Computational and Mathematical Methods in Medicine

Functional Dynamics of Proteins


Publishing date
25 May 2012
Status
Published
Submission deadline
25 Jan 2012

Lead Editor

1Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 300, Taiwan

2Department of Chemistry, Rice University, Houston, TX, USA

3Institute of Biological Chemistry, Academia Sinica, Taiwan

4College of Nursing and Health Professions, University of Southern Indiana, Evansville, USA


Functional Dynamics of Proteins

Description

Atomic thermal fluctuations and protein domain motions, basic consequence of the definition of temperature, are essential to protein functions. The vibrant nature of proteins poses a challenge to rational drug design where the synthetic chemical probes/drugs have to hit the “moving targets.” “Healthy” protein dynamics, resulting from a delicate interplay between conformational selection and induced fit, are essential to precise enzymatic reactions and molecular recognitions. Atoms in enzymes are believed to function as an interacting network and are therefore allosterically regulated. Molecular motions that could promote catalyzed chemical reactions vary in sizes, from side chain flipping, domain rearrangement, to collective motions that involve the entire protein. The time scales of these motions can span from picoseconds to milliseconds, which calls for variety of spectroscopic technology and simulation schemes to proper address the dynamics occurring in hierarchical time and space.

With the rising interest in protein dynamics that are known crucial to drug design and disease-related protein-protein interaction/recognition, we herein call for manuscripts that report studies revealing the relation between protein dynamics and their functions. Reviews that summarize the advancement of spectroscopic technology and theoretical methods that address the importance of functional dynamics are welcome. Potential topics include, but are not limited to:

  • Advanced spectroscopic and theoretical methods that characterize local and global dynamics
  • Conformational changes found or predicted in the protein-ligand interactions and how the understandings of protein/ligand dynamics can facilitate the rational drug design
  • Structure ↔ dynamics ↔ function relationship reported for a particular system
  • Single molecule experiments that report the time and spatial distribution of interesting molecular events
  • Nonequilibrium dynamics including protein folding/misfolding/unfolding
  • Databases and web servers that store and generate dynamics data of protein, DNA/RNAs, and other biomolecules
  • Dynamics and conformational changes that are observed and predicted in the protein-protein interaction and protein-ligand docking
  • Discussions and systematic reviews of aforementioned topics (reviews)

Before submission authors should carefully read over the journal's Author Guidelines, which are located at http://www.hindawi.com/journals/cmmm/guidelines/. Prospective authors should submit an electronic copy of their complete manuscript through the journal Manuscript Tracking System at http://mts.hindawi.com/ according to the following timetable:


Articles

  • Special Issue
  • - Volume 2012
  • - Article ID 242903
  • - Editorial

Functional Dynamics of Proteins

Lee-Wei Yang | Silvina Matysiak | ... | Yasumasa Joti
  • Special Issue
  • - Volume 2012
  • - Article ID 781456
  • - Research Article

Coarse-Grained Simulation of Myosin-V Movement

Zoe Katsimitsoulia | William R. Taylor
  • Special Issue
  • - Volume 2012
  • - Article ID 151854
  • - Research Article

Molecular Dynamics Simulation of HIV Fusion Inhibitor T-1249: Insights on Peptide-Lipid Interaction

A. M. T. Martins do Canto | A. J. Palace Carvalho | ... | Luís M. S. Loura
  • Special Issue
  • - Volume 2012
  • - Article ID 541594
  • - Research Article

Implication of Crystal Water Molecules in Inhibitor Binding at ALR2 Active Site

Hymavati | Vivek Kumar | M. Elizabeth Sobhia
  • Special Issue
  • - Volume 2012
  • - Article ID 805827
  • - Review Article

Analyzing Effects of Naturally Occurring Missense Mutations

Zhe Zhang | Maria A. Miteva | ... | Emil Alexov
  • Special Issue
  • - Volume 2012
  • - Article ID 569870
  • - Review Article

Revealing −1 Programmed Ribosomal Frameshifting Mechanisms by Single-Molecule Techniques and Computational Methods

Kai-Chun Chang
  • Special Issue
  • - Volume 2012
  • - Article ID 790281
  • - Research Article

Membrane Protein Stability Analyses by Means of Protein Energy Profiles in Case of Nephrogenic Diabetes Insipidus

Florian Heinke | Dirk Labudde
Computational and Mathematical Methods in Medicine
 Journal metrics
Acceptance rate38%
Submission to final decision61 days
Acceptance to publication39 days
CiteScore1.840
Impact Factor1.563
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