Visualizing global properties of a molecular dynamics trajectory

Molecular dynamics (MD) trajectories are very large data sets that contain substantial information about the dynamic behavior of a protein. Condensing these data into a form that can provide intuitively useful understanding of the molecular behavior during the trajectory is a substantial challenge that has received relatively little attention. Here, we introduce the sigma‐r plot, a plot of the standard deviation of intermolecular distances as a function of that distance. This representation of global dynamics contains within a single, one‐dimensional plot, the average range of motion between pairs of atoms within a macromolecule. Comparison of sigma‐r plots calculated from 10 ns trajectories of proteins representing the four major SCOP fold classes indicates diversity of dynamic behaviors which are recognizably different among the four classes. Differences in domain structure and molecular weight also produce recognizable features in sigma‐r plots, reflective of differences in global dynamics. Plots generated from trajectories with progressively increasing simulation time reflect the increased sampling of the structural ensemble as a function of time. Single amino acid replacements can give rise to changes in global dynamics detectable through comparison of sigma‐r plots. Dynamic behavior of substructures can be monitored by careful choice of interatomic vectors included in the calculation. These examples provide demonstrations of the utility of the sigma‐r plot to provide a simple measure of the global dynamics of a macromolecule. Proteins 2016; 84:82–91. © 2015 Wiley Periodicals, Inc.     

Visualizing global properties of large complex networks

For complex biological networks, graphical representations are highly desired for understanding some design principles, but few drawing methods are available that capture topological features of a large and highly heterogeneous network, such as a protein interaction network. Here we propose the circular perspective drawing (CPD) method to visualize global structures of large complex networks. The presented CPD combines the quasi-continuous search (QCS) analogous to the steepest descent method with a random node swapping strategy for an enhanced calculation speed. The CPD depicts a network in an aesthetic manner by showing connection patterns between different parts of the network instead of detailed links between nodes. Global structural features of networks exhibited by CPD provide clues toward a comprehensive understanding of the network organizations. Availability: Software is freely available at http://www.cadlive.jp.     

Visualizing circuits and systems using transgenic reporters of neural activity

Genetically encoded sensors of neural activity enable visualization of circuit-level function in the central nervous system. Although our understanding of the molecular events that regulate neuronal firing, synaptic function, and plasticity has expanded rapidly over the past 15 years, an appreciation for how cellular changes are functionally integrated at the circuit level has lagged. A new generation of tools that employ fluorescent sensors of neural activity promises unique opportunities to bridge the gap between cellular level and system level analysis. This review will focus on genetically encoded sensors. A primary advantage of these indicators is that they can be nonselectively introduced to large populations of cells using either transgenic-mediated or viral-mediated approaches. This ability removes the nontrivial obstacles of how to get chemical indicators into cells of interest, a problem that has dogged investigators who have been interested in mapping neural function in the intact CNS. Five different types of approaches and their relative utility will be reviewed here: first, reporters of immediate-early gene (IEG) activation using promoters such as c-fos and arc; second, voltage-based sensors, such as GFP-coupled Na+ and K+ channels; third, Cl*-based sensors; fourth, Ca2+-based sensors, such as Camgaroo and the troponin-based TN-L15; and fifth, pH-based sensors, which have been particularly useful for examining synaptic activity of highly convergent afferents in sensory systems in vivo. Particular attention will be paid to reporters of IEG expression, because these tools employ the built-in threshold function that occurs with activation of gene expression, provoking new experimental questions by expanding the timescale of analysis for circuit-level and system-level functional mapping.     

Visualizing protein motion in Couette flow by all-atom molecular dynamics

In living cells, biomacromolecules are exposed to a highly crowded environment. The cytoplasm, the nucleus, and other organelles are highly viscous fluids that differ from dilute in vitro conditions. Viscosity, a measure of fluid internal friction, directly affects the forces that act on immersed macromolecules. Although active motion of this viscous fluid – cytoplasmic streaming – occurs in many plant and animal cells, the effect of fluid motion (flow) on biomolecules is rarely discussed. Recently NMR experiments that apply a shearing flow in situ have been used for protein studies. While these NMR experiments have succeeded in spectroscopically tracking protein aggregation in real time, they do not provide a visual picture of protein motion under shear. To fill this gap, here we have used molecular dynamics simulations to study the motion of three proteins of different size and shape in a simple shearing flow. The proteins exhibit a superposition of random diffusion and shear-flow-induced rotational motion. Random rotational diffusion dominates at lower shear stresses, whereas an active “rolling motion” along the axis of the applied flow occurs at higher shear stress. Even larger shear stresses perturb protein secondary structure elements resulting in local and global unfolding. Apart from shear-induced unfolding, our results imply that, in an ideal Couette flow field biomolecules undergo correlated motion, which should enhance the probability of inter-molecular interaction and aggregation. Connecting biomolecular simulation with experiments applying shear flow in situ appears to be a promising strategy to study protein alignment, deformation, and dynamics under shear.     

Study on mechanical properties of polyethylene with chain branching in atomic scale by molecular dynamics simulation

The effects of length and content of chain branching on the mechanical properties of polyethylene (PE) in atomic scale were examined by molecular dynamics (MD) simulations. Methyl-, ethyl- and butyl-groups were adopted as branched chains to distribute along PE backbones. Plastic flow deformation was captured by providing a uniaxial tensile loading at a given strain rate, which shows the characteristic of rate dependence. Current results are in reasonable agreements with existing experimental data. The statistical results show that the longer length of chain branching induces lower equilibrium density and higher yield strength of branched PE. In addition, higher content of chain branching brings higher equilibrium density and lower yield strength of branched PE. It is assumed that the distribution of dihedral angles influences the deformation of PE definitely. The non-bond interactions contribute to the load-bearing capacity of PE largely. Branched PE shows big differences on mechanical behaviours comparing with the linear one. Chain branching distribution also greatly affects the performance of PE, which needs a further discussion.     

Influence of alkaline concentration on molecular association structure and viscoelastic properties of curdlan aqueous systems

Curdlan is an extracellular polysaccharide produced from soil microorganism Alcaligens faecalis var. 10C3K, and the linear structure consists of β-1,3-glycoside linkages. Curdlan is not soluble in water but it is soluble in alkaline aqueous solution, and we can obtain the gel when curdlan alkaline solution is heated above 60°C or neutralized by acids. In the present study, the gelation mechanism and dispersing structure of curdlan in the alkaline solutions are studied in terms of correlation between the molecular association structure and viscoelastic properties, using static light scattering and rheological measurements. The degree of association for the curdlan molecules in dilute solution increases with decreasing alkaline concentration. The viscoelastic properties also depend strongly on the alkaline concentration. The concentrated curdlan solution shows almost Newtonian flow at high alkaline concentrations and shows a gel-like behavior at low alkaline concentrations. It was elucidated that the molecular association in the dilute solution reflects on the viscoelastic properties of the concentrated solution and that the gelation mechanism is related to the association structure of curdlan molecules. In the case of lower NaOH concentration systems, the molecular association is likely to consist of a hydrophobic core and hydrophilic surface. The gelation mechanism above 60°C is considered to include the dissociation process of the molecular association and reformation of the network structure. © 1997 John Wiley & Sons, Inc. Biopoly 42: 479–487, 1997     

Visualizing DNA domains and sequences by microscopy: a fifty-year history of molecular cytogenetics.

This short review presents a historical perspective of chromosome research during the last 50 years. It shows how molecular knowledge and technology of DNA entered cytogenetics step by step making it now daily practice in almost every modern chromosome lab. A crucial milestone in these decades has been the development of in situ protocols by Pardue and Gall, among others, initially only with isotopic labels, and without fluorescence microscopy and sophisticated detection systems. But these very first in situ hybridizations played a decisive role in the discovery of chromosome banding profiles, which were obtained under specific chemical, physical, or enzymatic conditions, thus effecting stainability of specific chromosome regions. In the decades thereafter, numerous technical improvements were achieved leading to complex multi-colour fluorescence in situ hybridization (FISH) protocols for mammals, plants, and insects. Highly improved detection systems of the FISH signals further allowed detection of DNA targets of up to 50 bp, whereas other protocols, which were developed to stretch chromatin fibres to the full length of native DNA, improved spatial resolution of adjacent targets in the light microscope to 1 kb.     

Formaldehyde-induced mutagenesis in Saccharomyces cerevisiae: molecular properties and the roles of repair and bypass systems

Although DNA-protein cross-links (DPCs) pose a significant threat to genome stability, they remain a poorly understood class of DNA lesions. To define genetic impacts of DPCs on eukaryotic cells in molecular terms, we used a sensitive Saccharomyces cerevisiae frameshift-detection assay to analyze mutagenesis by formaldehyde (HCHO), and its response to nucleotide excision repair (NER) and translesion DNA synthesis (TLS). Brief exposure to HCHO was mutagenic for NER-defective rad14 strains but not for a corresponding RAD14 strain, nor for a rad14 strain lacking both Polζ and Polη TLS polymerases. This confirmed that HCHO-generated DNA lesions can trigger error-prone TLS and are substrates for the NER pathway. Sequencing revealed that HCHO-induced single-base-pair insertions occurred primarily at one hotspot; most of these insertions were also complex, changing an additional base-pair nearby. Most of the HCHO-induced mutations required both Polζ and Polη, providing a striking example of cooperativity between these two TLS polymerases during bypass of a DNA lesion formed in vivo. The similar molecular properties of HCHO-induced and spontaneous complex +1 insertions detected by this system suggest that DPCs which form in vivo during normal metabolism may contribute characteristic events to the spectra of spontaneous mutations in NER-deficient cells.     

The sociobiology of molecular systems

It is often assumed that molecular systems are designed to maximize the competitive ability of the organism that carries them. In reality, natural selection acts on both cooperative and competitive phenotypes, across multiple scales of biological organization. Here I ask how the potential for social effects in evolution has influenced molecular systems. I discuss a range of phenotypes, from the selfish genetic elements that disrupt genomes, through metabolism, multicellularity and cancer, to behaviour and the organization of animal societies. I argue that the balance between cooperative and competitive evolution has shaped both form and function at the molecular scale.     

Measuring molecular elasticity by atomic force microscope cantilever fluctuations

In single-molecule mechanics experiments the molecular elasticity is usually measured from the deformation in response to a controlled applied force, e.g., via an atomic force microscope cantilever. We have tested the validity of an alternative method based on a recently developed theory. The concept is to measure the change in thermal fluctuations of the cantilever tip with and without its coupling to a rigid surface via the molecule. The new method was demonstrated by its application to the elasticity measurements of L- and P-selectin complexed with P-selectin glycoprotein ligand-1 or their respective antibodies, which showed values comparable to those measured from the slope of the force-extension curve. L- and P-selectin were found to behave as nearly linear springs capable of sustaining large forces and strains without sudden unfolding. The measured spring constants of approximately 4 and approximately 1 pN/nm for L- and P-selectin, respectively, suggest that a physiological force of approximately 100 pN would result in an approximately 200% strain for the respective selectins.     

Sensing specific molecular interactions with the atomic force microscope

One of the unique features of the atomic force microscope (AFM) is its capacity to measure interactions between tip and sample with high sensitivity and unparalleled spatial resolution. Since the development of methods for the functionalization of the tips, the versatility of the AFM has been expanded to experiments where specific molecular interactions are measured. For illustration, we present measurements of the interaction between complementary strands of DNA. A necessary prerequisite for the quantitative analysis of the interaction force is knowledge of the spring constant of the cantilevers. Here, we compare different techniques that allow for the in situ measurement of the absolute value of the spring constant of cantilevers.     

Detection and localization of single molecular recognition events using atomic force microscopy

Because of its piconewton force sensitivity and nanometer positional accuracy, the atomic force microscope (AFM) has emerged as a powerful tool for exploring the forces and the dynamics of the interaction between individual ligands and receptors, either on isolated molecules or on cellular surfaces. These studies require attaching specific biomolecules or cells on AFM tips and on solid supports and measuring the unbinding forces between the modified surfaces using AFM force spectroscopy. In this review, we describe the current methodology for molecular recognition studies using the AFM, with an emphasis on strategies available for preparing AFM tips and samples, and on procedures for detecting and localizing single molecular recognition events.