scholarly journals Modeling and Molecular Dynamics of the 3D Structure of the HPV16 E7 Protein and Its Variants

2021 ◽  
Vol 22 (3) ◽  
pp. 1400
Author(s):  
Ciresthel Bello-Rios ◽  
Sarita Montaño ◽  
Olga Lilia Garibay-Cerdenares ◽  
Lilian Esmeralda Araujo-Arcos ◽  
Marco Antonio Leyva-Vázquez ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
3D Structure ◽  
Epidemiological Studies ◽  
Dynamics Simulation ◽  
Structural Refinement ◽  
Oncogenic Potential ◽  
Structural Differences ◽  
Reference Protein ◽  
E6 And E7 ◽  
First Time

The oncogenic potential of high-risk human papillomavirus (HPV) is predicated on the production of the E6 and E7 oncoproteins, which are responsible for disrupting the control of the cell cycle. Epidemiological studies have proposed that the presence of the N29S and H51N variants of the HPV16 E7 protein is significantly associated with cervical cancer. It has been suggested that changes in the amino acid sequence of E7 variants may affect the oncoprotein 3D structure; however, this remains uncertain. An analysis of the structural differences of the HPV16 E7 protein and its variants (N29S and H51N) was performed through homology modeling and structural refinement by molecular dynamics simulation. We propose, for the first time, a 3D structure of the E7 reference protein and two of Its variants (N29S and H51N), and conclude that the mutations induced by the variants in N29S and H51N have a significant influence on the 3D structure of the E7 protein of HPV16, which could be related to the oncogenic capacity of this protein.

scholarly journals Modeling and Molecular Dynamics of the 3D Structure of the HPV16 E7 Protein and Its Variants

2020 ◽  
Author(s):  
Ciresthel Bello-Rios ◽  
Sarita Montaño ◽  
Olga Lilia Garibay-Cerdenares ◽  
Lilian Esmeralda Araujo-Arcos ◽  
Marco Antonio Leyva-Vázquez ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
3D Structure ◽  
Epidemiological Studies ◽  
Dynamics Simulation ◽  
Structural Refinement ◽  
Oncogenic Potential ◽  
Structural Differences ◽  
Reference Protein ◽  
E6 And E7 ◽  
First Time

The oncogenic potential of high-risk HPVs is focused on producing the E6 and E7 oncoproteins responsible for disrupting the control of the cell cycle. Epidemiological studies propose the presence of the N29S and H51N variants of the HPV16 E7 protein as a significant association with cervical cancer. It has been suggested that changes in the amino acid sequence of E7 variants may affect the oncoprotein 3D structure; however, this remains unknown. Analysis of the structural differences of the HPV16 E7 protein and its variants (N29S and H51N) was performed through homology modeling and structural refinement by molecular dynamics simulation. We propose for the first time a 3D structure of the E7 reference protein and two of its variants (N29S and H51N) and conclude that the mutations induced by the variants in N29S and H51N have a significant influence on the 3D structure of the E7 protein of HPV16, which could be related to the oncogenic capacity of this protein.

Multicanonical Molecular Dynamics Simulation Study of the Liquid-Solid and Solid-Solid Transitions in Lennard-Jones Clusters

2011 ◽  
Author(s):  
Toshihiro Kaneko ◽  
Kenji Yasuoka ◽  
Ayori Mitsutake ◽  
Xiao Cheng Zeng
Keyword(s):  
Molecular Dynamics ◽  
Heat Capacity ◽  
Transition Temperature ◽  
Peak Position ◽  
Temperature Curve ◽  
Dynamics Simulation ◽  
Lennard Jones ◽  
Dynamics Simulations ◽  
First Time ◽  
Good Agreement

Multicanonical molecular dynamics simulations are applied, for the first time, to study the liquid-solid and solid-solid transitions in Lennard-Jones (LJ) clusters. The transition temperatures are estimated based on the peak position in the heat capacity versus temperature curve. For LJ31, LJ58 and LJ98, our results on the solid-solid transition temperature are in good agreement with previous ones. For LJ309, the predicted liquid-solid transition temperature is also in agreement with previous result.

A systematic study on the intradiffusion and structure of N,N-dimethylformamide–water mixtures: by experiment and molecular dynamics simulation

RSC Advances ◽  
2016 ◽  
Vol 6 (88) ◽  
pp. 85603-85611 ◽  
Author(s):  
Jinyang Wang ◽  
Wei Gao ◽  
Haimin Zhong ◽  
Canjian Liang ◽  
Xiaojuan Chen ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Systematic Study ◽  
Dynamics Simulation ◽  
Pgse Nmr ◽  
First Time

Intradiffusion coefficients ofN,N-dimethylformamide (DDMF) and water (DW) in their mixtures were measured as a function of temperature, pressure and composition for the first time using the PGSE-NMR technique.

scholarly journals Electrostatics of Tau Protein by Molecular Dynamics

Biomolecules ◽  
2019 ◽  
Vol 9 (3) ◽  
pp. 116 ◽  
Author(s):  
Tarsila Castro ◽  
Florentina-Daniela Munteanu ◽  
Artur Cavaco-Paulo
Keyword(s):  
Molecular Dynamics ◽  
3D Structure ◽  
Three Dimensional ◽  
Dynamics Simulation ◽  
Microtubule Assembly ◽  
Interaction Sites ◽  
Disordered Protein ◽  
Fluid Environment ◽  
Function Relationship ◽  
Insight Into

Tau is a microtubule-associated protein that promotes microtubule assembly and stability. This protein is implicated in several neurodegenerative diseases, including Alzheimer’s. To date, the three-dimensional (3D) structure of tau has not been fully solved, experimentally. Even the most recent information is sometimes controversial in regard to how this protein folds, interacts, and behaves. Predicting the tau structure and its profile sheds light on the knowledge about its properties and biological function, such as the binding to microtubules (MT) and, for instance, the effect on ionic conductivity. Our findings on the tau structure suggest a disordered protein, with discrete portions of well-defined secondary structure, mostly at the microtubule binding region. In addition, the first molecular dynamics simulation of full-length tau along with an MT section was performed, unveiling tau structure when associated with MT and interaction sites. Electrostatics and conductivity were also examined to understand how tau affects the ions in the intracellular fluid environment. Our results bring a new insight into tau and tubulin MT proteins, their characteristics, and the structure–function relationship.

Constant-Temperature Molecular-Dynamics Simulation of the 2D Melting Transition of Rb and K

1992 ◽  
Vol 291 ◽  
Author(s):  
J. D. Fan ◽  
Zhi-Xiong Cai
Keyword(s):  
Molecular Dynamics ◽  
Constant Temperature ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Melting Transition ◽  
Histogram Method ◽  
Graphite Intercalation ◽  
2D System ◽  
Incommensurate Structures ◽  
First Time

ABSTRACTThe energy histogram method, introduced by Ferrenberg and Swendsen [Phys. Rev. Lett., 61, 2635, (1988) and 63, 1195, (1989)], was applied for the first time to the constant temperature molecular dynamics (MD) simulation of a two-dimensional (2D) system with incommensurate structures. We performed MD simulations for the stage-2 graphite intercalation compounds (GIC's) with Rb or K being the intercalants (Rb-GIC's and K- GIC's). The temperature dependence of the specific heat, Cv, is calculated for various sizes up to 864 atoms. The melting temperature was found to be 158 K for Rb-GIC's and 119 K for K-GIC's, respectively, which are in agreement with the experimental observations.

PHOTOACOUSTIC MEASUREMENT AND MOLECULAR DYNAMICS SIMULATION FOR THERMAL CONDUCTIVITY OF Al0.3Ga0.7As

2003 ◽  
Vol 14 (01) ◽  
pp. 61-72 ◽  
Author(s):  
S. CHITRA ◽  
A. JALAL ◽  
K. RAMACHANDRAN ◽  
S. RAJAGOPAL
Keyword(s):  
Thermal Conductivity ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Thermal Property ◽  
Dynamics Simulation ◽  
Experimental Setup ◽  
Photoacoustic Technique ◽  
Photoacoustic Measurement ◽  
First Time

The thermal conductivity of Al 0.3 Ga 0.7 As is studied using photoacoustic technique and molecular dynamics simulation. Tersoff's potential is used for the simulation, for the first time, to this alloy. Thermal conductivity, determined experimentally by photoacoustic technique using our experimental setup, agrees well with the molecular dynamics simulation and literature values. The results are compared with the host GaAs and the role of DX centers in thermal property is discussed.

scholarly journals Mechanism unravelling for ultrafast and selective 99TcO4− uptake by a radiation-resistant cationic covalent organic framework: a combined radiological experiment and molecular dynamics simulation study

2019 ◽  
Vol 10 (15) ◽  
pp. 4293-4305 ◽  
Author(s):  
Linwei He ◽  
Shengtang Liu ◽  
Long Chen ◽  
Xing Dai ◽  
Jie Li ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Sorption Kinetics ◽  
Dynamics Simulation ◽  
Uptake Capacity ◽  
Covalent Organic Framework ◽  
Radiation Resistant ◽  
First Time ◽  
Exchange Selectivity ◽  
Organic Framework

Separation of TcO4– by a cationic covalent organic framework is achieved for the first time, showing advantages of extremely fast sorption kinetics, ultrahigh uptake capacity, good anion-exchange selectivity, and excellent radiation resistance.

Interactions of molecular ions with model phospholipid membranes

2011 ◽  
Vol 76 (6) ◽  
pp. 695-711 ◽  
Author(s):  
Michal Petrov ◽  
Lukasz Cwiklik ◽  
Pavel Jungwirth
Keyword(s):  
Molecular Dynamics ◽  
Molecular Ions ◽  
The Other ◽  
Dynamics Simulation ◽  
Phospholipid Membrane ◽  
Biophysical Properties ◽  
Ion Specificity ◽  
Biologically Relevant ◽  
Lipid Diffusion ◽  
First Time

The affinities of a series of biologically relevant ions for a hydrated phospholipid membrane were investigated using molecular dynamics simulation. Interactions of molecular ions, such as guanidinium, tetramethylammonium, and thiocyanate with the bilayer were computationally characterized for the first time. Simulations reveal strong ion specificity. On one hand, ions like guanidinium and thiocyanate adsorb relatively strongly to the headgroup region of the membrane. On the other hand, potassium or chloride interact very weakly with the phospholipids and merely act as neutralizing counterions. Calculations also show that these ions affect differently biophysical properties of the membrane, such as lipid diffusion, headgroup hydration and tilt angle.

scholarly journals Inhibition of Mycobacterium-RmlA by Molecular Modeling, Dynamics Simulation, and Docking

2016 ◽  
Vol 2016 ◽  
pp. 1-13 ◽  
Author(s):  
N. Harathi ◽  
Madhusudana Pulaganti ◽  
C. M. Anuradha ◽  
Suresh Kumar Chitta
Keyword(s):  
Drug Targets ◽  
Rational Design ◽  
3D Structure ◽  
Reliability Assessment ◽  
Comparative Modeling ◽  
Structure And Function ◽  
Dynamics Simulation ◽  
Structural Refinement ◽  
And Function ◽  
Key Residues

The increasing resistance to anti-tb drugs has enforced strategies for finding new drug targets against Mycobacterium tuberculosis (Mtb). In recent years enzymes associated with the rhamnose pathway in Mtb have attracted attention as drug targets. The present work is on α-D-glucose-1-phosphate thymidylyltransferase (RmlA), the first enzyme involved in the biosynthesis of L-rhamnose, of Mtb cell wall. This study aims to derive a 3D structure of RmlA by using a comparative modeling approach. Structural refinement and energy minimization of the built model have been done with molecular dynamics. The reliability assessment of the built model was carried out with various protein checking tools such as Procheck, Whatif, ProsA, Errat, and Verify 3D. The obtained model investigates the relation between the structure and function. Molecular docking interactions of Mtb-RmlA with modified EMB (ethambutol) ligands and natural substrate have revealed specific key residues Arg13, Lys23, Asn109, and Thr223 which play an important role in ligand binding and selection. Compared to all EMB ligands, EMB-1 has shown better interaction with Mtb-RmlA model. The information thus discussed above will be useful for the rational design of safe and effective inhibitors specific to RmlA enzyme pertaining to the treatment of tuberculosis.

scholarly journals Ab Initio Molecular Dynamics Simulation of Tribochemical Reactions Involving Phosphorus Additives at Sliding Iron Interfaces

2018 ◽  
Author(s):  
Sophie Loehlé ◽  
M. C. Righi
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Dynamics Simulation ◽  
Ab Initio Molecular Dynamics ◽  
Molecular Dissociation ◽  
Iron Phosphide ◽  
Dynamics Simulations ◽  
Activation Times ◽  
First Time ◽  
Dissociation Barrier

We performed for the first time to our knowledge fully ab initio molecular dynamics simulations of additive tribochemistry in boundary lubrication conditions. We consider an organophosphourus additive that has been experimentally shown to reduce friction in steel-on-steel sliding contacts thanks to the tribologically-induced formation of an iron phosphide tribofilm. The simulations allow us to observe in real time the molecular dissociation at the sliding iron interface under pressure and to understand the mechanism of iron phosphide formation. We discuss the role played by the mechanical stress by comparing the activation times for molecular dissociation observed in the tribological simulations at different applied loads with that expected on the basis of the dissociation barrier.

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