The recently developed CMAP correction to the CHARMM22 force field (C22) is evaluated from 25 ns molecular dynamics simulations on hen lysozyme. Substantial deviations from experimental backbone root mean-square fluctuations and N-H NMR order parameters obtained in the C22 trajectories (especially in the loops) are eliminated by the CMAP correction. Thus, the C22/CMAP force field yields improved dynamical and structural properties of proteins in molecular dynamics simulations.

The formation of a complex between Rac1 and the cytoplasmic domain of plexin-B1 is one of the first documented cases of a direct interaction between a small guanosine 5′-triphosphatase (GTPase) and a transmembrane receptor. Structural studies have begun to elucidate the role of this interaction for the signal transduction mechanism of plexins. Mapping of the Rac1 GTPase surface that contacts the Rho GTPase binding domain of plexin-B1 by solution NMR spectroscopy confirms the plexin domain as a GTPase effector protein. Regions neighboring the GTPase switch I and II regions are also involved in the interaction and there is considerable interest to examine the changes in protein dynamics that take place upon complex formation. Here we present main-chain nitrogen-15 relaxation measurements for the unbound proteins as well as for the Rho GTPase binding domain and Rac1 proteins in their complexed state. Derived order parameters, S 2 , show that considerable motions are maintained in the bound state of plexin. In fact, some of the changes in S 2 on binding appear compensatory, exhibiting decreased as well as increased dynamics. Fluctuations in Rac1, already a largely rigid protein on the picosecond-nanosecond timescale, are overall diminished, but isomerization dynamics in the switch I and II regions of the GTPase are retained in the complex and appear to be propagated to the bound plexin domain. Remarkably, fluctuations in the GTPase are attenuated at sites, including helices α6 (the Rho-specific insert helix), α7 and α8, that are spatially distant from the interaction region with plexin. This effect of binding on long-range dynamics appears to be communicated by hinge sites and by subtle conformational changes in the protein. Similar to recent studies on other systems, we suggest that dynamical protein features are affected by allosteric mechanisms. Altered protein fluctuations are likely to prime the Rho GTPase-plexin complex for interactions with additional binding partners.

We investigate ps-ns dynamics of the Rho-GTPase Binding Domain (RBD) of plexin-B1, which plays a key role in plexin-mediated cell signaling. Backbone 15N relaxation data of the dimeric RBD are analyzed with the model-free (MF) method, and with the slowly relaxing local structure/molecular dynamics (SRLS-MD) approach. Independent analysis of the MD trajectories, based on the MF paradigm, is also carried out. MF is a widely popular and simple method, SRLS is a general approach, and SRLS-MD is an integrated approach we developed recently. Corresponding parameters from the RBD dimer, a previously studied RBD monomer mutant, and the previously studied complex of the latter with the GTPase Rac1, are compared. The L2, L3 and L4 loops of the plexin-B1 RBD are involved in interactions with other plexin domains, GTPase binding, and RBD dimerization, respectively. Peptide groups in the loops of both the monomeric and dimeric RBD are found to experience weak and moderately asymmetric local ordering centered approximately at the Ci-1α-Ciα axes, and ns backbone motion. Peptide groups in the α-helices and the β-strands of the dimer (the β-strands of the monomer) experience strong and highly asymmetric local ordering centered approximately at the Ci-1α-Ciα axes (N–H bonds). N–H fluctuations occur on the ps time-scale. An allosteric pathway for GTPase binding, providing new insights into plexin function, is delineated.

This study deals with a spin system constituted of three nonequivalent protons, two of them originating from para-hydrogen (p-H(2)) after a hydrogenation reaction carried out in the earth magnetic field. It is shown that three singlet states are created provided indirect (J) couplings exist between the three spins, implying hyperpolarization transfer toward the third spin. Upon insertion of the sample in the NMR (Nuclear Magnetic Resonance) high field magnet, the following events occur: (i) the longitudinal two-spin orders which are parts of the singlet states survive; (ii) the other two terms (of these singlet states) tend to be destroyed by magnetic field gradients but at the same time are partly converted into differences of longitudinal polarizations. Nuclear spin relaxation is studied by appropriate NMR measurements when evolution takes place in the high field magnet or in the earth field. In the former case, relaxation is classical although complicated by numerous relaxation rates associated with both longitudinal two-spin orders and longitudinal polarizations. In the latter case, an equilibration between the singlet states first occur, their disappearance being thereafter driven by relaxation rates which remain very small because of the absence of any dipolar contribution. Thus, even in the case of a three-spin system, long-lived states exist; this unexpected property could be very useful for many applications.

Proton nuclear spin relaxation has been for the first time extensively used for a structural and dynamical study of low-molecular-weight organogels. The gelator in the present study is a modified phenylalanine amino acid bearing a naphthalimide moiety. From T(1) (spin-lattice relaxation time in the laboratory frame) and T(1ρ) (spin-lattice relaxation time in the rotating frame) measurements, it is shown that the visible gelator NMR spectrum below the liquid-gel transition temperature corresponds to a so-called isotropic compartment, where gelator molecules behave as in a liquid phase but exchange rapidly with the molecules constituting the gel structure. This feature allows one to derive, from accessible parameters, information about the gel itself. Nuclear Overhauser effect spectroscopy (NOESY) experiments have been exploited in view of determining not only cross-relaxation rates but also specific longitudinal rates. The whole set of relaxation parameters (at 25 °C) leads to a correlation time of 5 ns for gelator molecules within the gel structure and 150 ps for gelator molecules in the isotropic phase. This confirms, on one hand, the flexibility of the organogel fibers and, on the other hand, the likely presence of clusters in the isotropic phase. Concerning cross-relaxation rates, a thorough theoretical investigation in multispin systems of direct and relayed correlations in a NOESY spectrum allows one to make conclusions about contacts (around 2-3 Å) not only between naphtalimide moieties of different gelator molecules but also between the phenyl ring and the naphtalimide moiety again of different gelator molecules. As a result, not only is the head-to-tail structure of amino acid columns confirmed but also the entangling of nearby columns by the naphthalimide moieties is demonstrated.

Combinations of experimentally derived data from nuclear magnetic resonance spectroscopy and analyses of molecular dynamics trajectories increasingly allow us to obtain a detailed description of the molecular mechanisms by which proteins function in signal transduction. This chapter provides an introduction into these two methodologies, illustrated by example of a small GTPase–effector interaction. It is increasingly becoming clear that new insights are provided by the combination of experimental and computational methods. Understanding the structural and protein dynamical contributions to allostery will be useful for the engineering of new binding interfaces and protein functions, as well as for the design/in silico screening of chemical agents that can manipulate the function of small GTPase–protein interactions in diseases such as cancer.

Peptide self-assemblies have attracted intense research interests in the last decades thanks to their implications in key biological processes (e.g., amyloid formation) and for their use in the biotechnological and...

An organogelation process depends on the gelator-solvent pair. This study deals with the solvent dynamics once the gelation process is completed. The first approach used is relaxometry, i.e., the measurement of toluene proton longitudinal relaxation time T(1) as a function of the proton NMR resonance frequency (here in the 5 kHz to 400 MHz range). Pure toluene exhibits an unexpected T(1) variation, which has been identified as paramagnetic relaxation resulting from an interaction of toluene with dissolved oxygen. In the gel phase, this contribution is retrieved with, in addition, a strong decay at low frequencies assigned to toluene molecules within the gel fibers. Comparison of dispersion curves of pure toluene and toluene in the gel phase leads to an estimate of the proportion of toluene embedded within the organogel (found around 40%). The second approach is based on carbon-13 T(1) and nuclear Overhauser effect measurements, the combination of these two parameters providing direct information about the reorientation of C-H bonds. It appears clearly that reorientation of toluene is the same in pure liquid and in the gel phase. The only noticeable changes in carbon-13 longitudinal relaxation times are due to the so-called chemical shift anisotropy (csa) mechanism and reflect slight modifications of the toluene electronic distribution in the gel phase. NMR diffusion measurements by the pulse gradient spin-echo (PGSE) method allow us to determine the diffusion coefficient of toluene inside the organogel. It is roughly two-thirds of the one in pure toluene, thus indicating that self-diffusion is the only dynamical parameter to be slightly affected when the solvent is inside the gel structure. The whole set of experimental observations leads to the conclusion that, once the gel is formed, the solvent becomes essentially passive, although an important fraction is located within the gel structure.