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Int. J. Mol. Sci. 2016, 17(10), 1741; doi:10.3390/ijms17101741

Structural Interface Forms and Their Involvement in Stabilization of Multidomain Proteins or Protein Complexes

1
Department of Rehabilitation, Hospital in Przemyśl, Monte Cassino 18, 37-700 Przemyśl, Poland
2
Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University, Łojasiewicza 11, 30-348 Krakow, Poland
3
Department of Bioinformatics and Telemedicine, Jagiellonian University–Medical College, Łazarza 16, 31-530 Krakow, Poland
4
Chair of Medical Biochemistry, Jagiellonian University–Medical College, Kopernika 7, 31-034 Krakow, Poland
*
Author to whom correspondence should be addressed.
Academic Editor: Christo Z. Christov
Received: 14 August 2016 / Revised: 30 September 2016 / Accepted: 11 October 2016 / Published: 18 October 2016
(This article belongs to the Section Physical Chemistry, Theoretical and Computational Chemistry)
View Full-Text   |   Download PDF [9116 KB, uploaded 18 October 2016]   |  

Abstract

The presented analysis concerns the inter-domain and inter-protein interface in protein complexes. We propose extending the traditional understanding of the protein domain as a function of local compactness with an additional criterion which refers to the presence of a well-defined hydrophobic core. Interface areas in selected homodimers vary with respect to their contribution to share as well as individual (domain-specific) hydrophobic cores. The basic definition of a protein domain, i.e., a structural unit characterized by tighter packing than its immediate environment, is extended in order to acknowledge the role of a structured hydrophobic core, which includes the interface area. The hydrophobic properties of interfaces vary depending on the status of interacting domains—In this context we can distinguish: (1) Shared hydrophobic cores (spanning the whole dimer); (2) Individual hydrophobic cores present in each monomer irrespective of whether the dimer contains a shared core. Analysis of interfaces in dystrophin and utrophin indicates the presence of an additional quasi-domain with a prominent hydrophobic core, consisting of fragments contributed by both monomers. In addition, we have also attempted to determine the relationship between the type of interface (as categorized above) and the biological function of each complex. This analysis is entirely based on the fuzzy oil drop model. View Full-Text
Keywords: hydrophobic core; homodimers; utrophin; dystrophin; domain; hydrophobicity; interface hydrophobic core; homodimers; utrophin; dystrophin; domain; hydrophobicity; interface
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

Dygut, J.; Kalinowska, B.; Banach, M.; Piwowar, M.; Konieczny, L.; Roterman, I. Structural Interface Forms and Their Involvement in Stabilization of Multidomain Proteins or Protein Complexes. Int. J. Mol. Sci. 2016, 17, 1741.

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