Iterative cluster-NMA: A tool for generating conformational transitions in proteins.

Proteins
Adam D SchuylerGregory S Chirikjian

Abstract

Computational models provide insight into the structure-function relationship in proteins. These approaches, especially those based on normal mode analysis, can identify the accessible motion space around a given equilibrium structure. The large magnitude, collective motions identified by these methods are often well aligned with the general direction of the expected conformational transitions. However, these motions cannot realistically be extrapolated beyond the local neighborhood of the starting conformation. In this article, the iterative cluster-NMA (icNMA) method is presented for traversing the energy landscape from a starting conformation to a desired goal conformation. This is accomplished by allowing the evolving geometry of the intermediate structures to define the local accessible motion space, and thus produce an appropriate displacement. Following the derivation of the icNMA method, a set of sample simulations are performed to probe the robustness of the model. A detailed analysis of beta1,4-galactosyltransferase-T1 is also given, to highlight many of the capabilities of icNMA. Remarkably, during the transition, a helix is seen to be extended by an additional turn, emphasizing a new unknown role for secondary struc...Continue Reading

References

Feb 5, 1985·Journal of Molecular Biology·M LevittP S Stern
Jun 1, 1983·Proceedings of the National Academy of Sciences of the United States of America·N GoT Nishikawa
Nov 1, 1983·Proceedings of the National Academy of Sciences of the United States of America·B Brooks, M Karplus
Jun 1, 1994·Journal of Molecular Graphics·J SchlitterP Krüger
Mar 5, 1993·Journal of Molecular Biology·M M Tirion, D ben-Avraham
Nov 5, 1997·Current Opinion in Structural Biology·A G Palmer
May 14, 1999·Current Opinion in Structural Biology·S Doniach, P Eastman
Sep 24, 1999·Journal of Molecular Biology·N Kannan, S Vishveshwara
Dec 11, 1999·Nucleic Acids Research·H M BermanP E Bourne
Aug 31, 2000·Nature Structural Biology·H R Saibil
Feb 13, 2001·Biophysical Journal·A R AtilganI Bahar
Apr 5, 2001·Protein Engineering·F Tama, Y H Sanejouand
May 31, 2001·Journal of Molecular Graphics & Modelling·M F ThorpeL A Kuhn
Aug 29, 2001·Nature Structural Biology·S W Englander, M M Krishna
Sep 18, 2001·Methods : a Companion to Methods in Enzymology·T Ha
Mar 14, 2002·Proceedings of the National Academy of Sciences of the United States of America·A J RaderM F Thorpe
Aug 31, 2002·Biophysical Journal·Moon K KimGregory S Chirikjian
Oct 26, 2002·Journal of Molecular Graphics & Modelling·Moon K KimRobert L Jernigan
Oct 21, 2003·Proceedings of the National Academy of Sciences of the United States of America·O MiyashitaP G Wolynes
Nov 18, 2003·Journal of Biomolecular Structure & Dynamics·Moon K KimGregory S Chirikjian
Nov 25, 2003·Journal of Molecular Graphics & Modelling·Adam D Schuyler, Gregory S Chirikjian
Jan 18, 2005·Trends in Biochemical Sciences·Pradman K QasbaElizabeth Boeggeman
Feb 22, 2005·Biophysical Journal·Wenjun Zheng, Bernard R Brooks
Apr 19, 2005·Biophysical Journal·Moon K KimGregory S Chirikjian
Apr 20, 2005·Current Opinion in Structural Biology·Valentina Tozzini
Jul 2, 2005·Journal of Molecular Graphics & Modelling·Adam D Schuyler, Gregory S Chirikjian
Sep 6, 2005·Journal of Molecular Biology·Paul Maragakis, Martin Karplus
Sep 7, 2005·Current Opinion in Structural Biology·Ivet Bahar, A J Rader
Sep 10, 2005·Biophysical Journal·K V Brinda, Saraswathi Vishveshwara
Dec 20, 2005·Biophysical Journal·Paula Petrone, Vijay S Pande
Mar 23, 2006·Acta Crystallographica. Section D, Biological Crystallography·Jay I JeongGregory S Chirikjian

❮ Previous
Next ❯

Citations

Apr 22, 2009·The Journal of Physical Chemistry. B·Adam D SchuylerEva L Feldman
Jun 24, 2011·Journal of Biomolecular Structure & Dynamics·Ji Guo SuCun Xin Wang
Jul 14, 2012·Reports on Progress in Physics·Paul C WhitfordJosé N Onuchic
Sep 10, 2010·Journal of Physics. Condensed Matter : an Institute of Physics Journal·Gregory S Chirikjian
May 28, 2010·BMC Structural Biology·Nurit HaspelLydia E Kavraki
Dec 22, 2015·Journal of Molecular Biology·Michael T ZimmermannRobert L Jernigan
Aug 18, 2010·Proteins·Daniel W FarrellM F Thorpe
Oct 19, 2010·Protein Science : a Publication of the Protein Society·Gareth Williams, Andrew J Toon
Aug 19, 2016·BMC Genomics·Emmanuel SapinAmarda Shehu
Mar 24, 2016·PLoS Computational Biology·Tadeo E SaldañoSebastian Fernandez-Alberti
Jul 20, 2018·International Journal of Molecular Sciences·Seyed Majid Saberi Fathi, Jack A Tuszynski
Jun 14, 2014·BMC Bioinformatics·Mikel DiezAlfonso Hernández
Nov 17, 2016·The Journal of Chemical Physics·Patrice Koehl
Jun 7, 2019·BMC Bioinformatics·David MorrisAmarda Shehu
Mar 29, 2020·Journal of Chemical Information and Modeling·Tadeo E SaldañoSebastian Fernandez-Alberti

❮ 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.