Coordination and control inside simple biomolecular machines.
Biomolecular machines can achieve physiological functions precisely and efficiently, though they always operate under fluctuations and noises. We review two types of simple machinery that we have recently studied. The machinery can be regarded as molecular motors. They transform chemical free energy from NTP hydrolysis to mechanical work. One type belongs to small monomeric helicases that move directionally along single-stranded nucleic acid, and may further unwind the duplex part for gene replication or repair. The other type belongs to ring-shaped NTPase motors that also move or transport nucleic acid or protein substrate in a directional manner, such as for genome packaging or protein degradation. The central issue in this review is on how the machinery coordinates essential degrees of freedom during the mechanochemical coupling process. Further concerns include how the coordination and control are manifested in experiments, and how they can be captured well in modeling and computational research. We employed atomistic molecular dynamics simulations, coarse-grained analyses, and stochastic modeling techniques to examine the molecular machines at multiple resolutions and timescales. Detailed descriptions on how the protein interacts with its substrate at interface, as well as how multiple protein subunits are coordinated are summarized.
Beijing Computational Science Research Center, No 3 Heqing Road, Haidian District, Beijing, 100084, China, jinyu@csrc.ac.cn.
Jin
J
Yu
D000255:Adenosine Triphosphate / Q000737:chemistry; D001426:Bacterial Proteins / Q000737:chemistry*; D001692:Biological Transport; D004265:DNA Helicases / Q000737:chemistry*; D004277:DNA, Single-Stranded / Q000737:chemistry; D006868:Hydrolysis; D007700:Kinetics; D056004:Molecular Dynamics Simulation; D020409:Molecular Motor Proteins / Q000737:chemistry*; D043583:Nucleoside-Triphosphatase / Q000737:chemistry*; D011487:Protein Conformation; D021122:Protein Subunits / Q000737:chemistry*; D013269:Stochastic Processes; D013816:Thermodynamics; D017361:Viral Nonstructural Proteins / Q000737:chemistry*; D014764:Viral Proteins / Q000737:chemistry*; D012697:Serine Endopeptidases; D053487:DEAD-box RNA Helicases; D000085242:Viral Proteases
D000255:Adenosine Triphosphate; D001426:Bacterial Proteins; D004265:DNA Helicases; D004277:DNA, Single-Stranded; D020409:Molecular Motor Proteins; D043583:Nucleoside-Triphosphatase; D021122:Protein Subunits; D017361:Viral Nonstructural Proteins; D014764:Viral Proteins; C084422:NS3 protein, hepatitis C virus; D012697:Serine Endopeptidases; D053487:DEAD-box RNA Helicases; D000085242:Viral Proteases; C084217:pcrA protein, Bacteria