Primary/Secondary Structures

 

I.                   Terminology

II.                Secondary Structure Algorithm

a.      “Algorithm for Ribbon Models of Proteins.” Mike Carson, Charles E. Bugg. University of Alabama-Birmingham (html)

b.      “ A dynamic programming algorithm for RNA structure prediction including pseudoknots” (pdf, ps)

III.             Summary of Papers

a.      “A Generalization of Algebraic Surface Drawing.” JamesF. Blinn. Jet Propulstion Laboratory (Shubing Wang)

b.      “Adaptive Multilevel Finite Element Solution of the Poisson – Boltzmann Equation II. Refinement at Solvent –Accessible Surfaces in Biomolecular Systems.” N. Bakers, M. Holst, E. Wang (1999) (Yufeng Zhang)

c.  “HelixHunterP: Parallel Implementation of HelixHunter using Pthreads.” Matthew Baker, Wen Jiang. May 1999. (doc)

IV.              Secondary Structure Tools

 

 

I. Terminology

 

Consider the example of triosephosphate isomerase. The protein has the following primary sequence:

APRKFFVGGNWKMNGDKKSLGELIHTLNGAKLSADTEVVCGAPSIYLDFAR

QKLDAKIGVAAQNCYKVPKGAFTGEISPAMIKDIGAAWVILGHSERRHVFGES

DELIGQKVAHALAEGLGVIACIGEKLDEREAGITEKVVFEQTKAIADNVKDW

SKVVLAYEPVWAIGTGKTATPQQAQEVHEKLRGWLKSHVSDAVAQSTRI

IYGGSVTGGNCKELASQHDVDGFLVGGASLKPEFVDIINAKH

The three dimensional structure has been determined by X-ray crystallography and is shown below:

Figure 1. Various representations of a protein three-dimensional structure. The X-ray crystal structure of triosephosphate isomerase (1TIM) shown in the same orientation (clockwise from upper left) using all 3711 atoms (including hydrogen) in CPK format, using all 988 backbone heavy atoms N, CA, C, O in wire frame format, using all 247 CA atoms, and in cartoon format produced with Molscript (Kraulis, 1991).

amino acids – organic molecules possessing both carboxyl and amino groups

polymer – long molecule consisting of many identical or similar building blocks linked by covalent bonds, much as a train consists of chain of cars. A protein consists of one or more polypeptides folded and coiled into specific 3-d shapes(conformations)

polypeptide – polymer of amino acids connected in a specific sequence

peptide bonds – when two amino acids are positioned so that the carboxyl group of one is adjacent to an amino group of another

primary structure: The chemical structure of the polypeptide chain or chains in a given protein - i.e., the number and sequence of amino acid residues linked together by peptide bonds.

secondary structure: Any such folding which is brought about by linking the carbonyl and imide groups of the backbone together by means of hydrogen bonds.

tertiary structure: A organization of secondary structures linked by "looser segments" of the polypeptide chain stabilized (primarily) by sidechain interactions. Disulfide bonds are included in this level.

quaternary structure: The aggregation of separate polypeptide chains into the functional protein

Formation of Secondary Structure

Coils and folds are a result of hydrogen bonds at regular intervals along the polypeptide backbone.  Both the oxygen and nitrogen atoms have relatively weak negative charges.  The weakly positive hydrogen atom attached to the nitrogen atom has an affinity for the oxygen atom of a nearby peptide bond.  Individual these bonds are weak but over a long region of a polypeptide chain support a particular shape for that part of the protein -> helices, sheets, turns

Types of Secondary Structure

I.                    Helices 

In a helical conformation, the relationship of one peptide unit to the next is the same for all alpha-carbons. This means that the dihedral angle pairs phi and psi (phii, psii) are the same for each residue in the helical conformation. Helices are classified as repetitive secondary structure since their backbone phi and psi angles repeat (for the geometrically ideal, right-handed, alpha helix, these values are phi = -57.8 and psi = -47.0)

II.                 Sheets - antiparallel, parallel, twists, bulges, strand connections

The beta strand is then like the alpha helix, a repeating secondary structure. However, since there are no intrasegment hydrogen bonds and van der Waals interactions between atoms of neighboring residues are not significant due to the extended nature of the chain, this extended conformation is only stable as part of a beta sheet where contributions from hydrogen bonds and van der Waals interactions between aligned strands exert a stabilizing influence

III.               Turns

 

II. Secondary Structure Algorithm

This data file contains information about the types of atoms, the amino acid sequence, the atomic connectivity, geometrical data, and the coordinates of each atom of different proteins. This data is obtained through a process of amino acid sequencing, crystallization of the protein, and the assignment of position using crystallography or nuclear magnetic resonance

III. Summary of Papers

IV. Secondary Structure tools: