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bioRxiv2016

Measuring experimental cyclohexane-water distribution coefficients for the SAMPL5 challenge

Small molecule distribution coefficients between immiscible nonaqueuous and aqueous phases--such as cyclohexane and water--measure the degree to which small molecules prefer one phase over another at a given pH. As distribution coefficients capture both thermodynamic effects (the free energy of transfer between phases) and chemical effects (protonation state and tautomer effects in aqueous solution), they provide an exacting test of the thermodynamic and chemical accuracy of physical models without the long correlation times inherent to the prediction of more complex properties of relevance to drug discovery, such as protein-ligand binding affinities. For the SAMPL5 challenge, we carried out a blind prediction exercise in which participants were tasked with the prediction of distribution coefficients to assess its potential as a new route for the evaluation and systematic improvement of predictive physical models. These measurements are typically performed for octanol-water, but we opted to utilize cyclohexane for the nonpolar phase. Cyclohexane was suggested to avoid issues with the high water content and persistent heterogeneous structure of water-saturated octanol phases, since it has greatly reduced water content and a homogeneous liquid structure. Using a modified shake-flask LC-MS/MS protocol, we collected cyclohexane/water distribution coefficients for a set of 53 druglike compounds at pH 7.4. These measurements were used as the basis for the SAMPL5 Distribution Coefficient Challenge, where 18 research groups predicted these measurements before the experimental values reported here were released. In this work, we describe the experimental protocol we utilized for measurement of cyclohexane-water distribution coefficients, report the measured data, propose a new bootstrap-based data analysis procedure to incorporate multiple sources of experimental error, and provide insights to help guide future iterations of this valuable exercise in predictive modeling.\n\nAbbreviations used in this paper

Biophysics↗

bioRxiv2016

The mitotic spindle in the one-cell C. elegans embryo is positioned with high precision and stability

Precise positioning of the mitotic spindle is important for specifying the plane of cell division, which in turn determines how the cytoplasmic contents of the mother cell are partitioned into the daughter cells, and how the daughters are positioned within the tissue. During metaphase in the early C. elegans embryo, the spindle is aligned and centered on the anterior-posterior axis by a microtubule-dependent machinery that exerts restoring forces when the spindle is displaced from the center. To investigate the accuracy and stability of centering, we tracked the position and orientation of the mitotic spindle during the first cell division with high temporal and spatial resolution. We found that the precision is remarkably high: the cell-to-cell variation in the transverse position of the center of the spindle during metaphase, as measured by the standard deviation, was only 1.5% of the length of the short axis of the cell. Spindle position is also very stable: the standard deviation of the fluctuations in transverse spindle position during metaphase was only 0.5% of the short axis of the cell. Assuming that stability is limited by fluctuations in the number of independent motor elements such as microtubules or dyneins underlying the centering machinery, we infer that the number is on the order of one thousand, consistent with the several thousand of astral microtubules in these cells. Astral microtubules grow out from the two spindle poles, make contact with the cell cortex, and then shrink back shortly thereafter. The high stability of centering can be accounted for quantitatively if, while making contact with the cortex, the astral microtubules buckle as they exert compressive, pushing forces. We thus propose that the large number of microtubules in the asters provides a highly precise mechanism for positioning the spindle during metaphase while assembly is completed prior to the onset of anaphase.

Biophysics↗

bioRxiv2016

The Influence of Canalization on the Robustness of Boolean Networks

Time- and state-discrete dynamical systems are frequently used to model molecular networks. This paper provides a collection of mathematical and computational tools for the study of robustness in Boolean network models. The focus is on networks governed by k-canalizing functions, a recently introduced class of Boolean functions that contains the well-studied class of nested canalizing functions. The activities and sensitivity of a function quantify the impact of input changes on the function output. This paper generalizes the latter concept to c-sensitivity and provides formulas for the activities and c-sensitivity of general k-canalizing functions as well as canalizing functions with more precisely defined structure. A popular measure for the robustness of a network, the Derrida value, can be expressed as a weighted sum of the c-sensitivities of the governing canalizing functions, and can also be calculated for a stochastic extension of Boolean networks. These findings provide a computationally efficient way to obtain Derrida values of Boolean networks, deterministic or stochastic, that does not involve simulation.

Biophysics↗

bioRxiv2016

Antibody-Based Affinity Cryo-Electron Microscopy at 2.6 Å Resolution

The affinity cryo-electron microscopy (cryo-EM) approach has been explored in recent years to simplify and improve the sample preparation for cryo-EM. Despite the demonstrated successes for low-concentration and unpurified specimens, the lack of near-atomic structures using this approach has led to a common perception of affinity cryo-EM as a niche technique incapable of reaching high resolutions. Here, we report a ~2.6 [A] structure solved using the antibody-based affinity grid approach with a Tulane virus sample of low concentration. This is the first near-atomic structure solved using the affinity cryo-EM approach. Quantitative analyses of the structure indicate data and reconstruction quality comparable to conventional grid preparation method using samples at high concentration. With the shifting of bottlenecks of cryo-EM structural studies to sample grid preparation, our demonstration of the sub-3 [A] capability of affinity cryo-EM approach indicates its potential in revolutionizing cryo-EM sample preparation for a broader spectrum of specimens.

Biophysics↗

bioRxiv2016

Transport efficiency of membrane-anchored kinesin-1 motors depends on motor density and diffusivity

In eukaryotic cells, membranous vesicles and organelles are transported by ensembles of motor proteins. These motors, such as kinesin-1, have been well characterized in vitro as single molecules or as ensembles rigidly attached to non-biological substrates. However, the collective transport by membrane-anchored motors, i.e. motors attached to a fluid lipid bilayer, is poorly understood. Here, we investigate the influence of motors anchorage to a lipid bilayer on the collective transport characteristics. We reconstituted membrane-anchored gliding motility assays using truncated kinesin-1 motors with a streptavidin-binding-peptide tag that can attach to streptavidin-loaded, supported lipid bilayers. We found that the diffusing kinesin-1 motors propelled the microtubules in presence of ATP. Notably, we found the gliding velocity of the microtubules to be strongly dependent on the number of motors and their diffusivity in the lipid bilayer. The microtubule gliding velocity increased with increasing motor density and membrane viscosity, reaching up to the stepping velocity of single-motors. This finding is in contrast to conventional gliding motility assays where the density of surface-immobilized kinesin-1 motors does not influence the microtubule velocity over a wide range. We reason, that the transport efficiency of membrane-anchored motors is reduced because of their slippage in the lipid bilayer, an effect which we directly observed using singlemolecule fluorescence microscopy. Our results illustrate the importance of the motor-cargo coupling, which potentially provides cells with an additional means of regulating the efficiency of cargo transport.

Biophysics↗

bioRxiv2016

Structure of Topologically Associating Domains and gene regulation embedded in the 5C data revealed by a polymer model and stochastic simulations

Chromatin organization is probed by chromosomal capture data, from which the encounter probability (EP) between genomic sites is represented in a large matrix. However, this matrix is obtained by averaging the EP over cell population, where diagonal blocks called TADs, contains hidden information about sub-chromatin organization. Our aim here is to elucidate the relationship between TADs structure and gene regulation. For this end, we reconstruct the chromatin dynamics from the EP matrix using polymer model and explore the transient properties, constrained by the statistics of the data. To construct the polymer, we use the EP decay in two steps: first, to account for TADs, we introduce random connectors inside a restricted region defining the TADs. Second, we account for long-range frequent specific genomic interactions in the polymer architecture. Finally, stochastic simulations show that only a small number of randomly placed connectors are required to reproduce the EP of TADs, and allow us to compute the mean first time and the conditional encounter probability of three key genomic sites to meet. These encounter times reveal how chromatin can self-regulate. The present polymer construction is generic and can be used to study steady-state and transient properties of chromatin constrained on 5C data.

Biophysics↗

bioRxiv2016

Crowding-induced transcriptional bursts dictate nucleosome and polymerase density profiles along genes

During transcription, RNA polymerase competes for space on the DNA with other DNA binding proteins and higher order DNA structures acting as roadblocks. Though it is known that individual polymerases often slow down when forcing roadblocks, the effect of crowding on transcription as a whole is not clear. Based on quantitative theoretical modeling, we show that interactions with roadblocks induce a strong kinetic attraction between polymerases, causing them to self-organize into pelotons. Peloton formation explains observed nucleosome and polymerase density profiles close to the initiation site on highly transcribed genes, and how these densities depend on induction levels. At termination, pelotons translate into transcriptional bursts that dispaly the same characteristics as those observed in vivo. Our model thus unifies common spatial and temporal transcription patterns as arising from a non-specific interaction between roadblocks and polymerases. The generality of our model suggests that peloton formation might be ubiquitous in systems where molecular motors interact with dynamic roadblocks.

Biophysics↗

bioRxiv2016

On numerical study of Parkinson tremor

Parkinsons disease and Parkinsons tremor are the two most common movement disorders, nor do we fully understand the origin of one of the diseases cardinal symptom: the Parkinsonian tremor. We study one mathematical model involved in Parkinsons disease and in the Parkinsonian tremor. In this paper, we use the Van der Pol equation to further understand this tremor as well as investigate different numerical approaches to solve the system and compare them.\n\nAMS Subject Classification 34L16; 34K28; 92B05

Biophysics↗

bioRxiv2016

Mechanisms of self-assembly and fibrillization of the prion-like domains

The mechanism of the self-assembly and fibrillization of the prion-like domains lies at the heart of their physiology and pathology. Here with the same methods previously established, we aimed to further decipher the mechanism by characterizing two prion-like sequences with the electrostatic properties very different from that of the full-length TDP-43 prion-like domain with a very basic pI value: namely the C-half of the TDP-43 prion-like domain only abundant in Gly, Ser, Asn and Gln with a pI of ~6.3, and the FUS prion-like domain enriched with Gly, Ser, Gln and Tyr with a pI of ~3.5. Interestingly, the C-half with the TDP-43 unique hydrophobic region removed is no longer able to form insoluble aggregates/fibrils but still capable of self-assembling into the reversible hydrogel with cross-{beta} structures, despite being much slower than the full-length. On the other hand, the FUS prion-like domain rapidly self-assembles into the reversible hydrogel with cross-{beta} fibrillar structures in 1 mM phosphate buffer at pH 6.8 but its self-assembly becomes very slow in 50 mM MES buffer at pH 5.5. Our study reveals that despite having completely different electrostatic properties, the full-length and C-half of the TDP-43 prion-like domain, as well as FUS prion-like domain all have the similar pH-dependence in self-assembly as we previously reported (Lim et al., [2016] PLOS Biol 14:e1002338). This unambiguously indicates that the self-assembly of the prion-like domains is not generally governed by the electrostatic interaction. Rather, their self-assembly and fibrillization are specified by the sequences despite being highly polar and degenerative. Furthermore, our study provides the first evidence that the formation of reversible hydrogel with cross-{beta} structures is separable from fibrillization of the prion-like domain. Finally, our results also successfully reconcile the previous discrepancy about the conformation and mechanism of the self-assembly of the FUS prion-like domain.

Biophysics↗

bioRxiv2016

Sensitivity in binding free energies due to protein reorganization

Tremendous recent improvements in computer hardware, coupled with advances in sampling techniques and force fields, are now allowing protein-ligand binding free energy calculations to be routinely used to aid pharmaceutical drug discovery projects. However, despite these recent innovations, there are still needs for further improvement in sampling algorithms to more adequately sample protein motion relevant to protein-ligand binding. Here, we report our work identifying and studying such clear and remaining needs in the apolar cavity of T4 Lysozyme L99A. In this study, we model recent experimental results that show the progressive opening of the binding pocket in response to a series of homologous ligands.1 Even while using enhanced sampling techniques, we demonstrate that the predicted relative binding free energies (RBFE) are sensitive to the initial protein conformational state. Particularly, we highlight the importance of sufficient sampling of protein conformational changes and demonstrate how inclusion of three key protein residues in the hot region of the FEP/REST simulation improves the sampling and resolves this sensitivity.

Biophysics↗

bioRxiv2016

Mutations in the catalytic domain of human β-cardiac myosin that cause early onset hypertrophic cardiomyopathy significantly increase the fundamental parameters that determine ensemble force and velocity

Hypertrophic cardiomyopathy (HCM) is a heritable cardiovascular disorder that affects 1 in 500 people. In infants it can be particularly severe and it is the leading cause of sudden cardiac death in pediatric populations. A high percentage of HCM is attributed to mutations in {beta}-cardiac myosin, the motor protein that powers ventricular contraction. This study reports how two mutations that cause early-onset HCM, D239N and H251N, affect the mechanical output of human {beta}-cardiac myosin at the molecular level. We observe extremely large increases (25% - 95%) in the actin gliding velocity, single molecule intrinsic force, and ATPase activity of the two mutant myosin motors compared to wild type myosin. In contrast to previous studies of HCM-causing mutations in human {beta}-cardiac myosin, these mutations were striking in that they caused changes in biomechanical parameters that were both greater in magnitude and more uniformly consistent with a hyper-contractile phenotype. In addition, S1-S2 binding studies revealed a significant decrease in affinity of the H251N motor for S2, suggesting that this mutation may further increase hyper-contractility by releasing active motors from a sequestered state. This report shows, for the first time, a clear and significant gain in function for all tested molecular biomechanical parameters due to HCM mutations in human {beta}-cardiac myosin.

Biophysics↗

bioRxiv2016

Coupled Nosé-Hoover equations of motions without time scaling

The Nose-Hoover (NH) equation of motion is widely used in molecular dynamics simulations. It enables us to set a constant temperature and produce the canonical distribution for a target physical system. For the purpose of investigating the physical system under fluctuating temperature, we have introduced a coupled Nose-Hoover equation in our previous work [J. Phys. A 48 455001 (2015)]. The coupled NH equation implements a fluctuating heat-bath temperature in the NH equation of the physical system, and also keeps a statistically complete description via an invariant measure of the total system composed of the physical system and a \"temperature system\". However, a difficulty lies in that the time development of the physical system may not correspond to the realistic physical process, because of the need of a scaled time average to compute thermodynamical quantities. The current work gives a solution by presenting a new scheme, which is free from the scaled time but retains the statistical description. By use of simple model systems, we validate the current scheme and compare with the original scheme. The sampling property of the current scheme is also clarified to investigate the effect of function setting used for the distribution of the total system.

Biophysics↗

bioRxiv2016

Modeling Hsp70/Hsp40 interaction by multi-scale molecular simulations and co-evolutionary sequence analysis

The interaction between the Heat Shock Proteins 70 and 40 is at the core of the ATPase regulation of the chaperone machinery that maintains protein homeostasis. However, the structural details of this fundamental interaction are still elusive and contrasting models have been proposed for the transient Hsp70/Hsp40 complexes. Here we combine molecular simulations based on both coarsegrained and atomistic models with co-evolutionary sequence analysis to shed light on this problem by focusing on the bacterial DnaK/DnaJ system. The integration of these complementary approaches resulted into a novel structural model that rationalizes previous experimental observations. We identify an evolutionary-conserved interaction surface formed by helix II of the DnaJ J-domain and a groove on lobe IIA of the DnaK nucleotide binding domain, involving the inter-domain linker.

Biophysics↗

bioRxiv2016

Intrinsic K-Ras dynamics: A novel molecular dynamics data analysis method shows causality between residue pairs

While mutant K-Ras is an important therapeutic target for human cancers, there are still no drugs that directly target it. Recent promising studies emphasize the significance of dynamics data to selectively target its active/inactive states. However, despite tremendous information on K-Ras, the direction of information flow in the allosteric regulation of its dynamics has not yet been elucidated. Here, we present a novel approach that identifies causality in correlated motions of proteins and apply it to K-Ras dynamics. Specifically, we analyze molecular dynamics simulations data and comprehensively investigate nucleotide-dependent intrinsic K-Ras activity. We show that GTP binding leads to characteristic residue correlations with relatively long decay times by stabilizing K-Ras motions. Furthermore, we identify for the first time driver-follower relationships of correlated motions in the regulation of K-Ras activity. Our results can be utilized for directly targeting mutant K-Ras in future studies.

Biophysics↗

bioRxiv2016

Ultraslow water-mediated transmembrane interactions regulate the activation of A2A adenosine receptor

Water molecules inside G-protein coupled receptor have recently been spotlighted in a series of crystal structures. To decipher the dynamics and functional roles of internal waters in GPCR activity, we studied A2A adenosine receptor using sec-molecular dynamics simulations. Our study finds that the amount of water flux across the transmembrane (TM) domain varies depending on the receptor state, and that the water molecules of the TM channel in the active state flow three times slower than those in the inactive state. Depending on the location in solvent-protein interface as well as the receptor state, the average residence time of water in each residue varies from [Formula] psec to [Formula] nsec. Especially, water molecules, exhibiting ultraslow relaxation ([Formula] nsec) in the active state, are found around the microswitch residues that are considered activity hotspots for GPCR function. A continuous allosteric network spanning the TM domain, arising from water-mediated contacts, is unique in the active state, underscoring the importance of slow waters in the GPCR activation.

Biophysics↗

bioRxiv2016

A FLIC motility assay reveals myosin-6 coordination limited by actin filament buckling

Teams of myosin motors carry out intracellular transport and contract the actin cytoskeleton. To fully understand the behavior of multi-myosin ensembles we need to know the properties of individual myosins and the mode of interaction between them. Current models of the interactions within the myosin complex treat the actin filament as a stiff rod, not contributing to the regulation of collective myosin dynamics. Here, we present data suggesting that force transduction through the actin filament is an important element of interaction within myosin-6 ensembles in vitro. Multiple myosin-6s coordinate their steps if they are separated by a short (and therefore high-force bearing) segment of actin. The measurements were performed using Fluorescence Interference Contrast Microscopy (FLIC) to measure small changes in the height of fluorescently labeled actin. Using FLIC, we assign the positions of myosins in a gliding filament assay geometry and measure their attachment time to actin. We also identify actin segments that are buckled or under tension. We show that myosin-6 holds actin about 10 nm above the surface. However, due to asynchronous myosin stepping, frequent buckles up to about 60 nm high appear. The buckle lifetime decreases as the distance between the myosin-6s is reduced, a sign of inter-motor coordination. Our data are consistent with coordinated stepping of closely spaced myosins, but uncoordinated motility with widely separated myosins where buckles can form. These features would be expected to operate on myosins in the cell, where motor spacing may vary considerably depending on the target organelle.\n\nSIGNIFICANCE STATEMENTMyosins are molecular motors that carry out intracellular transport. Interactions between the myosins are crucial for understanding their function. Using Fluorescence Interference Contrast (FLIC) microscopy we characterized the interaction between multiple myosin-6 motors immobilized to the surface of a slide and pulling the same actin filament. Our results point towards coordination of myosin steps as a mechanism governing the behavior of a multi-myosin complex. We also demonstrated the unique application of FLIC microscopy for highly parallel identification and measurement of single myosin motors in a gliding filament format. These features of FLIC enable a robust study of collective myosin dynamics.

Biophysics↗

bioRxiv2016

The hidden treasure in your data: Phasing with unexpected weak anomalous scatterers from routine datasets

Single wavelength anomalous dispersion (SAD) utilizing anomalous signal from native sulfurs, or other atoms with Z[≤]20, generally requires highly redundant data collected with relatively long wavelength X-rays. Here we present experiences with two proteins, where anomalous signal from serendipitously acquired surface bound calcium atoms with data redundancy as low as 10 was utilized to drive de novo structure determination. In both the cases, the calcium atoms were acquired from the crystallization solution, and data collection strategy was not optimized for exploiting the anomalous signal from these scatterers. The X-ray data were collected at 0.98[A] in one case and at 1.74[A] in the other (wavelength optimized for sulfur but anomalous signal from Ca was exploited for structure solution). Similarly, using a test case, we show that the data collected at ~1.0[A] wavelength, where the f\" value for sulfur is 0.28e, is sufficient for structure determination using intrinsic sulfur atoms from a strongly diffracting crystal. Interestingly, it was also observed that SHELXD was capable of generating a substructure solution from high-exposure data with a completeness of 70% for low-resolution reflections extending to 3.5[A], with relatively low redundancy (i.e., 6.0 fold). Considering the fact that many crystallization conditions contain anomalous scatterers such as Cl, Ca, Mn etc., it appears that the data from well diffracting crystals should be processed, with anomalous pairs kept separate, so as to detect any fortuitous signal that might be present, which could prove useful in either solving the structure de novo or in accurately assigning surface bound atoms.

Biophysics↗

bioRxiv2016

Dissection of molecular assembly dynamics by tracking orientation and position of single molecules in live cells

Regulation of order, such as orientation and conformation, drives the function of most molecular assemblies in living cells, yet remains difficult to measure accurately through space and time. We built an instantaneous fluorescence polarization microscope, which simultaneously images position and orientation of fluorophores in living cells with single-molecule sensitivity and a time resolution of 100ms. We developed image acquisition and analysis methods to track single particles that interact with higher-order assemblies of molecules. We tracked the fluctuations in position and orientation of molecules from the level of an ensemble of fluorophores down to single fluorophores. We tested our system in vitro using fluorescently labeled DNA and F-actin in which the ensemble orientation of polarized fluorescence is known. We then tracked the orientation of sparsely labeled F-actin network at the leading edge of migrating human keratinocytes, revealing the anisotropic distribution of actin filaments relative to the local retrograde flow of the F-actin network. Additionally, we analyzed the position and orientation of septin-GFP molecules incorporated in septin bundles in growing hyphae of a filamentous fungus. Our data indicate that septin-GFP molecules undergo positional fluctuations within, [~]350nm of the binding site and angular fluctuations within [~]30{degrees} of the central orientation of the bundle. By reporting position and orientation of molecules while they form dynamic higher-order structures, our approach can provide new insights into how micron-scale ordered assemblies emerge from nanoscale molecules in living cells.\n\nSignificance StatementIn living cells, the 3D architecture of molecular assemblies such as chromosomes, lipid bilayers, and the cytoskeleton is regulated through the interaction among their component molecules. Monitoring the position and orientation of constituent molecules is important for understanding the mechanisms that govern the structure and function of these assemblies. We have developed an instantaneous fluorescence polarization microscope to track the position and orientation of fluorescently labeled particles, including single molecules, which form micron-scale macromolecular assemblies in living cells. Our imaging approach is broadly applicable to the study of dynamic molecular interactions that underpin the function of micron-scale assemblies in living cells.

Biophysics↗