Motions of Alexis St. Martin's stomach

In addition to studies on the action of gastric juice, William Beaumont studied the motility of Alexis St. Martin's stomach. He documented the nature of fundal and antral motility and how antral contractions might convert an admixture of solid food and gastric juice into a uniform homogenous semifluid. Beaumont described forcible contractions of the antrum, closure of the pylorus during antral contraction, and the discriminatory nature of the pylorus. Beaumont may also have made the first observations of the gastric motor component of the interdigestive migrating motor complex.     

Correlated Inter-Domain Motions in Adenylate Kinase

Correlated inter-domain motions in proteins can mediate fundamental biochemical processes such as signal transduction and allostery. Here we characterize at structural level the inter-domain coupling in a multidomain enzyme, Adenylate Kinase (AK), using computational methods that exploit the shape information encoded in residual dipolar couplings (RDCs) measured under steric alignment by nuclear magnetic resonance (NMR). We find experimental evidence for a multi-state equilibrium distribution along the opening/closing pathway of Adenylate Kinase, previously proposed from computational work, in which inter-domain interactions disfavour states where only the AMP binding domain is closed. In summary, we provide a robust experimental technique for study of allosteric regulation in AK and other enzymes.     

钙调蛋白的功能性运动分析

目的:研究钙调蛋白(CaM)结构的动力学行为和运动趋势。方法:利用高斯网络模型(GNM)和各向异性网络模型(ANM),分析CaM在无钙和含钙2种形式下的功能运动。结果:CaM的慢运动模式显示,CaM的构象变化主要表现为2个结构域的运动;2种形式的CaM具有共同的铰链区,铰链区位于分子的中央接头,但二者具有不同的运动趋势。交叉相关图结果显示,CaM结合钙离子后,结构域内的相互作用会增强。结论:GNM和ANM结果可以解释先前报道的实验数据。结果有助于更好地了解CaM的构象转变规律,并会提高对CaM的底物识别和调节活动机制的理解。     

Motions of tropomyosin. Crystal as metaphor.

Movements of tropomyosin play an essential role in muscle regulation. This fibrous protein is a two-chain alpha-helical coiled coil that bonds head to tail to form cables wound in the two long grooves of the actin helix. The regulatory switch consists of tropomyosin and a "globular" Ca2+-sensitive protein complex called troponin. The structure of the tropomyosin filaments has now been determined by x-ray crystallography to approximately 15 A resolution. The complete sequence of alpha-tropomyosin is known; by using mercury markers on the cysteine residues the ends of the molecules in the filaments have been identified. Details of the coiled-coil structure have also been visualized by refinement of models against the diffraction data. The average pitch of the coiled coil is approximately 137 A, so that each tropomyosin molecule can make similar contacts with seven actin monomers. The electron density map also indicates that departures from the alpha-helical coiled coil occur in a few localized regions of the molecule, especially at the overlapping ends. Motions of tropomyosin in the crystal lattice are displaced by the character of the Bragg reflections and the strong diffuse scatter. These effects depend markedly on temperature. It appears that the molecular filaments fluctuate freely in a direction perpendicular to their axes. Moreover, the C-terminal half of the molecule "unfolds" to some degree at less than physiological temperatures. Crystallographic results on co-crystals of tropomyosin and a component of troponin (TnT) suggest that this subunit consists of structurally distinct domains, so that the troponin complex is not in fact simply "globular". The interactions of the extended alpha-helical region of TnT may "stiffen" tropomyosin and influence its motions. We picture the tropomyosin/troponin switch in muscle as a restless cable, perpetually making and breaking bonds as it vibrates on the thin filament. These movements of tropomyosin probably depend on two aspects of its design: the regular pattern of coiled-coil linkages with actin; and the aperiodic features that allow flexibility and motion.     

DSMM: a Database of Simulated Molecular Motions

We describe a Database of Simulated Molecular Motions (DSMM). This database is designed to serve as a single searchable site for locating movies and animations from simulations of biomolecules. DSMM is accessible via a webserver at: http://projects.villa-bosch.de/mcm/database/dsmm.     

An Efficient Timer and Sizer of Biomacromolecular Motions

1. Download : Download high-res image (92KB)
2. Download : Download full-size image

     

Coherent Motions in Confluent Cell Monolayer Sheets

Cell migration plays a pivotal role in many physiologically important processes such as embryogenesis, wound-healing, immune defense, and cancer metastasis. Although much effort has been directed toward motility of individual cells, the mechanisms underpinning collective cell migration remain poorly understood. Here we develop a collective motility model that incorporates cell mechanics and persistent random motions of individual cells to study coherent migratory motions in epithelial-like monolayers. This model, in absence of any external chemical signals, is able to explain coordinate rotational motion seen in systems ranging from two adherent cells to multicellular assemblies. We show that the competition between the active persistent force and random polarization fluctuation is responsible for the robust rotation. Passive mechanical coupling between cells is necessary but active chemical signaling between cells is not. The predicted angular motions also depend on the geometrical shape of the underlying substrate: cells exhibit collective rotation on circular substrates, but display linear back-and-forth motion on long and narrow substrates.     

Light-Scattering Spectrum Due to Wiggling Motions of Bacteria

Simple models are used to calculate the inelastic light scattering spectrum of motile bacteria when wiggling motions are included in addition to translational displacement. Computations of spectra lead to the conclusion that nontranslational motions can be neglected when swimming speeds are deduced from light-scattering data for normal vigorously motile strains. On the other hand, for slowly translating bacteria, or for strains exhibiting noticeable wiggling motion when viewed in a microscope, additional spectral components may be significant. Such components are best distinguished when measurements are made at small and intermediate scattering angles; at large angles the spectra have approximately the same scaling properties (functionals of Qt, Q being the Bragg wave vector) as those associated with simple translational motility.     

Coherent Motions in Confluent Cell Monolayer Sheets

Cell migration plays a pivotal role in many physiologically important processes such as embryogenesis, wound-healing, immune defense, and cancer metastasis. Although much effort has been directed toward motility of individual cells, the mechanisms underpinning collective cell migration remain poorly understood. Here we develop a collective motility model that incorporates cell mechanics and persistent random motions of individual cells to study coherent migratory motions in epithelial-like monolayers. This model, in absence of any external chemical signals, is able to explain coordinate rotational motion seen in systems ranging from two adherent cells to multicellular assemblies. We show that the competition between the active persistent force and random polarization fluctuation is responsible for the robust rotation. Passive mechanical coupling between cells is necessary but active chemical signaling between cells is not. The predicted angular motions also depend on the geometrical shape of the underlying substrate: cells exhibit collective rotation on circular substrates, but display linear back-and-forth motion on long and narrow substrates.     

Building Blocks,Hinge-Bending Motions and Protein Topology

Abstract

Here we show that the locations of molecular hinges in protein structures fall between building block elements. Building blocks are fragments of the protein chain which constitute local minima. These elements fold first. In the next step they associate through a combinatorial assembly process. While chain-linked building blocks may be expected to trial-associate first, if unstable, alternate more stable associations will take place. Hence, we would expect that molecular hinges will be at such inter-building block locations, or at the less stable, ‘unassigned’ regions.

On the other hand, hinge-bending motions are well known to be critical for protein function. Hence, protein folding and protein function are evolutionarily related. Further, the pathways through which proteins attain their three dimensional folds are determined by protein topology. However, at the same time the locations of the hinges, and hinge-bending motions are also an outcome of protein topology. Thus, protein folding and function appear coupled, and relate to protein topology. Here we provide some results illustrating such a relationship.     

Dynamic Motions of the HIV-1 Frameshift Site RNA

The HIV-1 frameshift site (FS) plays a critical role in viral replication. During translation, the HIV-1 FS transitions from a 3-helix to a 2-helix junction RNA secondary structure. The 2-helix junction structure contains a GGA bulge, and purine-rich bulges are common motifs in RNA secondary structure. Here, we investigate the dynamics of the HIV-1 FS 2-helix junction RNA. Interhelical motions were studied under different ionic conditions using NMR order tensor analysis of residual dipolar couplings. In 150 mM potassium, the RNA adopts a 43°(±4°) interhelical bend angle (β) and displays large amplitude, anisotropic interhelical motions characterized by a 0.52(±0.04) internal generalized degree of order (GDO_int) and distinct order tensor asymmetries for its two helices (η = 0.26(±0.04) and 0.5(±0.1)). These motions are effectively quenched by addition of 2 mM magnesium (GDO_int = 0.87(±0.06)), which promotes a near-coaxial conformation (β = 15°(±6°)) of the two helices. Base stacking in the bulge was investigated using the fluorescent purine analog 2-aminopurine. These results indicate that magnesium stabilizes extrahelical conformations of the bulge nucleotides, thereby promoting coaxial stacking of helices. These results are highly similar to previous studies of the HIV transactivation response RNA, despite a complete lack of sequence similarity between the two RNAs. Thus, the conformational space of these RNAs is largely determined by the topology of their interhelical junctions.     

Modeling the Correlation Functions of Conformational Motions in Proteins

Abstract

A first principles calculation of the correlation function for conformational motion (CM) in proteins is carried out within the framework of a microscopic model of a protein as a heterogeneous system. The fragments of the protein are assumed to be identical hard spheres undergoing the CM within their conformational potentials about some mean equilibrium positions assigned by the tertiary structure. The memory friction function (MFF) for the generalized Langevin equation describing the CM of the particle is obtained on the basis of the direct calculation which is feasible for the present model of the protein due to the existence of a natural large parameter, viz. the ratio of the minimal distance between the mean equilibrium positions of the particles (～7A) to the amplitude of their CM (<1A). A relationship between the MFF and the correlation functions of the CM of the particles is derived which makes their calculation to be a self-consistent mathematical problem. The general analysis of the MFF is exemplified by a simple model case in which the mean equilibrium positions of the particles form a regular lattice so that the correlation functions for all particles are the same. In this case the MFF is shown to be an infinite series of the powers of the auto-correlation function whose coefficients are independent on temperature. The latter is a result of the abstraction of the interaction potential by that of hard spheres which actually corresponds to the high temperature limit. On the examples of cubic and triangular lattices the coefficients are shown to be non-negative values which increase with the increase of the packing density of the particles and quickly tend to zero with the increase of their index. Thus the MFF can be approximated by a polynomial of the correlation function and the resulting mathematical equation is analogous to the one from the dynamic theory of liquids. The correlation function of the CM is obtained by numerical solution of the equation. At realistic packing densities for proteins it exhibits transparent non-exponential decay and includes two relaxation processes: the first one on the intermediate timescale (tens of picoseconds) and the second on the long timescale (its characteristic time is about tens of nanoseconds at small values of the friction coefficient and increases by orders of the magnitude with the increase of the latter). Thus the present approach provides the microscopic basis for previous phenomenologi- cal models of cooperative dynamics in proteins.     

Unraveling the Motions behind Enterovirus 71 Uncoating

Enterovirus 71 can be a severe pathogen in small children and immunocompromised adults. Virus uncoating is a critical step in the infection of the host cell; however, the mechanisms that control this process remain poorly understood. We applied normal mode analysis and perturbation response scanning to several complexes of the virus capsid and present a coarse-graining approach to analyze the full capsid. We show that our method offers an alternative to expressing the system as a set of rigid blocks and accounts for the interconnection between nodes within each subunit and protein interfaces across the capsid. In our coarse-grained approach, the modes associated with capsid expansion are captured in the first three nondegenerate modes and correspond to the changes observed in structural studies of the virus. We show that the resolution of the analysis may be modified without losing information on the global motions leading to uncoating. Perturbation response scanning revealed that a protomer cannot serve as a functional unit to explain deformations of the capsid. Instead, we define a pentamer as the minimum functional unit to investigate changes within the capsid. From the modal analysis and perturbation response scanning, we locate a hotspot region surrounding the fivefold axis. The range of the effect of these single, hotspot residues extend to 140 Å. The perturbation of internal capsid residues in this region displayed greatest propensity to capsid expansion, thus indicating the significant role that the RNA genome may play in triggering uncoating.     

Molecular Dynamics Simulation of Collective Motions in Binary Liquids

Collective dynamic properties of different kind of binary liquid mixtures have been investigated by molecular dynamics simulation. The study includes both the longitudinal and the transverse current spectra in simple liquid alloys, 1:1 molten salts and liquid binary mixtures of neutral particles with an ionic-like structure. These systems were chosen as representative of binary liquids with different static structures in order to analyse the effects of structural ordering on the mechanisms of dynamic collective properties. The effect of the mass asymmetry between the two species in the mixture has been also discussed from the results for two different mass ratios for each kind of structure. Two length scales have been considered. On the one hand, the hydrodynamic scale (low wave numbers), where the modes for the partial currents of the two species are characterised by very close frequencies. On the other hand, the molecular scale (higher wave numbers), where the characteristic frequencies for the two species show noticeable differences. Vibrational concentration current modes (optic modes) have been found in neutral mixtures though their influence is rather weak, being the collective dynamic properties of this kind of systems dominated by the mass current modes (acoustic modes). On the contrary, in mixtures of charged particles such as molten salts the contribution of the concentration (charge) currents to the collective dynamics is important and optic modes can be characterised by a well-defined frequency for a wide range of wave numbers. It has been observed that heavy particles have a more relevant role on the mass current correlations whereas light particles play a dominant role on the concentration current correlations. The overall results for the three kinds of liquid mixtures analysed in this paper show that both the longitudinal and transverse current spectra are little dependent on the static structure of the system whereas marked differences are revealed when the particles in the system are either neutral or carry an electric charge.     

Investigation of Domain Motions in Bacteriophage T4 Lysozyme

Abstract

Hinge-bending in T4 lysozyme has been inferred from single amino acid mutant crystalline allomorphs by Matthews and coworkers. This raises an important question: are the different conformers in the unit cell artifacts of crystal packing forces, or do they represent different solution state structures? The objective of this theoretical study is to determine whether domain motions and hinge-bending could be simulated in T4 lysozyme using molecular dynamics. An analysis of a 400 ps molecular dynamics simulation of the 164 amino acid enzyme T4 lysozyme is presented. Molecular dynamics calculations were computed using the Discover software package (Biosym Technologies). All hydrogen atoms were modeled explicitly with the inclusion of all 152 crystallographic waters at a temperature of 300 K. The native T4 lysozyme molecular dynamics simulation demonstrated hinge-bending in the protein. Relative domain motions between the N-terminal and C-terminal domains were evident. The enzyme hinge bending sites resulted from small changes in backbone atom conformations over several residues rather than rotation about a single bound. Two hinge loci were found in the simulation. One locus comprises residues 8–14 near the C-terminal of the A helix; the other site, residues 77–83 near the C-terminal of the C helix. Comparison of several snapshot structures from the dynamics trajectory clearly illustrates domain motions between the two lysozyme lobes. Time correlated atomic motions in the protein were analyzed using a dynamical cross-correlation map. We found a high degree of correlated atomic motions in each of the domains and, to a lesser extent, anticorrelated motions between the two domains. We also found that the hairpin loop in the N-terminal lobe (residues 19–24) acted as a mobile ‘flap’ and exhibited highly correlated dynamic motions across the cleft of the active site, especially with residue 142.     

Single-Molecule Motions of MHC Class II Rely on Bound Peptides

The major histocompatibility complex (MHC) class II protein can bind peptides of different lengths in the region outside the peptide-binding groove. Peptide-flanking residues (PFRs) contribute to the binding affinity of the peptide for MHC and change the immunogenicity of the peptide/MHC complex with regard to T cell receptor (TCR). The mechanisms underlying these phenomena are currently unknown. The molecular flexibility of the peptide/MHC complex may be an important determinant of the structures recognized by certain T cells. We used single-molecule x-ray analysis (diffracted x-ray tracking (DXT)) and fluorescence anisotropy to investigate these mechanisms. DXT enabled us to monitor the real-time Brownian motion of the peptide/MHC complex and revealed that peptides without PFRs undergo larger rotational motions than peptides with PFRs. Fluorescence anisotropy further revealed that peptides without PFRs exhibit slightly larger motions on the nanosecond timescale. These results demonstrate that peptides without PFRs undergo dynamic motions in the groove of MHC and consequently are able to assume diverse structures that can be recognized by T cells.