scholarly journals Computational Compensatory Mutation Discovery Approach: Predicting a PARP1 Variant Rescue Mutation

2021 ◽  
Author(s):  
Krithika Ravishankar ◽  
Xianli Jiang ◽  
Emmett M. Leddin ◽  
Faruck Morcos ◽  
G. Andrés Cisneros
Keyword(s):  
Dynamical Behavior ◽  
Md Simulations ◽  
Integrated Approach ◽  
Compensatory Mutation ◽  
Wild Type ◽  
Molecular Therapeutics ◽  
Mutation Discovery ◽  
Compensatory Mutations ◽  
Biophysical Effects ◽  
Compensatory Effect

The prediction of protein mutations that affect function may be exploited for multiple uses. In the context of disease variants, the prediction of compensatory mutations that reestablish functional phenotypes could aid in the development of genetic therapies. In this work, we present an integrated approach that combines coevolutionary analysis and molecular dynamics (MD) simulations to discover functional compensatory mutations. This approach is employed to investigate possible rescue mutations of a poly(ADP-ribose) polymerase 1 (PARP1) variant, PARP1 V762A, associated with lung cancer and follicular lymphoma. MD simulations show PARP1 V762A exhibits noticeable changes in structural and dynamical behavior compared with wild type PARP1. Our integrated approach predicts A755E as a possible compensatory mutation based on coevolutionary information, and molecular simulations indicate that the PARP1 A755E/V762A double mutant exhibits similar structural and dynamical behavior to WT PARP1. Our methodology can be broadly applied to a large number of systems where SNPs have been identified as connected to disease and can shed light on the biophysical effects of such changes as well as provide a way to discover potential mutants that could restore wild type-like functionality. This can in turn be further utilized in the design of molecular therapeutics that aim to mimic such compensatory effect.

scholarly journals Cholesterol Transport in Wild-Type NPC1 and P691S: Molecular Dynamics Simulations Reveal Changes in Dynamical Behavior

2020 ◽  
Vol 21 (8) ◽  
pp. 2962 ◽  
Author(s):  
Nadia Elghobashi-Meinhardt
Keyword(s):  
Molecular Dynamics ◽  
Dynamical Behavior ◽  
Structural Data ◽  
Md Simulations ◽  
Structural Features ◽  
Wild Type ◽  
Lipid Storage Disease ◽  
Signaling Mechanism ◽  
Lipid Trafficking ◽  
Dynamics Simulations

The Niemann–Pick C1 (NPC1) protein is the main protein involved in NPC disease, a fatal lysosomal lipid storage disease. NPC1, containing 1278 amino acids, is comprised of three lumenal domains (N-terminal, middle lumenal, C-terminal) and a transmembrane (TM) domain that contains a five helix bundle referred to as the sterol-sensing domain (SSD). The exact purpose of the SSD is not known, but it is believed that the SSD may bind cholesterol, either as a part of the lipid trafficking pathway or as part of a signaling mechanism. A recent cryo-EM structure has revealed an itraconazole binding site (IBS) in the SSD of human NPC1. Using this structural data, we constructed a model of cholesterol-bound wild-type (WT) and mutant P691S and performed molecular dynamics (MD) simulations of each cholesterol-bound protein. For WT NPC1, cholesterol migrates laterally, in the direction of the lipid bilayer. In the case of P691S, cholesterol is observed for the first time to migrate away from the SSD toward the N-terminal domain via a putative tunnel that connects the IBS with the lumenal domains. Structural features of the IBS are analyzed to identify the causes for different dynamical behavior between cholesterol-bound WT and cholesterol-bound P691S. The side chain of Ser691 in the P691S mutant introduces a hydrogen bond network that is not present in the WT protein. This change is likely responsible for the altered dynamical behavior observed in the P691S mutant and helps explain the disrupted cholesterol trafficking behavior observed in experiments.

scholarly journals Deciphering the Role of Residues Involved in Disorder-To-Order Transition Regions in Archaeal tRNA Methyltransferase 5

Genes ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 399
Author(s):  
Ambuj Srivastava ◽  
Dhanusha Yesudhas ◽  
Shandar Ahmad ◽  
M. Michael Gromiha
Keyword(s):  
Three Dimensional ◽  
Md Simulations ◽  
Order Transition ◽  
Free Form ◽  
Wild Type ◽  
Intrinsically Disordered ◽  
Intrinsically Disordered Regions ◽  
Type Complex ◽  
In The Wild ◽  
Trna Methyltransferase

tRNA methyltransferase 5 (Trm5) enzyme is an S-adenosyl methionine (AdoMet)-dependent methyltransferase which methylates the G37 nucleotide at the N1 atom of the tRNA. The free form of Trm5 enzyme has three intrinsically disordered regions, which are highly flexible and lack stable three-dimensional structures. These regions gain ordered structures upon the complex formation with tRNA, also called disorder-to-order transition (DOT) regions. In this study, we performed molecular dynamics (MD) simulations of archaeal Trm5 in free and complex forms and observed that the DOT residues are highly flexible in free proteins and become stable in complex structures. The energetic contributions show that DOT residues are important for stabilising the complex. The DOT1 and DOT2 are mainly observed to be important for stabilising the complex, while DOT3 is present near the active site to coordinate the interactions between methyl-donating ligands and G37 nucleotides. In addition, mutational studies on the Trm5 complex showed that the wild type is more stable than the G37A tRNA mutant complex. The loss of productive interactions upon G37A mutation drives the AdoMet ligand away from the 37th nucleotide, and Arg145 in DOT3 plays a crucial role in stabilising the ligand, as well as the G37 nucleotide, in the wild-type complex. Further, the overall energetic contribution calculated using MMPBSA corroborates that the wild-type complex has a better affinity between Trm5 and tRNA. Overall, our study reveals that targeting DOT regions for binding could improve the inhibition of Trm5.

Effects of viscosity and osmotic stress on the reaction of human butyrylcholinesterase with cresyl saligenin phosphate, a toxicant related to aerotoxic syndrome: kinetic and molecular dynamics studies

2013 ◽  
Vol 454 (3) ◽  
pp. 387-399 ◽  
Author(s):  
Patrick Masson ◽  
Sofya Lushchekina ◽  
Lawrence M. Schopfer ◽  
Oksana Lockridge
Keyword(s):  
Osmotic Stress ◽  
Osmotic Pressure ◽  
Active Site ◽  
Md Simulations ◽  
Catalytic Triad ◽  
Wild Type ◽  
Irreversible Inhibitor ◽  
Enzyme Active Site ◽  
Diffusion Controlled ◽  
Peripheral Site

CSP (cresyl saligenin phosphate) is an irreversible inhibitor of human BChE (butyrylcholinesterase) that has been involved in the aerotoxic syndrome. Inhibition under pseudo-first-order conditions is biphasic, reflecting a slow equilibrium between two enzyme states E and E′. The elementary constants for CSP inhibition of wild-type BChE and D70G mutant were determined by studying the dependence of inhibition kinetics on viscosity and osmotic pressure. Glycerol and sucrose were used as viscosogens. Phosphorylation by CSP is sensitive to viscosity and is thus strongly diffusion-controlled (kon≈108 M−1·min−1). Bimolecular rate constants (ki) are about equal to kon values, making CSP one of the fastest inhibitors of BChE. Sucrose caused osmotic stress because it is excluded from the active-site gorge. This depleted the active-site gorge of water. Osmotic activation volumes, determined from the dependence of ki on osmotic pressure, showed that water in the gorge of the D70G mutant is more easily depleted than that in wild-type BChE. This demonstrates the importance of the peripheral site residue Asp70 in controlling the active-site gorge hydration. MD simulations provided new evidence for differences in the motion of water within the gorge of wild-type and D70G enzymes. The effect of viscosogens/osmolytes provided information on the slow equilibrium E⇌E′, indicating that alteration in hydration of a key catalytic residue shifts the equilibrium towards E′. MD simulations showed that glycerol molecules that substitute for water molecules in the enzyme active-site gorge induce a conformational change in the catalytic triad residue His438, leading to the less reactive form E′.

scholarly journals Dynamical Behavior and Conformational Selection Mechanism of the Intrinsically Disordered Sic1 Kinase-Inhibitor Domain

Life ◽  
2020 ◽  
Vol 10 (7) ◽  
pp. 110 ◽  
Author(s):  
Davide Sala ◽  
Ugo Cosentino ◽  
Anna Ranaudo ◽  
Claudio Greco ◽  
Giorgio Moro
Keyword(s):  
Kinase Inhibitor ◽  
Dynamical Behavior ◽  
Md Simulations ◽  
Molecular Shape ◽  
Conformational Space ◽  
Coarse Grained ◽  
Conformational Ensemble ◽  
Selection Mechanism ◽  
Conformational Selection ◽  
Intrinsically Disordered

Intrinsically Disordered Peptides and Proteins (IDPs) in solution can span a broad range of conformations that often are hard to characterize by both experimental and computational methods. However, obtaining a significant representation of the conformational space is important to understand mechanisms underlying protein functions such as partner recognition. In this work, we investigated the behavior of the Sic1 Kinase-Inhibitor Domain (KID) in solution by Molecular Dynamics (MD) simulations. Our results point out that application of common descriptors of molecular shape such as Solvent Accessible Surface (SAS) area can lead to misleading outcomes. Instead, more appropriate molecular descriptors can be used to define 3D structures. In particular, we exploited Weighted Holistic Invariant Molecular (WHIM) descriptors to get a coarse-grained but accurate definition of the variegated Sic1 KID conformational ensemble. We found that Sic1 is able to form a variable amount of folded structures even in absence of partners. Among them, there were some conformations very close to the structure that Sic1 is supposed to assume in the binding with its physiological complexes. Therefore, our results support the hypothesis that this protein relies on the conformational selection mechanism to recognize the correct molecular partners.

Entropic effect and residue specific entropic contribution to the cooperativity in streptavidin–biotin binding

Nanoscale ◽  
2020 ◽  
Vol 12 (13) ◽  
pp. 7134-7145 ◽  
Author(s):  
Yalong Cong ◽  
Kaifang Huang ◽  
Yuchen Li ◽  
Susu Zhong ◽  
John Z. H. Zhang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Md Simulations ◽  
Specific Charge ◽  
Wild Type ◽  
Double Mutation ◽  
Biotin Binding ◽  
Entropic Effect ◽  
Entropic Contribution

Molecular dynamics (MD) simulations were performed employing the polarized protein-specific charge (PPC) to explore the origin of the cooperativity in streptavidin–biotin systems (wild type, two single mutations and one double-mutation).

scholarly journals Molecular Dynamics and Metadynamics Simulations of the Cellulase Cel48F

2014 ◽  
Vol 2014 ◽  
pp. 1-7 ◽  
Author(s):  
Osmair Vital de Oliveira
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Md Simulations ◽  
Cellulose Fibers ◽  
Mean Square ◽  
Mean Square Deviation ◽  
Wild Type ◽  
Sugar Chain ◽  
Alcohol Production ◽  
Sugar Chains

Molecular dynamics (MD) and metadynamics techniques were used to study the cellulase Cel48F-sugar. Cellulase is enzyme that breaks cellulose fibers into small sugar units and is potentially useful in second generation alcohol production. In MD simulations, the overall structure of equilibrated Cel48F did not significantly change along the trajectory, retaining root mean square deviation below 0.15 nm. A set of 15 residues interacting with the sugar chains via hydrogen bonding throughout the simulation was observed. The free energy of dissociation (ΔGdiss.) of the chains in the catalytic tunnel of Cel48F was determined by metadynamics. The ΔGdiss. values of the chains entering and leaving the wild-type Cel48F cavity were 13.9 and 62.1 kcal/mol, respectively. We also mutated the E542 and Q543 to alanine residue and obtained ΔGdiss. of 41.8 and 45.9 kcal/mol, respectively. These mutations were found to facilitate smooth dissociation of the sugar chain across the Cel48F tunnel. At the entry of the Cel48F tunnel, three residues were mutated to alanine: T110, T213, and L274. Contrary to the T110A-Cel48F, the mutants T213-Cel48F and L274-Cel48F prevented the sugar chain from passing across the leaving site. The present results can be a guideline in mutagenesis studies to improve processing by Cel48F.

A QM/MM MD study of the pH-dependent ring-opening catalysis and lid motif flexibility in glucosamine 6-phosphate deaminase

2014 ◽  
Vol 16 (34) ◽  
pp. 18406-18417 ◽  
Author(s):  
Yuan Zhao ◽  
Nanhao Chen ◽  
Ruibo Wu ◽  
Zexing Cao
Keyword(s):  
Ring Opening ◽  
Dynamical Behavior ◽  
Md Simulations ◽  
Ph Dependent

QM/MM MD and MM MD simulations reveal pH-dependent proton-shuttle ring-opening mechanisms of GlcN6P and dynamical behavior of the lid motif inSmuNagB.

scholarly journals Determination of Protein Structural Ensembles by Hybrid-Resolution SAXS Restrained Molecular Dynamics.

2019 ◽  
Author(s):  
Cristina Paissoni ◽  
Alexander Jussupow ◽  
Carlo Camilloni
Keyword(s):  
Dynamical Behavior ◽  
Computational Cost ◽  
Three Dimensional ◽  
Md Simulations ◽  
Coarse Grained ◽  
Conformational Ensemble ◽  
Biomolecular Systems ◽  
Conformational Ensembles ◽  
Independent Experimental Data

<div><div><div><p>SAXS experiments provide low-resolution but valuable information about the dynamics of biomolecular systems, which could be ideally integrated in MD simulations to accurately determine conformational ensembles of flexible proteins. The applicability of this strategy is hampered by the high computational cost required to calculate scattering intensities from three-dimensional structures. We previously presented a metainference-based hybrid resolution method that makes atomistic SAXS-restrained MD simulation feasible by adopting a coarse-grained approach to efficiently back-calculate scattering intensities; here, we extend this technique, applying it in the framework of multiple-replica simulations with the aim to investigate the dynamical behavior of flexible biomolecules. The efficacy of the method is assessed on the K63-diubiquitin multi-domain protein, showing that inclusion of SAXS-restraints is effective in generating reliable and heterogenous conformational ensemble, also improving the agreement with independent experimental data.</p></div></div></div>

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