scholarly journals SNP2SIM: A modular workflow for standardizing molecular simulation and functional analysis of protein variants

2018 ◽  
Author(s):  
Matthew D. McCoy ◽  
Vikram Shivakumar ◽  
Sridhar Nimmagadda ◽  
Mohsin Saleet Jafri ◽  
Subha Madhavan
Keyword(s):  
Molecular Dynamics ◽  
Protein Function ◽  
Molecular Mechanisms ◽  
Cancer Genomics ◽  
Atomic Scale ◽  
Protein Variant ◽  
Docking Simulations ◽  
Small Molecule Ligands ◽  
Dynamics Simulations ◽  
The Impact

AbstractMolecular simulations are used to provide insight into protein structure and function, and have the potential to provide important context when predicting the impact of sequence variation on protein function. In addition to understanding molecular mechanisms and interactions on the atomic scale, translational applications of those approaches include drug screening, development of novel molecular therapies, and treatment planning when selecting targeted therapies. Supporting the continued development of these applications, we have developed the SNP2SIM workflow generates reproducible molecular dynamics and molecular docking simulations for downstream functional variant analysis. Three modules execute molecular dynamics simulations of solvated protein variant structures, analyze the resulting trajectories for unique structural conformations, and bind small molecule ligands to representative variant scaffolds. In addition to availability as a command line workflow, SNP2SIM modules are also available as individual apps on the Seven Bridges Cancer Genomics Cloud.

Molecular Dynamics Study of Ion Impact Phenomena and Compressive Stress in Thin Films

1993 ◽  
Vol 317 ◽  
Author(s):  
N.A. Marks ◽  
P. Guan ◽  
D.R. Mckenzie ◽  
B.A. PailThorpe
Keyword(s):  
Molecular Dynamics ◽  
Three Dimensional ◽  
Carbon Films ◽  
Loss Mechanism ◽  
Ion Energy ◽  
Lennard Jones ◽  
Impact Phenomena ◽  
Ion Impact ◽  
Dynamics Simulations ◽  
The Impact

ABSTRACTMolecular dynamics simulations of nickel and carbon have been used to study the phenomena due to ion impact. The nickel and carbon interactions were described using the Lennard-Jones and Stillinger-Weber potentials respectively. The phenomena occurring after the impact of 100 e V to 1 keV ions were studied in the nickel simulations, which were both two and three-dimensional. Supersonic focussed collision sequences (or focusons) were observed, and associated with these focusons were unexpected sonic bow waves, which were a major energy loss mechanism for the focuson. A number of 2D carbon films were grown and the stress in the films as a function of incident ion energy was Measured. With increasing energy the stress changed from tensile to compressive and reached a maximum around 50 eV, in agreement with experiment.

scholarly journals Exploiting correlated molecular-dynamics networks to counteract enzyme activity–stability trade-off

2018 ◽  
Vol 115 (52) ◽  
pp. E12192-E12200 ◽  
Author(s):  
Haoran Yu ◽  
Paul A. Dalby
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Active Site ◽  
Dynamic Networks ◽  
Aromatic Aldehydes ◽  
Active Site Residues ◽  
Trade Off ◽  
Highly Correlated ◽  
Dynamics Simulations ◽  
The Impact

The directed evolution of enzymes for improved activity or substrate specificity commonly leads to a trade-off in stability. We have identified an activity–stability trade-off and a loss in unfolding cooperativity for a variant (3M) of Escherichia coli transketolase (TK) engineered to accept aromatic substrates. Molecular dynamics simulations of 3M revealed increased flexibility in several interconnected active-site regions that also form part of the dimer interface. Mutating the newly flexible active-site residues to regain stability risked losing the new activity. We hypothesized that stabilizing mutations could be targeted to residues outside of the active site, whose dynamics were correlated with the newly flexible active-site residues. We previously stabilized WT TK by targeting mutations to highly flexible regions. These regions were much less flexible in 3M and would not have been selected a priori as targets using the same strategy based on flexibility alone. However, their dynamics were highly correlated with the newly flexible active-site regions of 3M. Introducing the previous mutations into 3M reestablished the WT level of stability and unfolding cooperativity, giving a 10.8-fold improved half-life at 55 °C, and increased midpoint and aggregation onset temperatures by 3 °C and 4.3 °C, respectively. Even the activity toward aromatic aldehydes increased up to threefold. Molecular dynamics simulations confirmed that the mutations rigidified the active-site via the correlated network. This work provides insights into the impact of rigidifying mutations within highly correlated dynamic networks that could also be useful for developing improved computational protein engineering strategies.

scholarly journals Systematic Finite-Temperature Reduction of Crystal Energy Landscapes.

2020 ◽  
Author(s):  
Nicholas Francia ◽  
Louise S. Price ◽  
Jonas Nyman ◽  
Sarah (Sally) Price ◽  
Matteo Salvalaglio
Keyword(s):  
Molecular Dynamics ◽  
Finite Temperature ◽  
Structure Prediction ◽  
Lattice Energy ◽  
Biased Sampling ◽  
Energy Landscapes ◽  
Polymorphic Transformations ◽  
Temperature And Pressure ◽  
Dynamics Simulations ◽  
The Impact

<p>Crystal structure prediction methods are prone to overestimate the number of potential polymorphs of organic molecules. In this work, we aim to reduce the overprediction by systematically applying molecular dynamics simulations and biased sampling methods to cluster subsets of structures that can easily interconvert at finite temperature and pressure. Following this approach, we rationally reduce the number of predicted putative polymorphs in CSP-generated crystal energy landscapes. This uses an unsupervised clustering approach to analyze independent finite-temperature molecular dynamics trajectories and hence identify a representative structure of each cluster of distinct lattice energy minima that are effectively equivalent at finite temperature and pressure. Biased simulations are used to reduce the impact of limited sampling time and to estimate the work associated with polymorphic transformations. We demonstrate the proposed systematic approach by studying the polymorphs of urea and succinic acid, reducing an initial set of over 100 energetically plausible CSP structures to 12 and 27 respectively, including the experimentally known polymorphs. The simulations also indicate the types of disorder and stacking errors that may occur in real structures.<br></p>

Atomic-Scale Probing of Defect-Assisted Ga Intercalation Through Graphene Using ReaxFF Molecular Dynamics Simulations

2021 ◽  
Author(s):  
Nadire Nayir ◽  
Mert Y. Sengul ◽  
Anna L. Costine ◽  
Petra Reinke ◽  
Siavash Rajabpour ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Atomic Scale ◽  
Dynamics Simulations

Structure and dynamics of gold nanoparticles decorated with chitosan–gentamicin conjugates: ReaxFF molecular dynamics simulations to disclose drug delivery

2019 ◽  
Vol 21 (24) ◽  
pp. 13099-13108 ◽  
Author(s):  
Susanna Monti ◽  
Jiya Jose ◽  
Athira Sahajan ◽  
Nandakumar Kalarikkal ◽  
Sabu Thomas
Keyword(s):  
Drug Delivery ◽  
Molecular Dynamics ◽  
Gold Nanoparticles ◽  
Molecular Dynamics Simulations ◽  
Atomic Scale ◽  
Functionalized Gold Nanoparticles ◽  
Structure And Dynamics ◽  
Antibiotic Drug ◽  
Dynamics Simulations

Functionalized gold nanoparticles for antibiotic drug delivery: from the nanoscale to the atomic scale.

Conformational and aggregation properties of PffBT4T polymers: atomistic insight into the impact of alkyl-chain branching positions

2019 ◽  
Vol 7 (45) ◽  
pp. 14198-14204
Author(s):  
Lu Ning ◽  
Guangchao Han ◽  
Yuanping Yi
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Alkyl Chain ◽  
Temperature Dependent ◽  
Chain Branching ◽  
Alkyl Chains ◽  
Dynamics Simulations ◽  
The Impact ◽  
Insight Into

The impact of the branching positions of alkyl chains on temperature dependent aggregation is rationalized by atomistic molecular dynamics simulations.

scholarly journals Carbon Nanotube Peapods Under High-Strain Rate Conditions: A Molecular Dynamics Investigation

MRS Advances ◽  
2020 ◽  
Vol 5 (33-34) ◽  
pp. 1723-1730
Author(s):  
J. M. De Sousa ◽  
C. F. Woellner ◽  
L. D. Machado ◽  
P. A. S. Autreto ◽  
D. S. Galvao
Keyword(s):  
Molecular Dynamics ◽  
Carbon Nanotube ◽  
High Strain Rate ◽  
Strain Rate ◽  
High Strain ◽  
Optical Modulation ◽  
Carbon Structures ◽  
Dynamics Simulations ◽  
Forms Of Carbon ◽  
The Impact

ABSTRACTNew forms of carbon-based materials have received great attention, and the developed materials have found many applications in nanotechnology. Interesting novel carbon structures include the carbon peapods, which are comprised of fullerenes encapsulated within carbon nanotubes. Peapod-like nanostructures have been successfully synthesized, and have been used in optical modulation devices, transistors, solar cells, and in other devices. However, the mechanical properties of these structures are not completely elucidated. In this work, we investigated, using fully atomistic molecular dynamics simulations, the deformation of carbon peapods under high-strain rate conditions, which are achieved by shooting the peapods at ultrasonic velocities against a rigid substrate. Our results show that carbon peapods experience large deformation at impact, and undergo multiple fracture pathways, depending primarily on the relative orientation between the peapod and the substrate, and the impact velocity. Observed outcomes include fullerene ejection, carbon nanotube fracture, fullerene, and nanotube coalescence, as well as the formation of amorphous carbon structures.

‘Piperazining’ the catalytic gatekeepers: unraveling the pan-inhibition of SRC kinases; LYN, FYN and BLK by masitinib

2019 ◽  
Vol 11 (18) ◽  
pp. 2365-2380
Author(s):  
Aimen K Aljoundi ◽  
Clement Agoni ◽  
Fisayo A Olotu ◽  
Mahmoud ES Soliman
Keyword(s):  
Molecular Dynamics ◽  
B Cell ◽  
Molecular Dynamics Simulations ◽  
Molecular Mechanisms ◽  
Cell Lymphoma ◽  
B Cell Lymphoma ◽  
Dynamics Simulation ◽  
Large B Cell Lymphoma ◽  
Dynamics Simulations ◽  
Large B Cell

Aim: Blocking oncogenic signaling of B-cell receptor (BCR) has been explored as a viable strategy in the treatment of diffuse large B-cell lymphoma. Masitinib is shown to multitarget LYN, FYN and BLK kinases that propagate BCR signals to downstream effectors. However, the molecular mechanisms of its selectivity and pan-inhibition remain elusive. Materials & methods: This study therefore employed molecular dynamics simulations coupled with advanced post-molecular dynamics simulation techniques to unravel the structural mechanisms that inform the reported multitargeting ability of masitinib. Results: Molecular dynamics simulations revealed initial selective targeting of catalytic residues (Asp334/Glu335 – LYN; Asp130/Asp148/Glu54 – FYN; Asp89 – BLK) by masitinib, with high-affinity interactions via its piperazine ring at the entrance of the ATP-binding pockets, before systematic access into the hydrophobic deep pocket grooves. Conclusion: Identification of these ‘gatekeeper’ residues could open up a novel paradigm of structure-based design of highly selective pan-inhibitors of BCR signaling in the treatment of diffuse large B-cell lymphoma.

Sign in / Sign up

Export Citation Format

Share Document