Computing Reaction Pathways of Rare Biomolecular Transitions using Atomistic Force-Fields

Faccioli, Pietro; Beccara, S. a

doi:10.1016/j.bpc.2015.06.014

Cited by 8 publications

(7 citation statements)

References 29 publications

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“…However, single-molecule studies have shown that even for slow-folding proteins, actual transitions between unfolded and folded conformations are rapid (typically on the microsecond timescale) and similar to those of small fast-folding proteins (16). Therefore, if we can preferentially sample only the ''reactive'' parts of folding trajectories, it becomes feasible to accurately compute the folding pathways of even large proteins (17)(18)(19). In this work, we rely on a recently developed variational method called the bias functional (BF) approach (see Methods) to achieve this goal and sample transition paths.…”

Section: Introductionmentioning

confidence: 99%

All-Atom Simulations Reveal How Single-Point Mutations Promote Serpin Misfolding

Wang

Orioli

Ianeselli

et al. 2018

Biophysical Journal

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Protein misfolding is implicated in many diseases, including serpinopathies. For the canonical inhibitory serpin α-antitrypsin, mutations can result in protein deficiencies leading to lung disease, and misfolded mutants can accumulate in hepatocytes, leading to liver disease. Using all-atom simulations based on the recently developed bias functional algorithm, we elucidate how wild-type α-antitrypsin folds and how the disease-associated S (Glu264Val) and Z (Glu342Lys) mutations lead to misfolding. The deleterious Z mutation disrupts folding at an early stage, whereas the relatively benign S mutant shows late-stage minor misfolding. A number of suppressor mutations ameliorate the effects of the Z mutation, and simulations on these mutants help to elucidate the relative roles of steric clashes and electrostatic interactions in Z misfolding. These results demonstrate a striking correlation between atomistic events and disease severity and shine light on the mechanisms driving chains away from their correct folding routes.

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Section: Introductionmentioning

confidence: 99%

All-Atom Simulations Reveal How Single-Point Mutations Promote Serpin Misfolding

Wang

Orioli

Ianeselli

et al. 2018

Biophysical Journal

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“…Atomic simulation studies can take care of these factors but such studies are limited due to the high computational cost. However, using the effective force fields in the coarse‐grain models [31] can address this problem.…”

Section: Discussionmentioning

confidence: 99%

Simulation Study of the Conformational Properties of Diblock Polyelectrolytes in Salt Solutions

Dabhade

Chaudhury

2021

Chemistry An Asian Journal

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Coarse‐grained molecular dynamics simulations are performed to understand the behavior of diblock polyelectrolytes in solutions of divalent salt by studying the conformations of chains over a wide range of salt concentrations. The polymer molecules are modeled as bead spring chains with different charged fractions and the counterions and salt ions are incorporated explicitly. Upon addition of a divalent salt, the salt cations replace the monovalent counterions, and the condensation of divalent salt cations onto the polyelectrolyte increases, and the chains favor to collapse. The condensation of ions changes with the salt concentration and depends on the charged fraction. Also, the degree of collapse at a given salt concentration changes with the increasing valency of the counterion due to the bridging effect. As a quantitative measure of the distribution of counterions around the polyelectrolyte chain, we study the radial distribution function between monomers on different polyelectrolytes and the counterions inside the counterion worm surrounding a polymer chain at different concentrations of the divalent salt. Our simulation results show a strong dependence of salt concentration on the conformational properties of diblock copolymers and indicate that it can tune the self‐assembly behaviors of such charged polyelectrolyte block copolymers.

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“…The Attenuated Total Reflectance Fourier Transform Infrared Spectroscopy (ATR-FTIR), Raman and 1HNMR spectroscopies are used in order to observe the changes of molecular structures of these tissues. The effect of Near-Infrared (NIR) or IR-A, Short-Wavelength Infrared (SWIR) or IR-B, Mid-Wavelength Infrared (MWIR) or IR-C, Intermediate Infrared (IIR) or IR-C, Long-Wavelength Infrared (LWIR) or IR-C and Far-Infrared (FIR) lights was seen by noticing the changes of the Amide bands in absorption spectra of tissues, respectively [10][11][12][13][14][15][16][17][18][19]. (Figures 7-9).…”

Section: Editorialmentioning

confidence: 99%

Study of Irradiations to Enhance the Induces the Dissociation of Hydrogen Bonds between Peptide Chains and Transition from Helix Structure to Random Coil Structure Using ATRFTIR, Raman and 1HNMR Spectroscopies

Heidari¹

2016

J Biomol Res Ther

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Computing Reaction Pathways of Rare Biomolecular Transitions using Atomistic Force-Fields

Cited by 8 publications

References 29 publications

All-Atom Simulations Reveal How Single-Point Mutations Promote Serpin Misfolding

All-Atom Simulations Reveal How Single-Point Mutations Promote Serpin Misfolding

Simulation Study of the Conformational Properties of Diblock Polyelectrolytes in Salt Solutions

Study of Irradiations to Enhance the Induces the Dissociation of Hydrogen Bonds between Peptide Chains and Transition from Helix Structure to Random Coil Structure Using ATRFTIR, Raman and 1HNMR Spectroscopies

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