A solvent induced mechanism for conformational change

Insights into the Binding of Intrinsically Disordered Proteins from Molecular Dynamics Simulation

Intrinsically disordered proteins (IDPs) are a class of protein that, in the native state, possess no well-defined secondary or tertiary structure, existing instead as dynamic ensembles of conformations. They are biologically important, with approximately 20% of all eukaryotic proteins disordered, and found at the heart of many biochemical networks. To fulfil their biological roles, many IDPs need to bind to proteins and/or nucleic acids. And while unstructured in solution, IDPs typically fold into a well-defined three-dimensional structure upon interaction with a binding partner. The flexibility and structural diversity inherent to IDPs makes this coupled folding and binding difficult to study at atomic resolution by experiment alone, and computer simulation currently offers perhaps the best opportunity to understand this process. But simulation of coupled folding and binding is itself extremely challenging; these molecules are large and highly flexible, and their binding partners, such as DNA or cyclins, are also often large. Therefore, their study requires either or both simplified representations and advanced enhanced sampling schemes. It is not always clear that existing simulation techniques, optimized for studying folded proteins, are well-suited to IDPs. In this article, we examine the progress that has been made in the study of coupled folding and binding using molecular dynamics simulation. We summarise what has been learnt, and examine the state of the art in terms of both methodologies and models. We also consider the lessons to be learnt from advances in other areas of simulation and highlight the issues that remain of be addressed.

Matching of additive and polarizable force fields for multiscale condensed phase simulations

Inclusion of electronic polarization effects is one of the key aspects in which the accuracy of current biomolecular force fields may be improved. The principal drawback of such approaches is the computational cost, which typically ranges from 3 - 10 times that of the equivalent additive model, and may be greater for more sophisticated treatments of polarization or other many-body effects. Here, we present a multiscale approach which may be used to enhance the sampling in simulations with polarizable models, by using the additive model as a tool to explore configuration space. We use a method based on information theory to determine the charges for an additive model that has optimal overlap with the polarizable one, and we demonstrate the feasibility of enhancing sampling via a hybrid replica exchange scheme for several model systems. An additional advantage is that, in the process, we obtain a systematic method for deriving charges for an additive model that will be the natural complement to its polarizable parent. The additive charges are found by an effective coarse-graining of the polarizable force field, rather than by ad hoc procedures.

Investigations into conformational transitions and solvation structure of a 7-piperidino-5,9-methanobenzo[8] annulene in water

Solvation shell structure of a 7-piperidino-5,9-methanobenzo[8] annulene (PMA) in water has been investigated in ambient conditions using both molecular dynamics (MD) and Car-Parrinello molecular dynamics (CPMD) calculations. From the MD calculations, we find that this molecule exists in three major conformational states out of which two are in twist-boat forms and one in chair form. Due to the limited time scale accessible in CPMD simulations, we have studied all the three conformational states separately using CPMD. The molecular geometry, electronic charge distribution and solvation structure for all three forms are investigated. The stability order of the chair and twist-boat conformations in water solvent has been reversed when compared to the gaseous phase results and in the case of polar aprotic solvents (J. Org. Chem., 1999, 61, 5979). From the radial distribution function, we find that the solvent density around the chair form is significantly lower, which has to be directly related to the smaller solvent accessible area for this conformation and this is in complete agreement with earlier reports. Among the findings are that the solvation shell structure around the nitrogen atom in the chair form of PMA is considerably different from the open conformational forms or the twist-boat forms. The dipole moment for the closed form is found to be significantly larger when compared to the twist-boat forms.

Conformational polymorphism in organic crystals

Polymorphs are different crystalline modifications of the same chemical substance. When different conformers of the same molecule occur in different crystal forms, the phenomenon is termed conformational polymorphism. Occasionally, more than one conformer is present in the same crystal structure. The influence of molecular conformation changes on the formation and stability of polymorphs is the focus of this Account. X-ray crystal structures of conformational polymorphs were analyzed to understand the interplay of intramolecular (conformer) and intermolecular (lattice) energy in the crystallization and stability of polymorphs. Polymorphic structures stabilized by strong O-H...O/N-H...O hydrogen bonds, weak C-H...O interactions, and close packing were considered. 4,4-Diphenyl-2,5-cyclohexadienone (1) and bis(p-tolyl) ketone p-tosylhydrazone (3) are prototypes of C-H...O and N-H...O hydrogen-bonded structures. Distance-angle scatter plots of O-H...O and C-H...O hydrogen bonds extracted from the Cambridge Structural Database indicate that polymorphs with a larger number of symmetry-independent molecules (high Z') generally have better interactions when compared with the polymorphs with lower Z' values, with the implication that these symmetry-independent molecules have different conformations. Since molecular conformer (E(conf)) and crystal lattice (U(latt)) energy differences are of the same magnitude in organic crystals (typically <5 kcal mol(-1)), situations wherein these two factors compensate or cancel one another are illustrative. Calculation of conformer and lattice energies using Gaussian 03 and Cerius(2) in 23 recently published polymorph sets shows that a strained conformer (higher E(conf)) is stabilized by stronger interactions or better crystal packing (lower U(latt)) in two-thirds of the cases, whereas there is no energy balance in the remaining structures. Organic molecules with flexible torsions and low-energy conformers have a greater likelihood of exhibiting polymorphism because (1) different conformations lead to new hydrogen-bonding and close-packing modes and (2) the tradeoff reduces the total energy difference between alternative crystal structures. As a test case, polymorph promiscuity in fuchsones (6) is related to the conformational diversity at the exo-methylene phenyl rings and the small energy difference computed for dimethyl fuchsone polymorphs. These ideas find application in the design of putative pharmaceutical polymorphs and crystal structure prediction.

The effect of solvation on biomolecular conformation: 2-amino-1-phenylethanol

Small molecule neurotransmitters form one the most important classes of pharmaceutical molecules. While the behavior of these molecules in their neutral forms in the gas phase is well understood, their behavior in more biologically relevant scenarios (protonated and in aqueous solution) has received comparatively little attention. Here we address this problem by using molecular mechanics simulations to build up a detailed picture of the conformational behavior of 2-amino-1-phenylethanol, a noradrenaline analogue, in aqueous solution in both its neutral and protonated forms. For the sake of comparison, equivalent simulations are also performed on the gas-phase molecules and gas-phase hydrated clusters. These calculations reveal the important role that water has to play in determining the conformational preferences and dynamic behavior of the molecules. Water molecules are found to bridge between the various functional groups within the molecule, significantly affecting their relative stabilities in comparison to the gas-phase values. The reorganization of these solvation structures also provides a mechanism for conformational interconversion. The role of the solvent in mediating interactions between the various functional groups within the molecule suggests that in noradrenaline the catechol groups will be able to interact, albeit indirectly, with the other functional groups, thereby influencing the behavior of the molecule.