Reconciling Mediating and Slaving Roles of Water in Protein Conformational Dynamics

Citation: Zhao L, Li W, Tian P ( Reconciling Mediating and Slaving Roles of Water in Protein Conformational Dynamics Li Zhao 0 Wenzhao Li 0 Pu Tian 0 Pratul K. Agarwal, Oak Ridge National Laboratory, United States of America 0 1 College of Life Science, Jilin University , Changchun , China , 2 College of Life Science and MOE Key Laboratory of Molecular Enzymology and Engineering, Jilin University , Changchun , China Proteins accomplish their physiological functions with remarkably organized dynamic transitions among a hierarchical network of conformational substates. Despite the essential contribution of water molecules in shaping functionally important protein dynamics, their exact role is still controversial. Water molecules were reported either as mediators that facilitate or as masters that slave protein dynamics. Since dynamic behaviour of a given protein is ultimately determined by the underlying energy landscape, we systematically analysed protein self energies and protein-water interaction energies obtained from extensive molecular dynamics simulation trajectories of barstar. We found that protein-water interaction energy plays the dominant role when compared with protein self energy, and these two energy terms on average have negative correlation that increases with increasingly longer time scales ranging from 10 femtoseconds to 100 nanoseconds. Water molecules effectively roughen potential energy surface of proteins in the majority part of observed conformational space and smooth in the remaining part. These findings support a scenario wherein water on average slave protein conformational dynamics but facilitate a fraction of transitions among different conformational substates, and reconcile the controversy on the facilitating and slaving roles of water molecules in protein conformational dynamics. - Funding: This research was partially funded by a start-up fund from Jilin University, by the National Natural Science Foundation of China (Grant#:31270758), and by the Intramural program of the National Institutes of Diabetes, Digestive and Kidneys Diseases. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. . These authors contributed equally to this work. Protein dynamics is critical for their functions [14] and evolvability [5], and is to a great extent determined by the roughness of their potential energy surface (PES). Solvents play an indispensable role in shaping dynamic behaviour of proteins through molecular interactions that contribute to protein PES. Energy transferred from the first hydration shell to surface residues of cyclophilin A was computationally demonstrated to influence catalysis through network fluctuations [2]. It is well known that, due to the hierarchical nature of PES [6], conformational dynamics of native proteins is hierarchical and occurs on many different time scales corresponding to different types of molecular motions, including bond stretch and bending motions on femtoseconds, rotations of small groups (e.g. methyl) on picoseconds, side chain and backbone dihedral rotations on subnanoseconds to microseconds, and major domain motions up to multiple milliseconds. It is likely that water molecules play different roles in the above mentioned various type of dynamic processes. Coupling between the function and internal motions of proteins and their water environment has been intensively studied [713]. Two lines of evidences that have been presented by many experimental [1420] and computational [2127] reports supporting either mediating or slaving roles of water molecules are briefly summarized below. It was demonstrated by both experimental [14] and computational studies [22] that below glass transition temperature, protein dynamics is slaved(or caged) by surrounding frozen water molecules. Protein dynamics on 10 ps to 100 ps time scales was found to be closely correlated with dynamics of surrounding water hydrogen bond network and thus slaved by water molecules [23]. Water molecules relaxation was observed to correlate well with conformational transitions of myoglobin among statistical substates [16], which occur on time scales ranging from sub-nanoseconds to microseconds at the physiological temperature, suggesting the slaving role of water molecules on corresponding time scales. At physiological or room temperature, certain hydration level is essential for functions of many proteins [13,28]. Based on the analysis of crystallographic water molecules, it was proposed that water molecule lubricate folding of proteins through three bond centre hydrogen bonds [21]. Theoretical protein structure prediction studies [24] revealed that addition of water mediated potential in protein design facilitated search of the free energy minimum (i.e. native state), water molecules were also found to mediate native state dynamics of eglin C [26,27]. Raman optical activity studies [15] support the role of water molecules as lubricant of life. From an energy landscape perspective, observations along this line were explained with the belief that water molecules facilitates protein dynamics through effectively smoothing their PES. However, direct evidence supporting this concept is lacking. In this study, we generated collectively 5 microsecond molecular dynamics (MD) trajectories for a small globular protein barstar [29], which is synthesized by the bacterium Bacillus amyloilyquefaciens as an inhibitor of the ribonuclease protein barnase. By systematically analysing the time series (or evolution in conformational space) of relevant energy terms (protein self energy (Ep), protein-water interaction energy (Ep{w) and their sum (Etot)) obtained from MD trajectories, we found that while the negative correlation between Ep and Ep{w in most parts of conformational space provides possibility for PES smoothing, the dominance of sEp{w over sEp (s stands for standard deviation) resulting in a rougher PES on average, especially for picoseconds and longer time scales. These two aspects contribute to the end effects of water molecules on the PES of proteins, that is roughening the majority and smoothing the remaining part of the potential energy landscape. Thus, the conflicting roles of water in the protein conformational dynamics are reconciled with an energy landscape perspective. It is noted here that due to the constraint of computational resource, our analysis were limited to submicrosecond time scale, correspond to transitions covering a few hierarchies of statistical substates. The impact of water molecules on major domain motions that occur on milli-seconds and longer time scales and folding dynamics is beyond the scope of this study. The PES that underlies the dynamics of a protein molecule can be decomposed into two components, protein self energy (Ep) and protein-solvents interaction en (...truncated)