Dynameomics: mass annotation of protein dynamics and unfolding in water by high-throughput atomistic molecular dynamics simulations

Protein Engineering, Design & Selection : PEDS
David A C BeckV Daggett

Abstract

The goal of Dynameomics is to perform atomistic molecular dynamics (MD) simulations of representative proteins from all known folds in explicit water in their native state and along their thermal unfolding pathways. Here we present 188-fold representatives and their native state simulations and analyses. These 188 targets represent 67% of all the structures in the Protein Data Bank. The behavior of several specific targets is highlighted to illustrate general properties in the full dataset and to demonstrate the role of MD in understanding protein function and stability. As an example of what can be learned from mining the Dynameomics database, we identified a protein fold with heightened localized dynamics. In one member of this fold family, the motion affects the exposure of its phosphorylation site and acts as an entropy sink to offset another portion of the protein that is relatively immobile in order to present a consistent interface for protein docking. In another member of this family, a polymorphism in the highly mobile region leads to a host of disease phenotypes. We have constructed a web site to provide access to a novel hybrid relational/multidimensional database (described in the succeeding two papers) to view and ...Continue Reading

Citations

Dec 3, 2009·Journal of the American Chemical Society·Jason KeyKevin H Gardner
Aug 21, 2008·Proceedings of the National Academy of Sciences of the United States of America·David A C BeckValerie Daggett
Nov 12, 2010·Bioinformatics·R Dustin SchaefferValerie Daggett
Nov 6, 2010·Protein Engineering, Design & Selection : PEDS·R Dustin Schaeffer, Valerie Daggett
Jul 20, 2012·Journal of Bioinformatics and Computational Biology·Noah C Benson, Valerie Daggett
Feb 10, 2012·Journal of Biomedicine & Biotechnology·Olivier FisetteSébastien Morin
Feb 2, 2011·The Journal of Chemical Physics·Carlo CamilloniGuido Tiana
Aug 17, 2011·Journal of Structural Biology·Amanda L Jonsson, Valerie Daggett
Jul 14, 2010·Computational Biology and Chemistry·Hyun JooJerry Tsai
Jun 10, 2011·Journal of the American Chemical Society·Charles K Fisher, Collin M Stultz
Sep 18, 2008·Protein Science : a Publication of the Protein Society·Noah C Benson, Valerie Daggett
Feb 1, 2011·Protein Science : a Publication of the Protein Society·Alexander D Scouras, Valerie Daggett
Mar 19, 2014·Protein Science : a Publication of the Protein Society·Eric D MerkleyJoshua N Adkins
Aug 22, 2014·Protein Science : a Publication of the Protein Society·Steven J RysavyValerie Daggett
Apr 20, 2010·Structure·Marc W van der KampValerie Daggett
Aug 10, 2016·Protein Engineering, Design & Selection : PEDS·Dennis BromleyValerie Daggett
Apr 23, 2009·Biochimie·Guilhem FaureAlexandre G de Brevern
Jul 1, 2012·International Journal of Wavelets, Multiresolution and Information Processing·Noah C Benson, Valerie Daggett
Apr 5, 2017·The Journal of Physical Chemistry. B·Clare-Louise TowseValerie Daggett
Feb 28, 2017·Molecular Systems Design & Engineering·Matthew Carter Childers, Valerie Daggett
Jun 24, 2011·Journal of Biomolecular Structure & Dynamics·Ji Guo SuCun Xin Wang
Mar 19, 2014·Journal of Computational Chemistry·Jong Cheol JeongWonpil Im
Dec 24, 2019·Protein Engineering, Design & Selection : PEDS·Rudesh D ToofannyValerie Daggett
Dec 1, 2010·Biomolecular Concepts·Amanda L JonssonValerie Daggett
Jul 28, 2020·Protein Science : a Publication of the Protein Society·Dennis Bromley, Valerie Daggett
Nov 16, 2020·Protein Science : a Publication of the Protein Society·Cullen DemakisValerie Daggett
Oct 13, 2009·Journal of Chemical Theory and Computation·Willy WriggersDavid E Shaw

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.