Theoretical Studies of S100 Proteins using the Accelerated Molecular Dynamics and Nudged Elastic Band Methods

Abstract

The use of calcium as a secondary messenger is an important aspect of many biological pathways. Through binding calcium ions, some proteins can undergo conformation changes required for biological activity. Understanding the mechanisms by which calcium binding and conformation changes occur, we can better treat pathologies associated with these proteins. The S100 protein family is highly conserved and is implicated in a number of biological systems due to their interactions with effector proteins. These interactions are dependent on both calcium and target protein concentrations, inducing the formation of a hydrophobic patch region. In this work, accelerated molecular dynamics and nudged elastic band methods were applied to investigate the calcium induced conformation pathways of the S100A6 protein. Accelerated molecular dynamics was used in the isolation of structures suitable to act as starting and end points in nudged elastic band pathways and in mutation studies. Multiple nudged elastic band simulations were completed to obtain adequate sampling of the S100A6 conformation pathway. Pairwise distance calculations revealed distinct calcium binding site formation, occurring in a stepwise fashion. The calculation of distance and angle of the hydrophobic patch constituents revealed the presence of a long-lived intermediate conformation. MMGBSA calculations allowed for the identification of K31, D50, and E67 as important residue contributors to patch formation. Residues K31 and D50 were identified as key mechanisms responsible for secondary structure rearrangement and stabilization. Residue E67 was identified as a potential communication mechanism between calcium binding loops, potentially assisting in cooperative binding. Mutation to these residues strongly supported the identified roles of these residues. The application of SASA calculations in these mutated systems revealed significant changes due to the absence of these residues in both apo and holo conformations. Further, accelerated molecular dynamics and nudged elastic band methods were also applied to the S100B system. Structural start and end points used in nudged elastic band simulations were identified through accelerated molecular dynamics simulations. The goal of this study was to identify mechanisms comparable to those discovered in S100A6. Pairwise distance calculations revealed similar yet unique pathways of calcium binding site formation due to structural differences. The presence of a long-lived intermediate conformation was also identified in S100B through distance and angle calculations of secondary structure elements. MMGBSA calculations revealed mechanisms similar to those in S100A6 that include comparable residues. Residue K30 in S100B was identified to have remarkably similar behavior to K31 in S100A6, having key roles in both sensing initial calcium binding and formation of the hydrophobic patch region. Residue E52 and D55 in S100B were identified to have similar function to D50 in S100A6, functioning to stabilize the hydrophobic patch in conjunction with K30. Initial review of other S100 protein systems identified residues that appear comparable to both K31 and K30 in S100A6 and S100B, respectively. Further study of the S100 protein family is vital to understanding the role of these proteins in various pathologies and we believe many of the mechanisms identified in this work are present in other S100 proteins.