Special Issue "Advances in Molecular Recognition"

Guest Editor
Prof. Dr. A. Keith Dunker
Department of Biochemistry and Molecular Biology, Indiana University Schools of Medicine & Informatics, 410 W. 10th Street, Suite 5000, Indianapolis, IN 46202, USA
Website: http://compbio.iupui.edu/people/details/8
E-Mail:

Dear Colleagues,

Molecular recognition is the specific interaction of one molecule with another by means of noncovalent bonds and hydrophobic effects. Molecular recognition can lead to the formation of a stable or transient complex between the two molecules or can lead to more complex interactions that result in associated allostery, catalysis, or even assembly of molecular machines. The interacting molecular pair can vary widely in size and complexity, from small molecules or even metal ions, to large proteins, nucleic acids, lipid assemblies, and carbohydrates. Molecular recognition is the most fundamental process underpinning life. Virtually every cellular activity can be viewed as a spatially and temporally ordered series of molecular recognition steps involving two or more molecules at each step.

Over the years a variety of models have been proposed to explain molecular recognition from the most fundamental level to the highest level of complexity. These models include, for small molecules, stereochemical fit among others, and for biological molecules, the lock and key, induced fit, conformational selection and coupled binding and folding. Recently very detailed computational models are being explored that probe shape, hydrogen bonding, and charge complementarity. Given the recent advances in high level models and in experimental and computational techniques that identify and probe molecular recognition events, it is time for an update in this rapidly advancing area.

Prof. Dr. A. Keith Dunker
Guest Editor

Submission

All manuscripts should be submitted to ijms@mdpi.org with a copy to the Guest Editor. Manuscripts can be submitted until the deadline. Papers will be published continuously (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

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Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this Open Access journal is 1000 CHF per accepted paper.

• lock and key
• induced fit
• coupled binding and folding
• conformational selection
• multispecificity

Type of Paper: Review
Title: Structural Properties of Hubs in Protein-Protein Interaction Networks
Authors: Ashwini Patil ¹, Kengo Kinoshita ² and Haruki Nakamura ³
Affiliations: ¹ Human Genome Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokane-dai, Minato-ku, Tokyo 108-8639, Japan
² Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki-aza-aoba, Aoba-ku, Miyagi, 982-0036, Japan
³ Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan; E-Mail: harukin@protein.osaka-u.ac.jp
Abstract: Hubs are proteins with a large number of interactions in a protein-protein interaction network. They are the principal components of the interaction network and affect its function and stability. Their specific recognition of many different protein partners is of great interest from the structural viewpoint. Over the last few years, the structural properties of hubs have been extensively studied. We review the currently known features that are particular to hubs, possibly affecting their binding ability. Specifically, we look at the levels of intrinsic disorder, surface charge and domain distribution in hubs, as compared to non-hubs, along with differences in their functional domains.