ABSINTH: A new continuum solvation model for simulations of polypeptides in aqueous solutions

By A. Vitalis, Rohit V. Pappu. Journal of Computational Chemistry, 2009

364 citations recorded by the source corpus.

A new implicit solvation model for use in Monte Carlo simulations of polypeptides is introduced. The model is termed ABSINTH for self‐Assembly of Biomolecules Studied by an Implicit, Novel, and Tunable Hamiltonian. It is designed primarily for simulating conformational equilibria and oligomerization reactions of intrinsically disordered proteins in aqueous solutions. The paradigm for ABSINTH is conceptually similar to the EEF1 model of Lazaridis and Karplus (Proteins 1999, 35, 133). In ABSINTH, the transfer of a polypeptide solute from the gas phase into a continuum solvent is the sum of a direct mean field interaction (DMFI), and a term to model the screening of polar interactions. Polypeptide solutes are decomposed into a set of distinct solvation groups. The DMFI is a sum of contributions from each of the solvation groups, which are analogs of model compounds. Continuum‐mediated screening of electrostatic interactions is achieved using a framework similar to the one used for the DMFI. Promising results are shown for a set of test cases. These include the calculation of NMR coupling constants for short peptides, the assessment of the thermal stability of two small proteins, reversible folding of both an α‐helix and a β‐hairpin forming peptide, and the polymeric properties of intrinsically disordered polyglutamine peptides of varying lengths. The tests reveal that the computational expense for simulations with the ABSINTH implicit solvation model increase by a factor that is in the range of 2.5–5.0 with respect to gas‐phase calculations. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009

Subfields: Atomic and Molecular Physics, and Optics, Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/5c0e38392e5479f497b0d769092005c85b6a8998

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Atomic and Molecular Physics, and Optics

In Materials Chemistry

In Molecular Biology

Citations in the corpus

Conformations of intrinsically disordered proteins are influenced by linear sequence distributions of oppositely charged residues (2013, methodology): “We use the ABSINTH (self-assembly of biomolecules studied by an implicit, novel, and tunable Hamiltonian) implicit solvation model and force field paradigm (17), a combination that has yielded verifiably accurate results for other IDPs (7, 18).”
Physics-driven coarse-grained model for biomolecular phase separation with near-quantitative accuracy (2021, methodology): “We estimated the coil–globule transition temperature T θ with ABSINTH 69 , a continuum solvation all-atom model of proteins.”
A decade and a half of protein intrinsic disorder: Biology still waits for physics (2013, background): “[83] [84] [85] [86] [87] [88] Furthermore, even polyglycine was shown to have a tendency to form heterogeneous ensembles of collapsed structures in water.”
Sequence Determinants of Intracellular Phase Separation by Complex Coacervation of a Disordered Protein (2016, methodology): “Atomistic Simulations of NICD Simulations used the CAMPARI Monte Carlo (MC) modeling suite (http:// campari.sourceforge.net), with the ABSINTH implicit solvent model and force-field paradigm (Vitalis and Pappu, 2009).”