A molecular-level understanding of the function of a protein requires knowledge of both its structural and dynamic properties. NMR spectroscopy allows the measurement of generalized order parameters that provide an atomistic description of picosecond and nanosecond fluctuations in protein structure. Molecular dynamics (MD) simulation provides a complementary approach to the study of protein dynamics on similar time scales. Comparisons between NMR spectroscopy and MD simulations can be used to interpret experimental results and to improve the quality of simulation-related force fields and integration methods. However, apparent systematic discrepancies between order parameters extracted from simulations and experiments are common, particularly for elements of noncanonical secondary structure. In this paper, results from a 1.2 µs explicit solvent MD simulation of the protein ubiquitin are compared with previously determined backbone order parameters derived from NMR relaxation experiments [Tjandra, N.; Feller, S. E.; Pastor, R. W.; Bax, A. J. Am. Chem. Soc. 1995, 117, 12562-12566]. The simulation reveals fluctuations in three loop regions that occur on time scales comparable to or longer than that of the overall rotational diffusion of ubiquitin and whose effects would not be apparent in experimentally derived order parameters. A coupled analysis of internal and overall motion yields simulated order parameters substantially closer to the experimentally determined values than is the case for a conventional analysis of internal motion alone. Improved agreement between simulation and experiment also is encouraging from the viewpoint of assessing the accuracy of long MD simulations.

The accurate characterization of the structure and dynamics of proteins in disordered states is a difficult problem at the frontier of structural biology whose solution promises to further our understanding of protein folding and intrinsically disordered proteins. Molecular dynamics (MD) simulations have added considerably to our understanding of folded proteins, but the accuracy with which the force fields used in such simulations can describe disordered proteins is unclear. In this work, using a modern force field, we performed a 200 μs unrestrained MD simulation of the acid-unfolded state of an experimentally well-characterized protein, ACBP, to explore the extent to which state-of-the-art simulation can describe the structural and dynamical features of a disordered protein. By comparing the simulation results with the results of NMR experiments, we demonstrate that the simulation successfully captures important aspects of both the local and global structure. Our simulation was ~2 orders of magnitude longer than those in previous studies of unfolded proteins, a length sufficient to observe repeated formation and breaking of helical structure, which we found to occur on a multimicrosecond time scale. We observed one structural feature that formed but did not break during the simulation, highlighting the difficulty in sampling disordered states. Overall, however, our simulation results are in reasonable agreement with the experimental data, demonstrating that MD simulations can already be useful in describing disordered proteins. Finally, our direct calculation of certain NMR observables from the simulation provides new insight into the general relationship between structural features of disordered proteins and experimental NMR relaxation properties.

Changes in residual conformational entropy of proteins can be significant components of the thermodynamics of folding and binding. Nuclear magnetic resonance (NMR) spin relaxation is the only experimental technique capable of probing local protein entropy, by inference from local internal conformational dynamics. To assess the validity of this approach, the picosecond-to-nanosecond dynamics of the arginine side-chain Nε-Hε bond vectors of E. coli ribonuclease H (RNase H) were determined by NMR spin relaxation and compared to the mechanistic detail provided by molecular dynamics (MD) simulations. The results indicate that arginine Nε spin relaxation primarily reflects persistence of guanidinium salt bridges and correlates well with simulated side-chain conformational entropy. In particular cases, the simulations show that the aliphatic part of the arginine side chain can retain substantial disorder while the guanidinium group maintains its salt bridges; thus, the Nε-Hε bond-vector orientation is conserved and side-chain flexibility is concealed from Nε spin relaxation. The MD simulations and an analysis of a rotamer library suggest that dynamic decoupling of the terminal moiety from the remainder of the side chain occurs for all five amino acids with more than two side-chain dihedral angles (R, K, E, Q and M). Dynamic decoupling thus may represent a general biophysical strategy for minimizing the entropic penalties of folding and binding.

Molecular dynamics (MD) simulations and nuclear magnetic resonance spin-relaxation measurements provide detailed insights into ps-ns structural dynamics of proteins. An analysis of discrepancies between the two methods is presented for the B3 immunoglobulin-binding domain of streptococcal protein G. MD simulations using three MD force fields (OPLS-AA, AMBER ff99SB, and AMBER ff03) overestimate the flexibility of backbone N--H vectors at the borders of secondary structure and in loops when compared with experimentally determined backbone amide generalized order parameters (Hall and Fushman, J Am Chem Soc 2006; 12:7855-7870). Comparison with a previous study of residual dipolar coupling constants (Bouvignies et al., Proc Natl Acad Sci USA 2005;102:13885-13890) indicates that slower timescale motions do not account for the discrepancies. Structural analysis reveals that relative imbalance between the description of hydrogen bonding and other terms of modern force fields may be responsible for disagreement.

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Investigations of membrane proteins pose one of the biggest current challenges in structural biology. Recent advances in protein production techniques based on cell-free transcription/translation methods have, however, opened new opportunities in this area. Here, we report an efficient protocol for the backbone assignment of membrane proteins as the first step of NMR-based structure determination.

Molecular dynamics (MD) simulations have been employed to study the conformational dynamics of the partially disordered DNA binding basic leucine zipper domain of the yeast transcription factor GCN4. We demonstrate that back-calculated NMR chemical shifts and spin-relaxation data provide complementary probes of the structure and dynamics of disordered protein states and enable comparisons of the accuracy of multiple MD trajectories. In particular, back-calculated chemical shifts provide a sensitive probe of the populations of residual secondary structure elements and helix capping interactions, while spin-relaxation calculations are sensitive to a combination of dynamic and structural factors. Back calculated chemical shift and spin-relaxation data can be used to evaluate the populations of specific interactions in disordered states and identify regions of the phase space that are inconsistent with experimental measurements. The structural interactions that favor and disfavor helical conformations in the disordered basic region of the GCN4 bZip domain were analyzed in order to assess the implications of the structure and dynamics of the apo form for the DNA binding mechanism. The structural couplings observed in these experimentally validated simulations are consistent with a mechanism where the binding of a preformed helical interface would induce folding in the remainder of the protein, supporting a hybrid conformational selection / induced folding binding mechanism.

It is widely believed that female and male leaders have fundamentally different characteristics and styles, which are thought to explain why organizations with more gender-diverse top management teams perform somewhat better. Unfortunately, few studies have concretely specified such differences or examined whether men and women in leadership roles, particularly executives, indeed differ on core psychological characteristics such as personality traits. Drawing on three alternative perspectives on the roles of personality and gender in leadership ascendancy, this study (a) examined whether men and women are more similar among executives than among non-executive employees, and (b) tested whether similar traits distinguish executives from lower-level employees across genders. Data were from a large (N = 577) sample of European executives (434 male, 143 female) and 52,139 non-executive employees (34,496 male, 17,643 female) who completed high-stakes personality assessments. Results generally supported a gender-similarities perspective. Gender differences on leadership emergence-relevant traits (i.e., Conscientiousness, Emotional Stability, Extraversion) were smaller among executives compared to non-executives. Further, similar traits distinguished executives from non-executives across genders. Both male and female executives tend to demonstrate an archetypical "leader personality" focused on assertiveness, high-level strategic thinking, and decisiveness. However, results also showed that hierarchical level differences in personality were much more strongly pronounced among women than men. Implications for gender equity in organizational leadership are discussed.