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)

C6. Quarternary Structure

Primary structure is the linear sequence of the protein. Secondary structure is the repetitive structure formed from H-bonds among backbone amide H and carbonyl O atoms. Tertiary structure is the overall 3D structure of the protein. Quaternary structure is the overall structure that arises when tertiary structures aggregate to self to form homodimers, homotrimers, or homopolymers OR aggregate with different proteins to form heteropolymers.

Quaternary Structure from ExPAYs

Globular versus fibril structures

We will deal exclusively with proteins which have a "globular" tertiary structure in this course. However, there are many proteins that form elongated fibrils with properties like elasticity, which measures the extent of deformation with a given force and subsequent return to the original state. Elastic molecules must store energy (go to a higher energy state) when the elongating force is applied, and the energy must be released on return to the equilibrium resting structure. Structures that can store energy and release it when subjected to a force have resiliency. Proteins that stretch with an applied forces include elastin (in blood vessels, lungs and skins where elasticity is required), resilin in insects (which stretches on wing beating), silk, found in spider web) and fibrillin found in most connective tissues and cartilage. Some proteins have high resiliency (90% in elastin and resilin), while others are only partially resilient (35% in silk, which have a tensile strength approaching that of stainless steel. In contrast to rubber, which has an amorphous structure which imparts elasticity, these proteins, although they have a dissimilar amino acid sequence, seem to have a common structure inferred from their DNA sequences. In some (like fibrillin), the protein has a folded b-sheet domain which unfold like a stretched accordion. Others (like elastin and spider silk) have b-sheet domain and other secondary structures (a-helices and (b turns) along with Pro and Ala repetitions. Researcher are studying these structures to help in the synthesis of new elastic and resilient products

Comprehensive Database for Protein Analysis - Biozon
SCOP: Structural Characterization of Proteins - Database showing folds, superfamiles, families, and domains

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