Molecular Dynamics (MD) plays a fundamental role in characterizing protein disordered states that are emerging as crucial actors in many biological processes. Here we assess the accuracy of three current force-fields in modeling disordered peptides by combining enhanced-sampling MD simulations with NMR data. These force-fields generate significantly different conformational ensembles, and AMBER03w [ Best and Mittal J. Phys. Chem. B 2010 , 114 , 14916 - 14923 ] provides the best agreement with experiments, which is further improved by adding the ILDN corrections [ Lindorff-Larsen et al. Proteins 2010 , 78 , 1950 - 1958 ].

No abstract

Allosteric regulation plays an important role in a myriad of biomacromolecular processes. Specifically, in a protein, the process of allostery refers to the transmission of a local perturbation, such as ligand binding, to a distant site. Decades after the discovery of this phenomenon, models built on static images of proteins are being reconsidered with the knowledge that protein dynamics plays an important role in its function. Molecular dynamics simulations are a valuable tool for studying complex biomolecular systems, providing an atomistic description of their structure and dynamics. Unfortunately, their predictive power has been limited by the complexity of the biomolecule free-energy surface and by the length of the allosteric timescale (in the order of milliseconds). In this work, we are able to probe the origins of the allosteric changes that transcription factor mixed lineage leukemia (MLL) causes to the interactions of KIX domain of CREB-binding protein (CBP) with phosphorylated kinase inducible domain (pKID), by combing allatom molecular dynamics with enhanced sampling methods recently developed in our group. We discuss our results in relation to previous NMR studies. We also develop a general simulations protocol to study allosteric phenomena and many other biological processes that occur in the micro/milliseconds timescale. metadynamics | replica exchange | protein conformational dynamics A llostery is a key process in cellular regulation (1-3), in which a perturbation by an effector leads to a functional change at a distant substrate binding site (4, 5) through alteration of the structure (6, 7) and/or dynamics of the protein (8). Although this process is well known and commonly observed in several biological contexts (9-12), its exact mechanism is still debated (13,14). Often, allostery has been related to changes in the dynamics of the protein (8,15). In this scenario, the role of the effector is to alter the distribution of conformations visited by the protein, enhancing the probability of those configurations for which binding of the ligand is more favorable (5,(16)(17)(18). It has been suggested that this process might take place via the interaction of the effector with an unstructured part of the protein. This change is then propagated to large distances via the more rigid parts of the protein (14). To validate this picture, it is important to study the dynamics of these biomolecur systems. Although much useful information on the conformational flexibility of a protein can be obtained from solution NMR, its limited time resolution prevents resolving the structure of those metastable states whose lifetime is shorter than a few milliseconds. The existence of these states can, however, be inferred from relaxation dispersion NMR, and their lifetime can be estimated (19)(20)(21)(22). Because these short-lived metastable states are not directly observable using standard NMR spectroscopic techniques, they are referred to as invisible states.An allosteric system in which the existence of such an invi...