Study of Loop Length & Residue Composition of β-Hairpin Motif Xin Zhan Nov 27, 2006 Xin Zhan CS 882 course project

Outline Research background about β-hairpin motif My task overview Preliminary results Future works Xin Zhan CS 882 course project

β-Hairpin Motif Simplest protein motif involving two beta strands [from Wikipedia] adjacent in primary sequence antiparallel linked by a short loop As isolated ribbon or part of beta sheet a special case of a turn direction of protein backbone reverses flanking secondary structure elements interact (hydrogen bonds) Xin Zhan CS 882 course project

Types of Turns β-turn (most common) δ-turn γ-turn α-turn π-turn ω-loop donor and acceptor residues of hydrogen bonds are separated by 3 residues (i i +3 H-bonding) δ-turn i i +1 H-bonding γ-turn i i +2 H-bonding α-turn i i +4 H-bonding π-turn i i +5 H-bonding ω-loop a longer loop with no internal hydrogen bonding Is characterized by… 1 Delta ; 2 gamma People have found beta and pi turn occurring in beta hairpin Xin Zhan CS 882 course project

Loop Length of β-Hairpin 70% hairpins with loop length ≤ 7 Most are 2 residues loops 2 residues loops prefer type I’ and II’ beta turns [Sibanda & Thornton 85’] People have found.. The authors also classify hairpins based on loop length and conformations of loop regions. Xin Zhan CS 882 course project

Turn Type of Two residue β-Hairpin (1) Types I‘ Residue 1 adopts left-handed alpha-helical conformation Preference for GLY, ASP, ASN Residue 2 nearly always GLY Type II’ Residue 1 only GLY Residue 2 polar amino acids such as SER, THR Type 1, residue 2: as the required phi and psi angles are well outside the allowed regions of the Ramachandran plot for amino acids with side chains. Type 1, residue 1: has a conformation which can only be adopted by glycine. This is because amino acids other than glycine would cause steric hindrance involving the residue's side chain and the main chain. Xin Zhan CS 882 course project

Turn Type of Two residue β-Hairpin (2) Residue 2 in type I’ and residue 1 in type II’ has a conformation which can only be adopted by GLY phi and psi angles are well outside the allowed regions of the Ramachandran plot for amino acids with side chains Type 1, residue 2: as the required phi and psi angles are well outside the allowed regions of the Ramachandran plot for amino acids with side chains. Type 1, residue 1: has a conformation which can only be adopted by glycine. This is because amino acids other than glycine would cause steric hindrance involving the residue's side chain and the main chain. Xin Zhan CS 882 course project

Three Residue β-Hairpin 1st residue adopts right-handed alpha-helical conformation 2nd in the region between alpha-helix and beta-sheet 3rd position prefer GLY, ASN, ASP 3rd: as this adopts phi and psi angles close to the left-handed helical conformation Xin Zhan CS 882 course project

Four Residue β-Hairpin 1st and 2nd residues adopting the alpha-helical conformation 3rd in the region between alpha-helix and beta-sheet 4th position prefer GLY, ASN, ASP 3rd: as this adopts phi and psi angles close to the left-handed helical conformation Xin Zhan CS 882 course project

Prediction of Turns [Chou 97’] Site-independent model based on knowledge that amino acid preferences at individual positions in ß-turns and does not consider any coupling between the residues in the sequence 1-4 & 2-3 correlation model based on residue coupling Sequence coupled model based on first-order markov chain involving conditional probabilities The existing prediction methods can be classified into 3 categories 1 model is based on knowledge that.. 2 model predict the ß-turns in proteins based on residue coupling. the coupling effect between the 1st and the 4th residues and that between the 2nd and the 3rd residues was given a special consideration. Xin Zhan CS 882 course project

β–Hairpin Revisited [Gunasekaran 97’] A data set of 250 non-homologous proteins For 3 residue loops, major conformational motif is αR-αR-αL (type I followed by a residue in a left-handed helical conformation) For 4 residue loops, αR-αR-αR-αL (π-turn motif) Small polar residue ASN, ASP, SER, THR, GLY and PRO are preferred in loop Identify several CYS-CYS pairs at the non-hydrogen bonded positions of beta stands Gave an reexamination of beta hairpin conformation. Xin Zhan CS 882 course project

β–Hairpin Folding Mechanism [Galzitskaya 02’] Review experimental and theoretical studies of β–hairpin folding mechanism Hydrogen-bond-centric model Formation of folding droplet starting from beta turn is the determining factor Hydrophobic-core-centric model A core structure formed by side chains from both strands comes first, then brings the two strands together to form hydrogen bonds The hydrogen-bond-centric model assumes that the formation of a folding droplet starting from the ß-turn is the determining factor in transition kinetics. The hydrophobic-core-centric model proposes that a core structure formed by side chains from both strands comes first, and then brings the two strands together to form hydrogen bonds. Xin Zhan CS 882 course project

My Task Overview 1116 proteins resolution ≤ 1.6 A Non-homologous Extract beta hairpins Identify loop length Classify hairpins based on loop length List is from PISCES, generated on Nov 11, 2006 Check secondary structures Select anti-parallel beta strands Verify no alpha helix between the strands Analysis residue preferences Cluster hairpins based on RMSD Xin Zhan CS 882 course project

Distribution of β–Hairpins Based on Loop Length Top 3 are 2 4 and 5 residues loops. Next I get a close look at them. Xin Zhan CS 882 course project

Amino Acids Distributions in Loop Regions The number of a residue i over the total number of residues in loop regions Only shows the top 10, the last 8 always has the highest ratio Charged Amino Acids: LYS GLU Hydrophobic amino acids: ALA Xin Zhan CS 882 course project

A.A. with hydrophilic side A. A. that are in between Xin Zhan CS 882 course project

Amino Acids Distributions in 2 Residues Loops The number of a residue i occurs at position j over the total number of residues at position j. GLY is favored , High beta turn propensity of GLY Xin Zhan CS 882 course project

Amino Acid Distributions in 4 Residues Loops Xin Zhan CS 882 course project

Position Preference of Amino Acids in 5 Residues Loops A residue’s preference for a loop position Fij is the number of times residue i occurs in a loop position j Di is the number of times residue i occurs in the loop region Xin Zhan CS 882 course project

Position Preference of Amino Acids in 5 Residues Loops Xin Zhan CS 882 course project

Considering Structural Similarity Further cluster beta hairpins based on structural similarity of loop region Analysis the amino acid distributions in each cluster That ‘s all the experimental result I will show today. Xin Zhan CS 882 course project

RMSD Measure the structure similarity between two proteins Given the position vectors of two sequences of amino acids V, W Xin Zhan CS 882 course project

Candidate Clustering Algorithms Partition methods K-means / Quality Threshold Hierarchical clustering method UPGMA / Diana Fuzzy logic based method Fuzzy c-means clustering / Fanny Neural network based methods SOM / SOTA SOM (self-organizing maps) and SOTA (self-organizing tree algorithm) Xin Zhan CS 882 course project

Reference Sibanda BL, Thornton JM. Beta-hairpin families in globular proteins. Nature 1985. 316(6024):170–174. Chou, K.C. and Blinn, J.R. Classification and prediction of beta-turn types. Protein Chem. 1997. 16, 575-595. Gunasekaran K, Ramakrishnan C, Balaram P. Beta-hairpins in proteins revisited: lessons for de novo design. Protein Eng. 1997 Oct;10(10):1131-41. Galzitskaya, O. V., J. Higo, and A. V. Finkelstein. 2002. Alpha-helix and beta-hairpin folding from experiment, analytical theory and molecular dynamics simulations. Curr. Protein Pept. Sci. 3:191–200. Xin Zhan CS 882 course project

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