Insight derived from molecular dynamics simulation into substrate-induced changes in protein motions of proteinase K

Journal of Biomolecular Structure & Dynamics
Yan TaoShu-Qun Liu

Abstract

Because of the significant industrial, agricultural and biotechnological importance of serine protease proteinase K, it has been extensively investigated using experimental approaches such as X-ray crystallography, site-directed mutagenesis and kinetic measurement. However, detailed aspects of enzymatic mechanism such as substrate binding, release and relevant regulation remain unstudied. Molecular dynamics (MD) simulations of the proteinase K alone and in complex with the peptide substrate AAPA were performed to investigate the effect of substrate binding on the dynamics/molecular motions of proteinase K. The results indicate that during simulations the substrate-complexed proteinase K adopt a more compact and stable conformation than the substrate-free form. Further essential dynamics (ED) analysis reveals that the major internal motions are confined within a subspace of very small dimension. Upon substrate binding, the overall flexibility of the protease is reduced; and the noticeable displacements are observed not only in substrate-binding regions but also in regions opposite the substrate-binding groove/pockets. The dynamic pockets caused by the large concerted motions are proposed to be linked to the substrate recognition...Continue Reading

References

Aug 1, 1988·Trends in Biochemical Sciences·J A Wells, D A Estell
Dec 1, 1988·European Journal of Biochemistry·C BetzelW Saenger
Jan 1, 1986·Journal of Cellular Biochemistry·H Neurath
Aug 20, 1985·Journal of Molecular Biology·H Tsukada, D M Blow
Aug 15, 1974·European Journal of Biochemistry·W EbelingH Lang
Jul 16, 1971·Biochemical and Biophysical Research Communications·U Wiegers, H Hilz
Apr 20, 1967·Biochemical and Biophysical Research Communications·I Schechter, A Berger
Apr 1, 1995·Nature Structural Biology·J R CollinsJ W Erickson
Dec 1, 1993·Proteins·A AmadeiH J Berendsen
Mar 1, 1997·Protein Science : a Publication of the Protein Society·R J Siezen, J A Leunissen
Dec 31, 1997·Biophysical Journal·D M van AaltenA Amadei
Oct 27, 1998·Trends in Biochemical Sciences·G Dodson, A Wlodawer
Feb 5, 1999·Journal of Molecular Biology·D W Miller, D A Agard
Jan 4, 2001·Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics·B Hess
Dec 2, 2004·Acta Crystallographica. Section D, Biological Crystallography·C Paul BarrettMartin E M Noble
Feb 8, 2005·The Journal of Biological Chemistry·C Paul Barrett, Martin E M Noble
Feb 1, 1958·Proceedings of the National Academy of Sciences of the United States of America·D E Koshland
Jan 18, 2007·Journal of Molecular Graphics & Modelling·Shu-Qun LiuYun-Xin Fu
Apr 4, 2007·Journal of Computational Chemistry·Carsten KutznerHelmut Grubmüller
Feb 20, 2008·Journal of Biomolecular Structure & Dynamics·Jeseong YoonSeokmin Shin
Apr 11, 2008·Journal of Biomolecular Structure & Dynamics·Arnau CordomíJuan J Perez
Jul 4, 2008·Journal of Biomolecular Structure & Dynamics·Boel Nyström MacchionLennart Nilsson
Jul 4, 2008·Journal of Biomolecular Structure & Dynamics·Uddhavesh B SonavaneRajendra R Joshi
Jul 4, 2008·Journal of Biomolecular Structure & Dynamics·Faramarz Mehrnejad, Nader Chaparzadeh
Jul 9, 2009·Journal of Biomolecular Structure & Dynamics·Arnau Cordomí, Juan J Perez
Jul 9, 2009·Journal of Biomolecular Structure & Dynamics·Jiapu Zhang
Oct 3, 2009·Journal of Biomolecular Structure & Dynamics·Jeseong YoonSeokmin Shin
Oct 3, 2009·Journal of Biomolecular Structure & Dynamics·D'Annessa IldaDesideri Alessandro

❮ Previous
Next ❯

Citations

Apr 8, 2011·Journal of Biomolecular Structure & Dynamics·Teodorico C RamalhoElaine F F da Cunha
Apr 8, 2011·Journal of Biomolecular Structure & Dynamics·Mao-Feng SunCalvin Yu-Chian Chen
Apr 8, 2011·Journal of Biomolecular Structure & Dynamics·Vinod JaniRajendra Joshi
Jul 9, 2013·Applied Microbiology and Biotechnology·Jinkui YangKe-Qin Zhang
Jun 25, 2015·Protein Science : a Publication of the Protein Society·Anna R BattTeaster Baird
Feb 21, 2014·Science China. Life Sciences·HuiMin LiShuQun Liu
Apr 12, 2015·European Biophysics Journal : EBJ·J Lesitha Jeeva Kumari, C Sudandiradoss
Jun 5, 2013·Journal of Biomolecular Structure & Dynamics·João T S CoimbraMaria J Ramos
Mar 27, 2013·Journal of Biomolecular Structure & Dynamics·Li-Quan YangShu-Qun Liu
Oct 30, 2016·International Journal of Biological Macromolecules·Mansoore Hosseini-KoupaeiFateme Davar
Feb 26, 2016·International Journal of Molecular Sciences·Peng SangShu-Qun Liu
Aug 31, 2011·Journal of Biomolecular Structure & Dynamics·Aline A OliveiraTanos C C França
Aug 31, 2011·Journal of Biomolecular Structure & Dynamics·Esmaeil BehmardSamad Jahandideh
Jan 3, 2012·Journal of Biomolecular Structure & Dynamics·Sundarapandian ThangapandianKeun Woo Lee
Jun 24, 2011·Journal of Biomolecular Structure & Dynamics·W JurkowskiI Roterman
Jun 24, 2011·Journal of Biomolecular Structure & Dynamics·Deok-Soo KimJong Bhak
Jun 24, 2011·Journal of Biomolecular Structure & Dynamics·Ji Guo SuCun Xin Wang
Jun 24, 2011·Journal of Biomolecular Structure & Dynamics·Rituraj PurohitRao Sethumadhavan
Feb 8, 2011·Journal of Biomolecular Structure & Dynamics·Zheng-Li ZhouYih Ho
Feb 8, 2011·Journal of Biomolecular Structure & Dynamics·Tung-Ti ChangCalvin Yu-Chian Chen
Feb 8, 2011·Journal of Biomolecular Structure & Dynamics·Xianjin XuCunxin Wang
Dec 15, 2010·Journal of Biomolecular Structure & Dynamics·Xing-Lai Ji, Shu-Qun Liu
Dec 15, 2010·Journal of Biomolecular Structure & Dynamics·Bornali ChakrabartiAsim K Bera
Apr 8, 2011·Journal of Biomolecular Structure & Dynamics·Maliheh S AtriAmir Niasari-Naslaji
Feb 8, 2011·Journal of Biomolecular Structure & Dynamics·Elif Ozkirimli Olmez, Burak Alakent
Jun 19, 2012·Journal of Biomolecular Structure & Dynamics·Shan ChangXu-hong Tian
Jun 13, 2012·Journal of Biomolecular Structure & Dynamics·Mahdi AlijanianzadehAli Akbar Moosavi-Movahedi
Feb 26, 2011·FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology·Lianming LiangKeqin Zhang
Aug 31, 2011·Journal of Biomolecular Structure & Dynamics·Ping LiCun Xin Wang
Jun 27, 2012·Journal of Biomolecular Structure & Dynamics·Guojun ShiSichuan Xu

❮ 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.