scholarly journals Toward Optimized Potential Functions for Protein–Protein Interactions in Aqueous Solutions: Osmotic Second Virial Coefficient Calculations Using the MARTINI Coarse-Grained Force Field

2013 ◽  
Vol 9 (9) ◽  
pp. 4176-4185 ◽  
Author(s):  
Austin C. Stark ◽  
Casey T. Andrews ◽  
Adrian H. Elcock
Keyword(s):  
Aqueous Solutions ◽  
Force Field ◽  
Protein Interactions ◽  
Virial Coefficient ◽  
Second Virial Coefficient ◽  
Potential Functions ◽  
Coarse Grained ◽  
Protein Protein Interactions

PACSAB: Coarse-Grained Force Field for the Study of Protein–Protein Interactions and Conformational Sampling in Multiprotein Systems

2015 ◽  
Vol 11 (12) ◽  
pp. 5929-5938 ◽  
Author(s):  
Agustí Emperador ◽  
Pedro Sfriso ◽  
Marcos Ariel Villarreal ◽  
Josep Lluis Gelpí ◽  
Modesto Orozco
Keyword(s):  
Force Field ◽  
Protein Interactions ◽  
Coarse Grained ◽  
Conformational Sampling ◽  
Protein Protein Interactions

scholarly journals Expansion of Intrinsically Disordered Proteins Increases the Range of Stability of Liquid–Liquid Phase Separation

Molecules ◽  
2020 ◽  
Vol 25 (20) ◽  
pp. 4705
Author(s):  
Adiran Garaizar ◽  
Ignacio Sanchez-Burgos ◽  
Rosana Collepardo-Guevara ◽  
Jorge R. Espinosa
Keyword(s):  
Phase Separation ◽  
Liquid Phase ◽  
Protein Interactions ◽  
Conformational Dynamics ◽  
Liquid Phase Separation ◽  
Phase Behaviour ◽  
Coarse Grained ◽  
Protein Protein Interactions ◽  
Intrinsically Disordered ◽  
Liquid Liquid Phase Separation

Proteins containing intrinsically disordered regions (IDRs) are ubiquitous within biomolecular condensates, which are liquid-like compartments within cells formed through liquid–liquid phase separation (LLPS). The sequence of amino acids of a protein encodes its phase behaviour, not only by establishing the patterning and chemical nature (e.g., hydrophobic, polar, charged) of the various binding sites that facilitate multivalent interactions, but also by dictating the protein conformational dynamics. Besides behaving as random coils, IDRs can exhibit a wide-range of structural behaviours, including conformational switching, where they transition between alternate conformational ensembles. Using Molecular Dynamics simulations of a minimal coarse-grained model for IDRs, we show that the role of protein conformation has a non-trivial effect in the liquid–liquid phase behaviour of IDRs. When an IDR transitions to a conformational ensemble enriched in disordered extended states, LLPS is enhanced. In contrast, IDRs that switch to ensembles that preferentially sample more compact and structured states show inhibited LLPS. This occurs because extended and disordered protein conformations facilitate LLPS-stabilising multivalent protein–protein interactions by reducing steric hindrance; thereby, such conformations maximize the molecular connectivity of the condensed liquid network. Extended protein configurations promote phase separation regardless of whether LLPS is driven by homotypic and/or heterotypic protein–protein interactions. This study sheds light on the link between the dynamic conformational plasticity of IDRs and their liquid–liquid phase behaviour.

The statistical mechanics of assemblies of axially symmetric molecules - II. Second virial coefficients

1954 ◽  
Vol 221 (1147) ◽  
pp. 508-516 ◽  
Keyword(s):  
Carbon Dioxide ◽  
General Theory ◽  
Force Field ◽  
Virial Coefficient ◽  
Second Virial Coefficient ◽  
Virial Coefficients ◽  
Intermolecular Potential ◽  
Crystal Data ◽  
Axially Symmetric ◽  
Second Virial Coefficients

A general theory of the second virial coefficient of axially symmetric molecules is developed, the directional part of the intermolecular field being treated as a perturbationon the central-force part. The method is applicable to any type of intermolecular potential, particular models of directional interaction being obtained by suitable choices of parameters. Simple expressions are given for the second virial coefficient due to several types of directional force. The theory is illustrated by some calculations on the force field of carbon dioxide and its relation to the second virial coefficient and crystal data. These indicate that there is strong quadrupole interaction between carbon dioxide molecules.

scholarly journals Modified Potential Functions Result in Enhanced Predictions of a Protein Complex by All-Atom MD Simulations, Confirming a Step-wise Association Process for Native PPIs

2018 ◽  
Author(s):  
Zhen-lu Li ◽  
Matthias Buck
Keyword(s):  
Electrostatic Interaction ◽  
Protein Interactions ◽  
Protein Complex ◽  
Complex Structure ◽  
Md Simulations ◽  
Potential Functions ◽  
Amino Acid Side Chain ◽  
Native Protein ◽  
Protein Protein Interactions ◽  
Steering Mechanism

ABSTRACTNative protein-protein interactions (PPIs) are the cornerstone for understanding the structure, dynamics and mechanisms of function of protein complexes. In this study, we investigate the association of the SAM domains of the EphA2 receptor and SHIP2 enzyme by performing a combined total of 48 μs all-atom molecular dynamics (MD) simulations. While the native SAM heterodimer is only predicted at a low rate of 6.7% with the original CHARMM36 force field, the yield is increased to 16.7% and to 18.3% by scaling the vdW solute-solvent interactions (better fitting the solvation free energy of amino acid side chain analogues) and by an increase of vdW radius of guanidinium interactions, and thus a dramatic reduction of electrostatic interaction between Arg and Glu/Asn in CHARMM36m, respectively. These modifications effectively improve the overly sticky association of proteins, such as ubiquitin, using the original potential function. By analyzing the 25 native SAM complexes formed in the simulations, we find that their formation involves a pre-orientation guided by electrostatic interaction, consistent with an electrostatic steering mechanism. The complex could then transform to the native protein interaction surfaces directly from a well pre-orientated position (Δinterface-RMSD < 5Å). In other cases, modest (< 90°) orientational and/or translational adjustments are needed (5 Å <Δi-RMSD <10 Å) to the native complex. Although the tendency for non-native complexes to dissociate has nearly doubled with the modified potential functions, a re-association to the correct complex structure is still rare. Instead a most non-native complexes are undergoing configurational changes/surface searching, which do not lead to native structures on a timescale of 250 ns. These observations provide a rich picture on mechanisms of protein-protein complex formation, and suggest that computational predictions of native complex protein-protein interactions could be improved further.

Dependence of the Second Virial Coefficient of Aqueous Solutions of Small Non-Electrolytes on Partial Molar Volume and Molecular Weight of the Solutes

1993 ◽  
Vol 46 (6) ◽  
pp. 929 ◽  
Author(s):  
K Kiyosawa
Keyword(s):  
Aqueous Solution ◽  
Molecular Weight ◽  
Aqueous Solutions ◽  
Molar Volume ◽  
Partial Molar Volume ◽  
Virial Coefficient ◽  
Van Der Waals ◽  
Second Virial Coefficient ◽  
Aqueous Systems ◽  
Quadratic Equations

The osmotic pressures of aqueous solutions of small non-electrolytes, namely ethane-1,2-diol, propane-1,2,3-triol, sucrose and raffinose , were found to be expressible by quadratic equations of the molar concentration, which indicate that these aqueous systems involve no term higher than the second virial coefficient A2. Analysis has shown that A2 mainly does not arise from non-ideality of the aqueous solutions, but its magnitude depends on the partial molar volume of the solute, more precisely on the molecular weight or van der Waals radius or volume of the solute in the aqueous solution.

scholarly journals Kinetic frustration by limited bond availability controls the LAT protein condensation phase transition on membranes

2021 ◽  
Author(s):  
Simou Sun ◽  
Trevor GrandPre ◽  
David T. Limmer ◽  
Jay T. Groves
Keyword(s):  
Phase Transition ◽  
T Cell Activation ◽  
Protein Interactions ◽  
Cell Activation ◽  
Coarse Grained ◽  
Structural Basis ◽  
Protein Protein Interactions ◽  
Kinetic Measurements ◽  
Coarse Grained Model ◽  
Intrinsically Disordered

AbstractLAT is a membrane-linked scaffold protein that undergoes a phase transition to form a two-dimensional protein condensate on the membrane during T cell activation. Governed by tyrosine phosphorylation, LAT recruits various proteins that ultimately enable condensation through a percolation network of discrete and selective protein-protein interactions. Here we describe detailed kinetic measurements of the phase transition, along with coarse-grained model simulations, that reveal LAT condensation is kinetically frustrated by the availability of bonds to form the network. Unlike typical miscibility transitions in which compact domains may coexist at equilibrium, the LAT condensates are dynamically arrested in extended states, kinetically trapped out of equilibrium. Modeling identifies the structural basis for this kinetic arrest as the formation of spindle arrangements, favored by limited multivalent binding interactions along the flexible, intrinsically disordered LAT protein. These results reveal how local factors controlling the kinetics of LAT condensation enable formation of different, stable condensates, which may ultimately coexist within the cell.

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