Low-Frequency Vibrational Spectrum of Water in the Hydration Layer of a Protein:  A Molecular Dynamics Simulation Study

Sudip Chakraborty; Sudipta Kumar Sinha; Sanjoy Bandyopadhyay

doi:10.1021/jp0746401

Low-Frequency Vibrational Spectrum of Water in the Hydration Layer of a Protein: A Molecular Dynamics Simulation Study

The Journal of Physical Chemistry B ◽

10.1021/jp0746401 ◽

2007 ◽

Vol 111 (48) ◽

pp. 13626-13631 ◽

Cited By ~ 32

Author(s):

Sudip Chakraborty ◽

Sudipta Kumar Sinha ◽

Sanjoy Bandyopadhyay

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Vibrational Spectrum ◽

Simulation Study ◽

Protein A ◽

Low Frequency ◽

Dynamics Simulation ◽

Hydration Layer

Download Full-text

Effect of conjugated (EK)10 peptide on structural and dynamic properties of ubiquitin protein: a molecular dynamics simulation study

Journal of Materials Chemistry B ◽

10.1039/d0tb00664e ◽

2020 ◽

Vol 8 (31) ◽

pp. 6934-6943

Author(s):

Qing Shao

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Simulation Study ◽

Dynamic Properties ◽

Protein A ◽

Dynamics Simulation ◽

Allosteric Effect ◽

Peptide Conjugation ◽

The Stability

Peptide conjugation modulates the stability and biological acitivty of proteins via the allosteric effect.

Download Full-text

Domain focused and residue focused phosphorylation effect on tau protein: A molecular dynamics simulation study

Journal of the Mechanical Behavior of Biomedical Materials ◽

10.1016/j.jmbbm.2020.104149 ◽

2021 ◽

Vol 113 ◽

pp. 104149

Author(s):

Md Ishak Khan ◽

Fuad Hasan ◽

Khandakar Abu Hasan Al Mahmud ◽

Ashfaq Adnan

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Simulation Study ◽

Tau Protein ◽

Protein A ◽

Dynamics Simulation

Download Full-text

Assembly of Transmembrane Domains of Human Papillomavirus Type 16 E5 Protein- a Molecular Dynamics Simulation Study

Biophysical Journal ◽

10.1016/j.bpj.2013.11.411 ◽

2014 ◽

Vol 106 (2) ◽

pp. 60a

Author(s):

Dhani R. Mahato ◽

Wolfgang B. Fischer

Keyword(s):

Molecular Dynamics ◽

Human Papillomavirus ◽

Molecular Dynamics Simulation ◽

Simulation Study ◽

Protein A ◽

Transmembrane Domains ◽

Dynamics Simulation ◽

Human Papillomavirus Type 16 ◽

E5 Protein

Download Full-text

Dielectric response and vibrational energy relaxation in photoactive yellow protein: A molecular dynamics simulation study

Chemical Physics Letters ◽

10.1016/j.cplett.2011.09.066 ◽

2011 ◽

Vol 516 (1-3) ◽

pp. 102-105 ◽

Cited By ~ 5

Author(s):

Ramachandran Gnanasekaran ◽

David M. Leitner

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Simulation Study ◽

Dielectric Response ◽

Vibrational Energy ◽

Protein A ◽

Energy Relaxation ◽

Dynamics Simulation ◽

Photoactive Yellow Protein ◽

Vibrational Energy Relaxation

Download Full-text

Influence of pressure on the low-frequency vibrational modes of lysozyme and water: A complementary inelastic neutron scattering and molecular dynamics simulation study

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.24189 ◽

2012 ◽

Vol 81 (2) ◽

pp. 326-340 ◽

Cited By ~ 22

Author(s):

Adrien Lerbret ◽

Alain Hédoux ◽

Burkhard Annighöfer ◽

Marie-Claire Bellissent-Funel

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Neutron Scattering ◽

Simulation Study ◽

Inelastic Neutron Scattering ◽

Low Frequency ◽

Inelastic Neutron ◽

Dynamics Simulation ◽

Vibrational Modes

Download Full-text

Temperature Dependence of Water Vibrational Spectrum: A Molecular Dynamics Simulation Study

The Journal of Physical Chemistry A ◽

10.1021/jp046158d ◽

2004 ◽

Vol 108 (50) ◽

pp. 11056-11062 ◽

Cited By ~ 98

Author(s):

Matej Praprotnik ◽

Dušanka Janežič ◽

Janez Mavri

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Vibrational Spectrum ◽

Temperature Dependence ◽

Simulation Study ◽

Dynamics Simulation

Download Full-text

Hydration Patterns of Graphene-Based Nanomaterials (GBNMs) Play a Major Role in the Stability of a Helical Protein: A Molecular Dynamics Simulation Study

Langmuir ◽

10.1021/la4033805 ◽

2013 ◽

Vol 29 (46) ◽

pp. 14230-14238 ◽

Cited By ~ 29

Author(s):

Lokesh Baweja ◽

Kanagasabai Balamurugan ◽

Venkatesan Subramanian ◽

Alok Dhawan

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Simulation Study ◽

Protein A ◽

Dynamics Simulation ◽

Helical Protein ◽

The Stability

Download Full-text

How graphene affects the misfolding of human prion protein: A combined experimental and molecular dynamics simulation study

Environmental Research ◽

10.1016/j.envres.2018.12.057 ◽

2019 ◽

Vol 171 ◽

pp. 1-10 ◽

Cited By ~ 2

Author(s):

Yongchang Zhu ◽

Jingjing Guo ◽

Ai Zhang ◽

Lanlan Li ◽

Xuewei Liu ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Prion Protein ◽

Simulation Study ◽

Protein A ◽

Dynamics Simulation ◽

Human Prion Protein

Download Full-text

Effect of temperature on the structure and hydration layer of TATA-box DNA: A molecular dynamics simulation study

Journal of Molecular Graphics and Modelling ◽

10.1016/j.jmgm.2016.03.005 ◽

2016 ◽

Vol 66 ◽

pp. 9-19 ◽

Cited By ~ 2

Author(s):

Sudipta Samanta ◽

Devanathan Raghunathan ◽

Sanchita Mukherjee

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Simulation Study ◽

Dynamics Simulation ◽

Tata Box ◽

Effect Of Temperature ◽

Hydration Layer

Download Full-text

Operation of Kelvin Effect in the Activities of an Antifreeze Protein: A Molecular Dynamics Simulation Study

The Journal of Physical Chemistry B ◽

10.1021/acs.jpcb.8b00846 ◽

2018 ◽

Vol 122 (12) ◽

pp. 3079-3087 ◽

Cited By ~ 4

Author(s):

Uday Sankar Midya ◽

Sanjoy Bandyopadhyay

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Simulation Study ◽

Protein A ◽

Antifreeze Protein ◽

Dynamics Simulation ◽

Kelvin Effect

Download Full-text