Simulating protein folding in different environmental conditions.
Molecular dynamics simulations have become an invaluable tool in investigating the dynamics of protein folding. However, most computational studies of protein folding assume dilute aqueous simulation conditions in order to reduce the complexity of the system under study and enhance the efficiency. Nowadays, it is evident that environmental conditions encountered in vivo (or even in vitro) play a major role in regulating the dynamics of protein folding especially when one considers the highly condensed environment in the cellular cytoplasm. In order to factor in these conditions, we can utilize the high efficiency of well-designed low resolution (coarse-grained) simulation models to reduce the complexity of these added protein-milieu interactions involving different time and length scales. The goal of this chapter is to describe some recently developed coarse-grained simulation techniques that are specifically designed to go beyond traditional aqueous solvent conditions. The chapter also gives the reader a flavor of the things that we can study using such "smart" low resolution models.
AMS Department, Khalifa University, 127788, Abu Dhabi, UAE, dirar.homouz@kustar.ac.ae.
Dirar
D
Homouz
D000942:Antigens, Bacterial / Q000737:chemistry*; D001059:Apoproteins / Q000737:chemistry*; D001426:Bacterial Proteins / Q000737:chemistry*; D025065:Borrelia burgdorferi / Q000737:chemistry; D002147:Calmodulin / Q000737:chemistry*; D005418:Flavodoxin / Q000737:chemistry*; D006801:Humans; D006860:Hydrogen Bonding; D008074:Lipoproteins / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D009994:Osmolar Concentration; D010735:Phosphoglycerate Kinase / Q000737:chemistry*; D011487:Protein Conformation; D017510:Protein Folding; D012997:Solvents / Q000737:chemistry; D055672:Static Electricity; D014508:Urea / Q000737:chemistry; D014867:Water / Q000737:chemistry
D000942:Antigens, Bacterial; D001059:Apoproteins; D001426:Bacterial Proteins; D002147:Calmodulin; D005418:Flavodoxin; D008074:Lipoproteins; D012997:Solvents; C105546:VlsE protein, Borrelia burgdorferi; C026932:apoflavodoxin; D014867:Water; D014508:Urea; D010735:Phosphoglycerate Kinase