title: SIRAH: a structurally unbiased coarse-grained force field for proteins with aqueous solvation and long-range electrostatics.
abstract: Modeling of macromolecular structures and interactions represents an important challenge for computational biology, involving different time and length scales. However, this task can be facilitated through the use of coarse-grained (CG) models, which reduce the number of degrees of freedom and allow efficient exploration of complex conformational spaces. This article presents a new CG protein model named SIRAH, developed to work with explicit solvent and to capture sequence, temperature, and ionic strength effects in a topologically unbiased manner. SIRAH is implemented in GROMACS, and interactions are calculated using a standard pairwise Hamiltonian for classical molecular dynamics simulations. We present a set of simulations that test the capability of SIRAH to produce a qualitatively correct solvation on different amino acids, hydrophilic/hydrophobic interactions, and long-range electrostatic recognition leading to spontaneous association of unstructured peptides and stable structures of single polypeptides and protein-protein complexes.
authors.affiliation: Institut Pasteur de Montevideo , Montevideo, Uruguay.|Department of Chemistry, King's College , London, United Kingdom.
authors.forename: Leonardo
authors.initials: L
authors.lastname: Darré
authors.affiliation: Institut Pasteur de Montevideo , Montevideo, Uruguay.
authors.forename: Matías Rodrigo
authors.initials: MR
authors.lastname: Machado
authors.affiliation: Institut Pasteur de Montevideo , Montevideo, Uruguay.
authors.forename: Astrid Febe
authors.initials: AF
authors.lastname: Brandner
authors.affiliation: Institut Pasteur de Montevideo , Montevideo, Uruguay.
authors.forename: Humberto Carlos
authors.initials: HC
authors.lastname: González
authors.affiliation: Institut Pasteur de Montevideo , Montevideo, Uruguay.
authors.forename: Sebastián
authors.initials: S
authors.lastname: Ferreira
authors.affiliation: Institut Pasteur de Montevideo , Montevideo, Uruguay.
authors.forename: Sergio
authors.initials: S
authors.lastname: Pantano
mesh_terms: D008958:Models, Molecular; D009994:Osmolar Concentration; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012995:Solubility; D055672:Static Electricity; D013696:Temperature; D014867:Water / Q000737:chemistry*
chemical_list: D011506:Proteins; D014867:Water