Escherichia coli adenylate kinase dynamics: comparison of elastic network model modes with mode-coupling (15)N-NMR relaxation data

Proteins
N Alpay TemizIvet Bahar

Abstract

The dynamics of adenylate kinase of Escherichia coli (AKeco) and its complex with the inhibitor AP(5)A, are characterized by correlating the theoretical results obtained with the Gaussian Network Model (GNM) and the anisotropic network model (ANM) with the order parameters and correlation times obtained with Slowly Relaxing Local Structure (SRLS) analysis of (15)N-NMR relaxation data. The AMPbd and LID domains of AKeco execute in solution large amplitude motions associated with the catalytic reaction Mg(+2)*ATP + AMP --> Mg(+2)*ADP + ADP. Two sets of correlation times and order parameters were determined by NMR/SRLS for AKeco, attributed to slow (nanoseconds) motions with correlation time tau( perpendicular) and low order parameters, and fast (picoseconds) motions with correlation time tau( parallel) and high order parameters. The structural connotation of these patterns is examined herein by subjecting AKeco and AKeco*AP(5)A to GNM analysis, which yields the dynamic spectrum in terms of slow and fast modes. The low/high NMR order parameters correlate with the slow/fast modes of the backbone elucidated with GNM. Likewise, tau( parallel) and tau( perpendicular) are associated with fast and slow GNM modes, respectively. Catalysis...Continue Reading

References

Jun 1, 1976·Biopolymers·M Go, N Go
Feb 5, 1985·Journal of Molecular Biology·M LevittP S Stern
Jan 1, 1984·CRC Critical Reviews in Biochemistry·W S Bennett, R Huber
Nov 1, 1983·Proceedings of the National Academy of Sciences of the United States of America·B Brooks, M Karplus
Jul 1, 1995·Protein Science : a Publication of the Protein Society·U Abele, G E Schulz
Mar 3, 1995·Journal of Molecular Biology·H J Müller-Dieckmann, G E Schulz
Dec 1, 1993·Proteins·A AmadeiH J Berendsen
Jun 7, 1994·Biochemistry·M GersteinC Chothia
Feb 23, 1996·Journal of Molecular Biology·G J SchlaudererG E Schulz
May 21, 1996·Biochemistry·M A SinevE Haas
Sep 23, 1997·Biochemical and Biophysical Research Communications·H J ZhangJ M Zhou
Jul 17, 1998·Nature Structural Biology·L E Kay
Dec 5, 1998·Biopolymers·J Elezgaray, Y H Sanejouand
Jan 29, 1999·Biochemistry and Cell Biology = Biochimie Et Biologie Cellulaire·L E Kay
Feb 19, 1999·Proteins·K HinsenM J Field
Mar 26, 1999·Biochemistry·I Bahar, R L Jernigan
Aug 31, 2000·Nature Structural Biology·R Ishima, D A Torchia
Feb 13, 2001·Biophysical Journal·A R AtilganI Bahar
Apr 28, 2001·Biophysical Journal·S KumarR Nussinov
May 8, 2001·Annual Review of Biophysics and Biomolecular Structure·A G Palmer
Jul 18, 2001·Journal of the American Chemical Society·V TugarinovE Meirovitch
Jul 27, 2001·Journal of the American Chemical Society·J J Prompers, R Brüschweiler
Jan 10, 2002·Biochemistry·O KeskinR L Jernigan
Mar 27, 2002·Journal of Computational Chemistry·Pemra DorukerIvet Bahar
Jun 11, 2002·Journal of Molecular Biology·Florence Tama, Charles L Brooks
Jun 13, 2002·Proceedings of the National Academy of Sciences of the United States of America·Dengming MingJianpeng Ma
Jun 27, 2002·Proceedings of the National Academy of Sciences of the United States of America·Dengming MingJianpeng Ma
Jul 19, 2002·Biophysical Journal·Ozlem KeskinDavid G Covell
Sep 5, 2002·Proteins·O KeskinD G Covell
Oct 24, 2002·Journal of the American Chemical Society·Fengli Zhang, Rafael Brüschweiler

❮ Previous
Next ❯

Citations

May 21, 2013·Progress in Biophysics and Molecular Biology·Yury E Shapiro
Jun 7, 2011·Journal of Chemical Information and Modeling·Aqeel AhmedHolger Gohlke
Sep 30, 2009·Chemical Reviews·Ivet BaharIndira H Shrivastava
Nov 26, 2008·The Journal of Biological Chemistry·Yan-Wen TanHaw Yang
Nov 10, 2011·Journal of Biomolecular Structure & Dynamics·Ragothaman M YennamalliTaner Z Sen
Apr 30, 2005·Bioinformatics·Lee-Wei YangIvet Bahar
May 28, 2013·Molekuliarnaia biologiia·G V NovikovK V Shaĭtan
May 28, 2010·BMC Structural Biology·Nurit HaspelLydia E Kavraki
Jul 15, 2006·PLoS Computational Biology·Jenny GuPhilip E Bourne
Nov 9, 2007·Proceedings of the National Academy of Sciences of the United States of America·Jeffrey A HansonHaw Yang
Nov 15, 2007·Proceedings of the National Academy of Sciences of the United States of America·Karunesh Arora, Charles L Brooks
Apr 7, 2011·Biochimica Et Biophysica Acta·Michael KovermannJochen Balbach
Sep 16, 2009·Journal of Molecular Biology·Oliver BecksteinThomas B Woolf
Dec 17, 2015·Journal of Computational Chemistry·Min LiFei Xia
Nov 10, 2015·The Journal of Physical Chemistry. B·Eva MeirovitchJordan H Chill
Nov 21, 2007·Current Opinion in Structural Biology·Ivet BaharDror Tobi
Jan 16, 2007·Journal of Molecular Biology·Paul C WhitfordJosé N Onuchic
Mar 4, 2008·Biophysical Journal·Ji Guo SuCun Xin Wang
Nov 8, 2006·Protein Science : a Publication of the Protein Society·Shenggen YaoRaymond S Norton
Aug 16, 2008·Proteins·Qingyi Yang, Kim A Sharp
Sep 8, 2010·Proteins·Canan AtilganAli Rana Atilgan
Aug 10, 2011·Protein Science : a Publication of the Protein Society·Lidio MeirelesIvet Bahar
Nov 16, 2004·Biophysical Journal·Alejandra Leo-MaciasAngel R Ortiz
Sep 7, 2005·Current Opinion in Structural Biology·Ivet Bahar, A J Rader
Sep 6, 2005·Journal of Molecular Biology·Paul Maragakis, Martin Karplus
Dec 20, 2005·Biophysical Journal·Paula Petrone, Vijay S Pande
May 27, 2015·Journal of Computer-aided Molecular Design·Hulya UnanMustafa Tekpinar
Aug 13, 2013·Neuron·Albert Y LauBenoît Roux
Aug 8, 2006·Biophysical Journal·Dmitry A KondrashovGeorge N Phillips

❮ 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.