Lecture21 - Lecture 21: Protein Structure Prediction I...

Info iconThis preview shows pages 1–3. Sign up to view the full content.

View Full Document Right Arrow Icon

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
This is the end of the preview. Sign up to access the rest of the document.

Unformatted text preview: Lecture 21: Protein Structure Prediction I Introduction to protein sequence and structure Protein secondary structure prediction Some slides adapted from notes created by Dr. Keith Dunker Protein Structure: Overview Dogma : amino acid sequence determines 3-dimensional protein structure We should, in theory, be able to predict structure from sequence Knowledge of protein structure will give information about protein function FUNCTION Currently, calculating a protein structure from first principles (Quantum theory) is too difficult and complex a problem Different sequences can yield the same structure The same sequences can yield different structures Difficulties in Protein Structure Prediction Levels of Protein Structure Primary (1) structure: amino acid sequence of protein Secondary (2) structure: local structure (alpha helices or beta strands) Tertiary (3) structure: 3-dimensional structure of protein Quaternary (4) structure: structure of a multiple protein complex 1 Structure: Amino Acid sequence The amino acid sequence of a protein specifies its 3-dimensional structure Each amino acid side-chain has different chemical properties that tend towards forming different types of structures Amino acids with large, nonpolar side-chains (L, W, etc) will tend to pack into the central hydrophobic regions of proteins Amino acids with polar or charged side-chains (E, K, etc) will tend to be on the hydrophilic surface of proteins W E Properties of Amino Acid Side-Chains Amino acid structures from: http://en.wikipedia.org/wiki/Proteinogenic_amino_acid Post-translational Modifications Post-translational modifications alter the chemical properties of the amino acid side-chain, and thus can change protein structure or interactions The addition or removal of post-translational modifications are catalyzed by enzymes Examples of post-translational modifications: Phosphorylation Acetylation Methylation Ubiquitination Glycosylation Farnesylation CH 2 OH Serine Phosphorylated Serine CH 2 O P O O- O- Peptide Bonds and Rotational Conformations Peptide bonds between amino acids have a partial double bond character, limiting rotational conformations of the protein chain The structure of the protein is determined by the Phi ( ! ) and Psi ( " ) dihedral angles for each amino acid in the protein ! " ! " Picture from http://www.tulane.edu/~biochem/med/second.htm 1 Structure: Amino Acid sequence The amino acid sequence of a protein specifies its 3-dimensional structure Each amino acid side-chain has different chemical properties that tend towards forming different types of structures Amino acids with large, nonpolar side-chains (L, W, etc) will tend to pack into the central hydrophobic regions of proteins Amino acids with polar or charged side-chains (E, K, etc) will tend to be on the hydrophilic surface of proteins W E Properties of Amino Acid Side-Chains Amino acid structures from: http://en.wikipedia.org/wiki/Proteinogenic_amino_acid Amino acid structures from: http://en....
View Full Document

This note was uploaded on 01/20/2012 for the course MBIOS 478 taught by Professor Staff during the Fall '11 term at Washington State University .

Page1 / 6

Lecture21 - Lecture 21: Protein Structure Prediction I...

This preview shows document pages 1 - 3. Sign up to view the full document.

View Full Document Right Arrow Icon
Ask a homework question - tutors are online