title: Functionally Relevant Specific Packing Can Determine Protein Folding Routes.
abstract: Functional residues can modulate the folding mechanisms of proteins. In some proteins, mutations to such residues can radically change the primary folding route. Is it possible then to learn more about the functional regions of a protein by investigating just its choice of folding route? The folding and the function of the protein Escherichia coli ribonuclease H (ecoRNase-H) have been extensively studied and its folding route is known to near-residue resolution. Here, we computationally study the folding of ecoRNase-H using molecular dynamics simulations of structure-based models of increasing complexity. The differences between a model that correctly predicts the experimentally determined folding route and a simpler model that does not can be attributed to a set of six aromatic residues clustered together in a region of the protein called CORE. This clustering, which we term "specific" packing, drives CORE to fold early and determines the folding route. Both the residues involved in specific packing and their packing are largely conserved across E. coli-like RNase-Hs from diverse species. Residue conservation is usually implicated in function. Here, the identified residues either are known to bind substrate in ecoRNase-H or pack against the substrate in the homologous human RNase-H where a substrate-bound crystal structure exists. Thus, the folding mechanism of ecoRNase-H is a byproduct of functional demands upon its sequence. Using our observations on specific packing, we suggest mutations to an engineered HIV RNase-H to make its function better. Our results show that understanding folding route choice in proteins can provide unexpected insights into their function.
authors.affiliation: National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bellary Road, Bangalore 560065, India; Manipal University, Madhav Nagar, Manipal 576104, India; Bioinformatics Institute (A*STAR), Singapore 138671, Singapore.
authors.forename: Shilpa
authors.initials: S
authors.lastname: Yadahalli
authors.affiliation: National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bellary Road, Bangalore 560065, India. Electronic address: shachi@ncbs.res.in.
authors.forename: Shachi
authors.initials: S
authors.lastname: Gosavi
mesh_terms: D000595:Amino Acid Sequence; D017124:Conserved Sequence; D004252:DNA Mutational Analysis; D004926:Escherichia coli / Q000235:genetics / Q000502:physiology*; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D050505:Mutant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D011487:Protein Conformation; D017510:Protein Folding; D016914:Ribonuclease H / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*
chemical_list: D050505:Mutant Proteins; D016914:Ribonuclease H; C078856:ribonuclease HI
keywords: E. coli RNase-H; computational protein folding; energetic heterogeneity; folding mechanism; substrate binding