Title

Structural features differentiate the mechanisms between 2S (2 state) and 3S (3 state) folding homodimers

Authors

Lei Li¹, Kannan Gunasekaran², Jacob Gah-Kok Gan¹, Cui Zhanhua¹, Paul Shapshak³, Meena Kishore Sakharkar¹, and Pandjassarame Kangueane^1*

Affiliation

¹School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore 639798; ²Basic Research Program, SAIC-Frederick, Inc., Laboratory of Experimental and Computational Biology, National Cancer Institute, Frederick, MD 21702, USA; ³Dementia/HIV Laboratory, Elliot Building Room 2013, Department of Psychiatry and Beh Sci, University of Miami Miller Medical School, 1800 NW 10th Avenue, Miami, Florida 33136

E-mail*

mpandjassarame@ntu.edu.sg; * Corresponding author

Article Type

Hypothesis

Date

received July 07, 2005; revised August 28, 2005; accepted September 2, 2005; published online September 2, 2005

Abstract

The formation of homodimer complexes for interface stability, catalysis and regulation is intriguing. The mechanisms of homodimer complexations are even more interesting. Some homodimers form without intermediates (two-state (2S)) and others through the formation of stable intermediates (three-state ((3S)). Here, we analyze 41 homodimer (25 `2S` and 16 `3S`) structures determined by X-ray crystallography to estimate structural differences between them. The analysis suggests that a combination of structural properties such as monomer length, subunit interface area, ratio of interface to interior hydrophobicity can predominately distinguish 2S and 3S homodimers. These findings are useful in the prediction of homodimer folding and binding mechanisms using structural data.

Keywords

Homodimer; structural difference; 2 state; 3 state; stable intermediate; folding mechanisms

Abbreviations

2S = 2 state homodimer; 3S = 3 state homodimer; 3SMI =  3 state homodimer with monomer intermediate; 3SDI = 3 state homodimer with dimer intermediate; ML =  monomer length; B/2 = subunit interface area; F_hp =  fraction of interface to interior hydrophobicity

Citation

Li et al., Bioinformation 1(2): 42-49 (2005)

Edited by

SANDEEP Kumar

ISSN

0973-2063

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.