Mohana Priya A

Department of Biotechnology

School of Bio Sciences and Technology

Vellore Campus

Nilofer c

Sukhwal a

Kangueane p

Fulltext

Vellore Institute of Technology (VIT) is a private university located in&nbsp;Tamil Nadu, India. Founded in 1984, as Vellore Engineering College, the institution offers 20 undergraduate, 34 postgraduate, four integrated and four research programs. It has campuses in Vellore, Amravati, Bhopal and Chennai.

VIT is one of the top ranked private universities in India according to NIRF, THE and QS Rankings.&nbsp;Govt. of India has recognized&nbsp;VIT, Vellore as an&nbsp;Institution of Eminence. This has allowed VIT to take independent quality initiatives and move up in world ranking.

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VIT University

Protein-protein interfaces are vdW dominant with selective H-bonds and (or) electrostatics towards broad functional specificity.

Bioinformation

Protein-Protein and Domain-Domain Interactions

Heterodimer Protein Complexes

Principles of Protein-Protein Interaction

The homodimers have essential role in catalysis and regulation. The homodimer folding mechanism through 2-state without stable intermediate (2S), 3-state with monomer intermediate (3SMI) and 3-state with dimer intermediate (3SDI) is fascinating. 23MI and 3SDI constitute 3-state (3S). Hence, it is important to differentiate 2S, 3SMI and 3SDI homodimers using structural features. We used the dataset of Li et al. [L. Li, K. Gunasekaran, J.G. Gan, C. Zhanhua, P. Shapshak, M.K. Sakharkar, P. Kangueane, Structural features differentiate the mechanisms between 2S and 3S folding of homodimers, Bioinformation 1 (2005) 42-49] consisting of twenty-five 2S, ten 3SMI and six 3SDI homodimer structures for the study. Interface to total (I/T) residues ratio is large for 2S than 3SMI and 3SDI. Interface to total residues ratio is similar for 3SMI (mean monomer length (ML) = 208) and 3SDI (mean monomer length (ML) = 404) despite difference in mean monomer size. Interface residues correlate with monomer size in 2S (Pearson's correlation coefficient (r); r2 = 0.41) and 3SMI (r2 = 0.52). This is not true for 3SDI with interface residues and monomer length (r2 = 0.17). Interface area (B/2) does not correlate with interface residues (r2 &lt; 0.001) and monomer size (r2 = 0.023) in 2S. This is despite a relationship with interface residues and monomer size (r2 = 0.41) in 2S. However, this is not true for 3SMI (r2 = 0.61 with interface residues and r2 = 0.25 with monomer size). In 3SDI, a different relationship is seen (r2 = 0.28 with interface residues and r2 = 0.09 with size). The mean hydrophobicity factor (Hf) is 3-fold less in 3S than 2S. Hf does not correlate with interface area in 2S (r2 = 0.03) and 3SDI (r2 = 0.0). However, a weak causal relation is seen in 3SMI (r2 = 0.23). Hydrophilic amino acid residues (E, R, K, S and Q) are prominent in 2S than 3S. Charged negative amino acid residues (D, E) are more than positive amino acid residues (R, K, H) in 2S and charged positive amino acid residues (R, K, H) are more than negative amino acid residues (D, E) in 3S. These features help to distinguish 2S, 3SMI and 3SDI providing insights to homodimer folding and binding. © 2009 Elsevier Inc. All rights reserved.

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Discrete structural features among interface residue-level classes

Protein-protein interfaces are vdW dominant with selective H-bonds and (or) electrostatics towards broad functional specificity

Journal	Bioinformation
Publisher	Biomedical Informatics
ISSN	0973-8894
Open Access	Yes