Free energy of conformational change in a single chain of polyvinylidene fluoride using molecular simulations

2021 ◽  
Vol 61 (4) ◽  
pp. 1270-1280
Author(s):  
Shubham Mireja ◽  
Devang V. Khakhar
Keyword(s):  
Free Energy ◽  
Conformational Change ◽  
Polyvinylidene Fluoride ◽  
Molecular Simulations ◽  
Single Chain

scholarly journals How proteins open fusion pores: insights from molecular simulations

2020 ◽  
Author(s):  
H. Jelger Risselada ◽  
Helmut Grubmüller
Keyword(s):  
Free Energy ◽  
Fusion Proteins ◽  
Graphics Processing Units ◽  
Fusion Reaction ◽  
Molecular Simulations ◽  
Minimum Free Energy ◽  
Free Energy Calculations ◽  
Coarse Grained ◽  
Fusion Pore ◽  
Graphics Processing

AbstractFusion proteins can play a versatile and involved role during all stages of the fusion reaction. Their roles go far beyond forcing the opposing membranes into close proximity to drive stalk formation and fusion. Molecular simulations have played a central role in providing a molecular understanding of how fusion proteins actively overcome the free energy barriers of the fusion reaction up to the expansion of the fusion pore. Unexpectedly, molecular simulations have revealed a preference of the biological fusion reaction to proceed through asymmetric pathways resulting in the formation of, e.g., a stalk-hole complex, rim-pore, or vertex pore. Force-field based molecular simulations are now able to directly resolve the minimum free-energy path in protein-mediated fusion as well as quantifying the free energies of formed reaction intermediates. Ongoing developments in Graphics Processing Units (GPUs), free energy calculations, and coarse-grained force-fields will soon gain additional insights into the diverse roles of fusion proteins.

scholarly journals Fracture of Elastomeric Materials by Crosslink Failure

2018 ◽  
Vol 85 (8) ◽  
Author(s):  
Yunwei Mao ◽  
Lallit Anand
Keyword(s):  
Free Energy ◽  
Failure Mode ◽  
Chain Scission ◽  
Progressive Damage ◽  
Central Feature ◽  
Single Chain ◽  
Elastomeric Material ◽  
Damage And Fracture ◽  
Elastomeric Materials ◽  
Covalent Crosslinks

If an elastomeric material is subjected to sufficiently large deformations, it eventually fractures. There are two typical micromechanisms of failure in such materials: chain scission and crosslink failure. The chain scission failure mode is mainly observed in polymers with strong covalent crosslinks, while the crosslink failure mode is observed in polymers with weak crosslinks. In two recent papers, we have proposed a theory for progressive damage and rupture of polymers with strong covalent crosslinks. In this paper, we extend our previous framework and formulate a theory for modeling failure of elastomeric materials with weak crosslinks. We first introduce a model for the deformation of a single chain with weak crosslinks at each of its two ends using statistical mechanics arguments, and then upscale the model from a single chain to the continuum level for a polymer network. Finally, we introduce a damage variable to describe the progressive damage and failure of polymer networks. A central feature of our theory is the recognition that the free energy of elastomers is not entirely entropic in nature; there is also an energetic contribution from the deformation of the backbone bonds in a chain and/or the crosslinks. For polymers with weak crosslinks, this energetic contribution is mainly from the deformation of the crosslinks. It is this energetic part of the free energy which is the driving force for progressive damage and fracture of elastomeric materials. Moreover, we show that for elastomeric materials in which fracture occurs by crosslink stretching and scission, the classical Lake–Thomas scaling—that the toughness Gc of an elastomeric material is proportional to 1/G0, with G0=NkBϑ the ground-state shear modulus of the material—does not hold. A new scaling is proposed, and some important consequences of this scaling are remarked upon.

HCO3(-)-dependent conformational change in gastric parietal cell AE2, a glycoprotein naturally lacking sialic acid

1996 ◽  
Vol 271 (2) ◽  
pp. G311-G321 ◽  
Author(s):  
A. S. Zolotarev ◽  
R. R. Townsend ◽  
A. Stuart-Tilley ◽  
S. L. Alper
Keyword(s):  
Sialic Acid ◽  
Conformational Change ◽  
Polyvinylidene Fluoride ◽  
Sodium Dodecyl ◽  
Monosaccharide Composition ◽  
Membrane Glycoproteins ◽  
Gastric Parietal Cell ◽  
Membrane Transport Proteins ◽  
Low Ionic Strength ◽  
Ribonuclease B

Although the AE1 chloride/bicarbonate exchanger of the red blood cell is among the most thoroughly investigated of membrane transport proteins, less is known about the related AE2 polypeptide of parietal cells. We have studied enzymatic deglycosylation of native AE2 polypeptide in gastric mucosal membranes from pig and rabbit. Deglycosylation of AE2 was maximal at low ionic strength. Deglycosylation of AE2 in membranes was preferentially inhibited by bicarbonate compared with other anions. This inhibition was maximal at alkaline pH and was not evident after detergent solubilization of AE2. Deglycosylation of AE2 increased its susceptibility to proteolytic degradation, but the presence of bicarbonate protected against this degradation. Bicarbonate failed to inhibit deglycosylation of the membrane glycoproteins AE1 and gastric H(+)-K(+)-adenosinetriphosphatase beta-subunit or deglycosylation of the soluble glycoproteins fetuin and ribonuclease B. These data suggest that bicarbonate induces a conformational change in AE2 that can protect the polypeptide from deglycosylation and proteolysis. Pig AE2 was purified in sodium dodecyl sulfate, and its monosaccharide composition was determined after blotting onto polyvinylidene fluoride membrane. AE2 was found to be devoid of sialic acid, with a composition suggestive of the presence of lactosamine-type chains.

scholarly journals Free Energy Landscape of Biomolecules from Multiple Non-Equilibrium Molecular Simulations

2009 ◽  
Vol 96 (3) ◽  
pp. 406a ◽  
Author(s):  
Shun Sakuraba ◽  
Akio Kitao
Keyword(s):  
Free Energy ◽  
Energy Landscape ◽  
Molecular Simulations ◽  
Free Energy Landscape ◽  
Non Equilibrium

scholarly journals Molecular-dynamics simulations of urea nucleation from aqueous solution

2014 ◽  
Vol 112 (1) ◽  
pp. E6-E14 ◽  
Author(s):  
Matteo Salvalaglio ◽  
Claudio Perego ◽  
Federico Giberti ◽  
Marco Mazzotti ◽  
Michele Parrinello
Keyword(s):  
Aqueous Solution ◽  
Free Energy ◽  
Molecular Simulations ◽  
Finite Size ◽  
Nucleation Theory ◽  
Classical Nucleation Theory ◽  
Science And Engineering ◽  
Finite Size Effects ◽  
Dynamics Simulations ◽  
Insight Into

Despite its ubiquitous character and relevance in many branches of science and engineering, nucleation from solution remains elusive. In this framework, molecular simulations represent a powerful tool to provide insight into nucleation at the molecular scale. In this work, we combine theory and molecular simulations to describe urea nucleation from aqueous solution. Taking advantage of well-tempered metadynamics, we compute the free-energy change associated to the phase transition. We find that such a free-energy profile is characterized by significant finite-size effects that can, however, be accounted for. The description of the nucleation process emerging from our analysis differs from classical nucleation theory. Nucleation of crystal-like clusters is in fact preceded by large concentration fluctuations, indicating a predominant two-step process, whereby embryonic crystal nuclei emerge from dense, disordered urea clusters. Furthermore, in the early stages of nucleation, two different polymorphs are seen to compete.

Oxygen Reduction Reaction of PEMFC Cathode by Molecular Simulations

2010 ◽  
Vol 105-106 ◽  
pp. 698-700
Author(s):  
Chuang Liu ◽  
Yu Hou Wu ◽  
Hong Sun ◽  
Yu Lan Tang
Keyword(s):  
Free Energy ◽  
Oxygen Reduction Reaction ◽  
Oxygen Reduction ◽  
Molecular Simulations ◽  
Control Process ◽  
Catalyst Layer ◽  
Reduction Reaction ◽  
Cathode Catalyst ◽  
Cathode Catalyst Layer ◽  
Fourth Step

Cathode catalyst layer plays an important role in PEMFC. Electrochemical reaction in cathode catalyst layer is a control process for the performance in PEMFC. In this paper, oxygen reduction reaction (ORR) is studied by molecular simulations based on a series pathway which consist of four steps. We calculated the free energy of four steps respectively by molecular simulations. Comparing free energy of our steps, we found that the fourth step can release more energy than the other steps. At the same time, we found that the energy released in ORR is decreased with the increase of temperature. The process of the first step in the series pathway release less energy than that of other steps. The results are very helpful for optimization of construction in the cathode and improving performance of PEM fuel cell.

scholarly journals Hormone-induced Conformational Change of the Purified Soluble Hormone Binding Domain of Follitropin Receptor Complexed with Single Chain Follitropin

2001 ◽  
Vol 276 (26) ◽  
pp. 23373-23381 ◽  
Author(s):  
Anja Schmidt ◽  
Robert MacColl ◽  
Barbara Lindau-Shepard ◽  
David R. Buckler ◽  
James A. Dias
Keyword(s):  
Conformational Change ◽  
Binding Domain ◽  
Hormone Binding ◽  
Single Chain ◽  
Hormone Binding Domain

Cationic carbosilane dendrimers and oligonucleotide binding: an energetic affair

Nanoscale ◽  
2015 ◽  
Vol 7 (9) ◽  
pp. 3876-3887 ◽  
Author(s):  
D. Marson ◽  
E. Laurini ◽  
P. Posocco ◽  
M. Fermeglia ◽  
S. Pricl
Keyword(s):  
Free Energy ◽  
Gene Delivery ◽  
Molecular Simulations ◽  
Molecular Parameter ◽  
Carbosilane Dendrimers ◽  
Free Energy Of Binding ◽  
Oligonucleotide Binding

Molecular simulations individuate the normalized effective free energy of binding as a critical molecular parameter in designing efficient nanovectors for gene delivery.

Sign in / Sign up

Export Citation Format

Share Document