Vivek Govind Kumar
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View article: Molecular Dynamics Investigation of the Influenza Hemagglutinin Conformational Changes in Acidic pH
Molecular Dynamics Investigation of the Influenza Hemagglutinin Conformational Changes in Acidic pH Open
The surface protein hemagglutinin (HA) of the influenza virus plays a pivotal role in facilitating viral infection by binding to sialic acid receptors on host cells. Its conformational state is pH-sensitive, impacting its receptor-binding …
View article: Molecular dynamics investigation of the influenza hemagglutinin conformational changes in acidic pH
Molecular dynamics investigation of the influenza hemagglutinin conformational changes in acidic pH Open
The surface protein hemagglutinin (HA) of the influenza virus plays a pivotal role in facilitating viral infection by binding to sialic acid receptors on host cells. Its conformational state is pH-sensitive, impacting its receptor-binding …
View article: cpSRP43 Is Both Highly Flexible and Stable: Structural Insights Using a Combined Experimental and Computational Approach
cpSRP43 Is Both Highly Flexible and Stable: Structural Insights Using a Combined Experimental and Computational Approach Open
The novel multidomain protein, cpSRP43, is a unique subunit of the post-translational chloroplast signal recognition particle (cpSRP) targeting pathway in higher plants. The cpSRP pathway is responsible for targeting and insertion of light…
View article: Binding affinity estimation from restrained umbrella sampling simulations
Binding affinity estimation from restrained umbrella sampling simulations Open
The protein–ligand binding affinity quantifies the binding strength between a protein and its ligand. Computer modeling and simulations can be used to estimate the binding affinity or binding free energy using data- or physics-driven metho…
View article: Binding Affinity Estimation from Restrained Umbrella Sampling Simulations
Binding Affinity Estimation from Restrained Umbrella Sampling Simulations Open
The protein-ligand binding affinity quantifies the binding strength between a protein and its ligand. Computer modeling and simulations can be used to estimate the binding affinity or binding free energy using data- or physics-driven metho…
View article: Prefusion spike protein conformational changes are slower in SARS-CoV-2 than in SARS-CoV-1
Prefusion spike protein conformational changes are slower in SARS-CoV-2 than in SARS-CoV-1 Open
Within the last 2 decades, severe acute respiratory syndrome coronaviruses 1 and 2 (SARS-CoV-1 and SARS-CoV-2) have caused two major outbreaks; yet, for reasons not fully understood, the coronavirus disease 2019 pandemic caused by SARS-CoV…
View article: Characterizing the roles of chemo-mechanical couplings in the differential behavior of SARS-CoV-1 and SARS-CoV-2 spike glycoprotein
Characterizing the roles of chemo-mechanical couplings in the differential behavior of SARS-CoV-1 and SARS-CoV-2 spike glycoprotein Open
View article: cpSRP43 is both highly flexible and stable: Structural insights using a combined experimental and computational approach
cpSRP43 is both highly flexible and stable: Structural insights using a combined experimental and computational approach Open
The novel multidomain protein, cpSRP43, is a unique subunit of the post-translational chloroplast signal recognition particle (cpSRP) targeting pathway in higher plants. The cpSRP pathway is responsible for targeting and insertion of light…
View article: Mechanistic Picture for Monomeric Human Fibroblast Growth Factor 1 Stabilization by Heparin Binding
Mechanistic Picture for Monomeric Human Fibroblast Growth Factor 1 Stabilization by Heparin Binding Open
Human fibroblast growth factor (FGF) 1 or hFGF1 is a member of the FGF family that is involved in various vital processes such as cell proliferation, cell differentiation, angiogenesis, and wound healing. hFGF1, which is associated with lo…
View article: Binding Affinity Estimation From Restrained Umbrella Sampling Simulations
Binding Affinity Estimation From Restrained Umbrella Sampling Simulations Open
The protein-ligand binding affinity quantifies the binding strength between a protein and its ligand. Computer modeling and simulations can be used to estimate the binding affinity or binding free energy using data- or physics-driven metho…
View article: Transient local secondary structure in the intrinsically disordered C-term of the Albino3 insertase
Transient local secondary structure in the intrinsically disordered C-term of the Albino3 insertase Open
View article: Characterization of the structural forces governing the reversibility of the thermal unfolding of the human acidic fibroblast growth factor
Characterization of the structural forces governing the reversibility of the thermal unfolding of the human acidic fibroblast growth factor Open
View article: Integrating Molecular Dynamics and smFRET Data to Study the Conformational Ensemble of the C-Terminus of Albino3 Protein
Integrating Molecular Dynamics and smFRET Data to Study the Conformational Ensemble of the C-Terminus of Albino3 Protein Open
View article: Comparing the Dynamic Differences between X-ray and Cryo-EM Structures of Cannabinoid Receptor 1 using Molecular Dynamics Simulations
Comparing the Dynamic Differences between X-ray and Cryo-EM Structures of Cannabinoid Receptor 1 using Molecular Dynamics Simulations Open
View article: An Investigation of the Disulfide Bridge Formation of a Thylakoid Protease using Nanosecond-Level MD Simulations
An Investigation of the Disulfide Bridge Formation of a Thylakoid Protease using Nanosecond-Level MD Simulations Open
View article: Differential Dynamic Behavior of Prefusion Spike Glycoproteins of Sars Coronaviruses 1 and 2
Differential Dynamic Behavior of Prefusion Spike Glycoproteins of Sars Coronaviruses 1 and 2 Open
View article: Molecular Dynamics Investigation of the Influenza Hemagglutinin Conformational Changes
Molecular Dynamics Investigation of the Influenza Hemagglutinin Conformational Changes Open
View article: An Investigation of the Conformational Dynamics of ABC Exporter PCAT1 using Microsecond-Level MD Simulations
An Investigation of the Conformational Dynamics of ABC Exporter PCAT1 using Microsecond-Level MD Simulations Open
View article: Differential Dynamic Behavior of Prefusion Spike Proteins of SARS Coronaviruses 1 and 2
Differential Dynamic Behavior of Prefusion Spike Proteins of SARS Coronaviruses 1 and 2 Open
The coronavirus spike protein, which binds to the same human receptor in both SARS-CoV-1 and 2, has been implied to be a potential source of their differential transmissibility. However, the mechanistic details of spike protein binding to …
View article: Mechanistic Picture for Monomeric Human Fibroblast Growth Factor 1 Stabilization by Heparin Binding
Mechanistic Picture for Monomeric Human Fibroblast Growth Factor 1 Stabilization by Heparin Binding Open
Human fibroblast growth factor (FGF) 1 or hFGF1 is a member of the FGF family that is involved in various vital processes such as cell proliferation, cell differentiation, angiogenesis and wound healing. hFGF1, which is associated with low…
View article: Effect of Cholesterol on the Structural Dynamics of Metabotropic Glutamate Receptor (mGluR1): A Molecular Dynamics Study
Effect of Cholesterol on the Structural Dynamics of Metabotropic Glutamate Receptor (mGluR1): A Molecular Dynamics Study Open
View article: The Role of a Crystallographically Unresolved Cytoplasmic Loop in Stabilizing the Bacterial Membrane Insertase YidC2
The Role of a Crystallographically Unresolved Cytoplasmic Loop in Stabilizing the Bacterial Membrane Insertase YidC2 Open
View article: An Effective Electric Dipole Model for Voltage-induced Gating Mechanism of Lysenin
An Effective Electric Dipole Model for Voltage-induced Gating Mechanism of Lysenin Open
Lysenin is a pore-forming toxin, which self-inserts open channels into sphingomyelin containing membranes and is known to be voltage regulated. The mechanistic details of its voltage gating mechanism, however, remains elusive despite much …
View article: The Role of a Crystallographically Unresolved Cytoplasmic Loop in Stabilizing the Bacterial Membrane Insertase YidC2
The Role of a Crystallographically Unresolved Cytoplasmic Loop in Stabilizing the Bacterial Membrane Insertase YidC2 Open
YidC, a bacterial member of the YidC/Alb3/Oxa1 insertase family, mediates membrane protein assembly and insertion. Cytoplasmic loops are known to have functional significance in membrane proteins such as YidC. Employing microsecond-level m…
View article: Mechanistic Study of a Peptidase Containing ABC-Transporter, Employing Microsecond Level Molecular Dynamics Simulations and Enhanced Sampling Techniques
Mechanistic Study of a Peptidase Containing ABC-Transporter, Employing Microsecond Level Molecular Dynamics Simulations and Enhanced Sampling Techniques Open
View article: A Comprehensive Investigation of the Stabilization of Monomeric Hfgf1 by Heparin Hexasaccharide using Microsecond-Level MD Simulations and Enhanced Sampling Techniques
A Comprehensive Investigation of the Stabilization of Monomeric Hfgf1 by Heparin Hexasaccharide using Microsecond-Level MD Simulations and Enhanced Sampling Techniques Open
View article: ALS-causing mutations in profilin-1 alter its conformational dynamics: A computational approach to explain propensity for aggregation
ALS-causing mutations in profilin-1 alter its conformational dynamics: A computational approach to explain propensity for aggregation Open
Profilin-1 (PFN1) is a 140-amino-acid protein with two distinct binding sites―one for actin and one for poly-L-proline (PLP). The best-described function of PFN1 is to catalyze actin elongation and polymerization. Thus far, eight DNA mutat…
View article: Using Molecular Dynamics Simulations to Compare the Stability of Lysenin Structures Obtained through X-ray Crystallography and Single-Particle Cryo-Electron Microscopy
Using Molecular Dynamics Simulations to Compare the Stability of Lysenin Structures Obtained through X-ray Crystallography and Single-Particle Cryo-Electron Microscopy Open