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Dihedral conformational transitions are analyzed systematically in a model globular protein, cytochrome P450cam, to examine their structural and chemical dependences through combined conventional molecular dynamics (cMD), accelerated molecular dynamics (aMD) and adaptive biasing force (ABF) simulations. The aMD simulations are performed at two acceleration levels, using dihedral and dual boost, respectively. In comparison with cMD, aMD samples protein dihedral transitions approximately two times faster on average using dihedral boost, and ∼ 3.5 times faster using dual boost. In the protein backbone, significantly higher dihedral transition rates are observed in the bend, coil, and turn flexible regions, followed by the β bridge and β sheet, and then the helices. Moreover, protein side chains of greater length exhibit higher transition rates on average in the aMD-enhanced sampling. Side chains of the same length (particularly Nχ = 2) exhibit decreasing transition rates with residues when going from hydrophobic to polar, then charged and aromatic chemical types. The reduction of dihedral transition rates is found to be correlated with increasing energy barriers as identified through ABF free energy calculations. These general trends of dihedral conformational transitions provide important insights into the hierarchical dynamics and complex free energy landscapes of functional proteins.

The startling diversity in αβ T‐cell receptor (TCR) sequences and structures complicates molecular‐level analyses of the specificity and sensitivity determining T‐cell immunogenicity. A number of three‐dimensional (3D) structures are now available of ternary complexes between TCRs and peptides: major histocompatibility complexes (pMHC). Here, to glean molecular‐level insights we analyze structures of TCRs bound to human class I nonamer peptide–MHC complexes. Residues at peptide positions 4–8 are found to be particularly important for TCR binding. About 90% of the TCRs hydrogen bond with one or both of the peptide residues at positions 4 and 8 presented by MHC allele HLA‐A2, and this number is still ~79% for peptides presented by other MHC alleles. Residue 8, which lies outside the previously‐identified central peptide region, is crucial for TCR recognition of class I MHC‐presented nonamer peptides. The statistics of the interactions also sheds light on the MHC residues important for TCR binding. The present analysis will aid in the structural modeling of TCR:pMHC complexes and has implications for the rational design of peptide‐based vaccines and T‐cell‐based immunotherapies. [ABSTRACT FROM AUTHOR]

Human interleukin‐6 (hIL‐6) is a multifunctional cytokine that regulates immune and inflammatory responses in addition to metabolic and regenerative processes and cancer. hIL‐6 binding to the IL‐6 receptor (IL‐6Rα) induces homodimerization and recruitment of the glycoprotein (gp130) to form a hexameric signaling complex. Anti‐IL‐6 and IL‐6R antibodies are clinically approved inhibitors of IL‐6 signaling pathway for treating rheumatoid arthritis and Castleman's disease, respectively. There is a potential to develop novel small molecule IL‐6 antagonists derived from understanding the structural basis for IL‐6/IL‐6Rα interactions. Here, we combine homology modeling with extensive molecular dynamics (MD) simulations to examine the association of hIL‐6 with IL‐6Rα. A comparison with MD of apo hIL‐6 reveals that the binding of hIL‐6 to IL‐6Rα induces structural and dynamic rearrangements in the AB loop region of hIL‐6, disrupting intraprotein contacts and increasing the flexibility of residues 48 to 58 of the AB loop. In contrast, due to the involvement of residues 59 to 78 in forming contacts with the receptor, these residues of the AB loop are observed to rigidify in the presence of the receptor. The binary complex is primarily stabilized by two pairs of salt bridges, Arg181 (hIL‐6)‐ Glu182 (IL‐6Rα) and Arg184 (hIL‐6)‐ Glu183 (IL‐6Rα) as well as hydrophobic and aromatic stacking interactions mediated essentially by Phe residues in both proteins. An interplay of electrostatic, hydrophobic, hydrogen bonding, and aromatic stacking interactions facilitates the formation of the hIL‐6/IL‐6Rα complex. [ABSTRACT FROM AUTHOR]

Actin is a major structural protein of the eukaryotic cytoskeleton and enables cell motility. Here, we present a model of the actin filament (F-actin) that not only incorporates the global structure of the recently published model by Oda et al. but also conserves internal stereochemistry. A comparison is made using molecular dynamics simulation of the model with other recent F-actin models. A number of structural determents such as the protomer propeller angle, the number of hydrogen bonds, and the structural variation among the protomers are analyzed. The MD comparison is found to reflect the evolution in quality of actin models over the last 6 years. In addition, simulations of the model are carried out in states with both ADP or ATP bound and local hydrogen-bonding differences characterized. Proteins 2011; © 2011 Wiley-Liss, Inc. [ABSTRACT FROM AUTHOR]

The assembly of monomeric G-actin into filamentous F-actin is nucleotide dependent: ATP-G-actin is favored for filament growth at the 'barbed end' of F-actin, whereas ADP-G-actin tends to dissociate from the 'pointed end.' Structural differences between ATP- and ADP-G-actin are examined here using multiple molecular dynamics simulations. The 'open' and 'closed' conformational states of G-actin in aqueous solution are characterized, with either ATP or ADP in the nucleotide binding pocket. With both ATP and ADP bound, the open state closes in the absence of actin-bound profilin. The position of the nucleotide in the protein is found to be correlated with the degree of opening of the active site cleft. Further, the simulations reveal the existence of a structurally well-defined, compact, 'superclosed' state of ATP-G-actin, as yet unseen crystallographically and absent in the ADP-G-actin simulations. The superclosed state resembles structurally the actin monomer in filament models derived from fiber diffraction and is putatively the polymerization competent conformation of ATP-G-actin. Proteins 2009. © 2008 Wiley-Liss, Inc. [ABSTRACT FROM AUTHOR]

Understanding X-ray crystallographic diffuse scattering is likely to improve our comprehension of equilibrium collective protein dynamics. Here, using molecular dynamics (MD) simulation, a detailed analysis is performed of the origins of diffuse scattering in crystalline Staphylococcal nuclease, for which the complete diffuse scattering pattern has been determined experimentally. The hydrogen-atom contribution and the scattering range over which the scattering can be considered to be a sum of solvent and protein scattering are determined. Two models of correlated protein motion are investigated by calculating the model-derived diffuse scattering and comparing with the scattering calculated directly from MD trajectories. In one model, previously used in diffuse scattering interpretation, the atomic displacement correlations decay isotropically with increasing separation. Model correlation lengths are obtained by refining the model scattering against the simulation-derived scattering pattern, and are found to be significantly different from those correlation lengths derived directly from the MD trajectories. Furthermore, the convergence between the model-derived and MD-derived scattering is poor. The second model, in which the displacement correlations are calculated from the principal components of the MD trajectories, is capable of fully reproducing the MD-derived diffuse scattering if the ≈50% lowest-frequency modes are included. However, a small number (≈10) of lowest-frequency and largest-amplitude modes dominates the diffuse scattering and thus the correlated protein motions. A detailed analysis of the principal components is performed. In particular, the effective free energy profile associated with each principle mode is analyzed and the eigenfrequency and damping coefficient computed using a model of Brownian dynamics. Those collective modes with effective frequencies below ≈0.5 THz, including those that determine the diffuse scattering, are overdamped. Proteins 2007. © 2006 Wiley-Liss, Inc. [ABSTRACT FROM AUTHOR]

Effective analysis of large-scale conformational transitions in macromolecules requires transforming them into a lower dimensional representation that captures the dominant motions. Herein, we apply and compare two different dimensionality reduction techniques, namely, principal component analysis (PCA), a linear method, and Sammon mapping, which is nonlinear. The two methods are used to analyze four different protein transition pathways of varying complexity, obtained by using either the conjugate peak refinement method or constrained molecular dynamics. For the return-stroke in myosin, both Sammon mapping and PCA show that the conformational change is dominated by a simple rotation of a rigid body. Also, in the case of the T→R transition in hemoglobin, both methods are able to identify the two main quaternary transition events. In contrast, in the cases of the unfolding transition of staphylococcal nuclease or the signaling switch of Ras p21, which are both more complex conformational transitions, only Sammon mapping is able to identify the distinct phases of motion. Proteins 2006. © 2006 Wiley-Liss, Inc. [ABSTRACT FROM AUTHOR]

The computation of minimum energy paths (MEPs) is an approach for gaining insight into protein conformational transitions that are too slow to be observed with unconstrained molecular dynamics simulations. MEPs have the advantage of providing the energy barrier of the rate-limiting step(s), allowing discrimination among different paths. Finding low-energy MEPs for complex transitions, such as those involving rearrangements of the backbone fold or repacking of buried side chains, has hitherto been unfeasible in a reliable, automated manner, the MEP often displaying unphysical behavior, such as the crossing of bonds. Here, this problem is addressed by combining a counterintuitive procedure for generating an initial guess of the path, in which all side chains are shrunk, with the conjugate peak refinement (CPR) method. The effectiveness of the approach is tested on the conformational switch in Ras p21. This conformational transition involves some partial unfolding and re-folding, a process for which a multitude of pathways are likely to exist and for which a single MEP does not provide a complete description. However, this transition requires some sterically demanding rearrangements, thus testing the ability of a method to find low-energy pathways free of structurally unphysical events. This is achieved by the present approach, which finds a path whose rate-limiting barrier is compatible with experiment. This demonstrates that the method can be used to compute plausible pathways for complex rearrangements in proteins in an automated manner that is unbiased by external driving constraints. Proteins 2005. © 2005 Wiley-Liss, Inc. [ABSTRACT FROM AUTHOR]

Understanding the energetic factors determining the positioning and orientation of single-helical peptides in membranes is of fundamental interest in structural biology. Here, a simple 5-slab continuum dielectric model for the membrane is examined that distinguishes between the solvent, headgroup, and core regions. An analytical solution for the electrostatic solvation of a single dipole and an all-atom model of N-methylacetamide are used to demonstrate the effect of the dielectric boundaries in the system on peptide dipole orientation. The dipole orientation energy is shown to dominate the electrostatic solvation energy of a polyalanine helix in the membrane. With an additional surface-area-dependent term to account for the cavity formation in the aqueous region, the continuum electrostatics description is used to examine several helical peptides, the atoms of which are explicitly represented with a molecular mechanics force field. The experimentally determined tilt angles of a number of peptides of alternating alanine and leucine residues, and of glycophorin and melittin, are accurately reproduced by the model. The factors determining the tilt angles and their fluctuations are analyzed. The tilt angles of the simpler peptides are found to increase approximately linearly with peptide length; this effect is also rationalized. The analysis and model presented here provide a step toward the prediction of helical membrane protein structure. Proteins 2005. © 2005 Wiley-Liss, Inc. [ABSTRACT FROM AUTHOR]