe the similarities between torsion angles and an energy vs torsion angle plot for the rotation of the C2-C3 torison angle with phi/psi angles of peptide bonds and the 2D plots off allowed conformations around a given amino acid in a protein (Ramachandran plot).
(from reading give explanation for observed propensities of amino acids for different secondary structure)

C5. Structual Clases of Proteins

Proteins can be divided into 3 classes of protein, depending on their characteristic secondary structure. Click below for Chime structures showing examples of these proteins.

alpha proteins - consist of predominately alpha helix.

Jmol: Updated cytochrome B562 Jmol14 (Java) | JSMol (HTML5)

Jmol: Updated met-myoglobin Jmol14 (Java) | JSMol (HTML5)

alpha/beta proteins - consist of a common of alpha and beta structure. These are the most common class.

Jmol: Updated triose phosphate isomerase Jmol14 (Java) | JSMol (HTML5)

Jmol: Updated hexokinase Jmol14 (Java) | JSMol (HTML5)

beta proteins - consist of predominantly beta structure.

Jmol: Updated superoxide dismutase Jmol14 (Java) | JSMol (HTML5)

Jmol: Updated human IgG1 antibodyJmol14 (Java) | JSMol (HTML5)

Jmol: Updated retinol binding proteinJmol14 (Java) | JSMol (HTML5)

fatty acid binding proteins; Peptide-N(4)-(N-Acetyl-b-D-Glucosaminyl) Asparagine Amidase (PNGase F) - under construction.

Tertiary Protein Structure and Folds from ExPAYs
Principles of Protein Structure on the Web

A more complete classification of protein structure has been developed based on the following hierarchy of organization: Class, Architecture, Topology, and Homologous Superfamilies - CATH.

Class: the highest level of organization which consists of four classes - mainly alpha, mainly beta, alpha-beta, and few secondary structures
Architecture (40 types): describes the shape of domain based on secondary structures but doesn't describe how they are connected. Ex: beta barrel, beta propellor
Topology (or fold group, 1233 types): members in topology groups have a common fold or topology in the "core" of the domain structure.
Homologous Superfamilies (2386 types): These groups are homologous in sequence or structure and derive from a common precursor gene/protein.

Structural Biology Knowledge Base

Here are some 3D structures resources, accessible through a sequence or ID-based search. and collated in Nature's Structural Biology Knowledge Base.

Biological Magnetic Resonance Data Bank
CATH - structural classification of manually curated classification of protein domain structures
DisProt - Database of Protein Disorder
Gene3D - CATH domain assignments for protein sequences
NESG Functional Annotation Database - Computational analysis of function of protein of unknown function
Membrane proteins of known 3D structure
RCSB PDB - Protein Data Bank USA
PDBe - Protein Databank Europe
PDBj - Protein Databank Japan
PDBsum - a pictorial database that provides an at-a-glance overview of the contents of each 3D structure deposited in the Protein Data Bank
PROCOGNATE - database of cognate ligands for the domains of enzyme structures in CATH, SCOP and Pfam
SCOP - Structural Classification of Proteins: detailed and comprehensive description of the structural and evolutionary relationships between all proteins whose structures are known
SMART (Simple Modular Architecture Research Tool) - allows the identification and annotation of genetically mobile domains and the analysis of domain architectures

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