SEARCH · Search bioRxiv

Results for “Biophysics”

Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,279 records · Page 71Linked to original sources

bioRxiv2018

Volvox barberi flocks, forming near-optimal, two-dimensional, polydisperse lattice packings

Volvox barberi is a multicellular green alga forming spherical colonies of 10000-50000 differentiated somatic and germ cells. Here, I show that these colonies actively self-organize over minutes into \"flocks\" that can contain more than 100 colonies moving and rotating collectively for hours. The colonies in flocks form two-dimensional, irregular, \"active crystals\", with lattice angles and colony diameters both following log-normal distributions. Comparison with a dynamical simulation of soft spheres with diameters matched to the Volvox samples, and a weak long-range attractive force, show that the Volvox flocks achieve optimal random close-packing. A dye tracer in the Volvox medium revealed large hydrodynamic vortices generated by colony and flock rotations, providing a likely source of the forces leading to flocking and optimal packing.

biophysics↗

bioRxiv2018

Conformational flexibility of collagen molecules: composition and environmental effects

The predominant structural protein in vertebrates is collagen, which plays a key role in extracellular matrix and connective tissue mechanics. Despite its prevalence and physical importance in biology, the mechanical properties of molecular collagen are far from established. The flexibility of its triple helix is unresolved, with descriptions from different experimental techniques ranging from flexible to semirigid. Furthermore, it is unknown how collagen type (homo-vs. heterotrimeric) and source (tissue-derived vs. recombinant) influence flexibility. Using SmarTrace, a chain tracing algorithm we devised, we performed statistical analysis of collagen conformations collected with atomic force microscopy (AFM) to determine the proteins mechanical properties. Our results show that types I, II and III collagens - the key fibrillar varieties - exhibit molecular flexibilities that are very similar. However, collagen conformations are strongly modulated by salt, transitioning from compact to extended as KCl concentration increases, in both neutral and acidic pH. While analysis with a standard worm-like chain model suggests that the persistence length of collagen can attain almost any value within the literature range, closer inspection reveals that this modulation of collagens conformational behaviour is not due to changes in flexibility, but rather arises from the induction of curvature (either intrinsic or induced by interactions with the mica surface). By modifying standard polymer theory to include innate curvature, we show that collagen behaves as an equilibrated curved worm-like chain (cWLC) in two dimensions. Analysis within the cWLC model shows that collagens curvature depends strongly on pH and salt, while its persistence length does not. Thus, we find that triple-helical collagen is well described as semiflexible, irrespective of source, type, pH and salt environment. These results demonstrate that collagen is more flexible than its conventional description as a rigid rod, which may have implications for its cellular processing and secretion.

biophysics↗

bioRxiv2018

Effect of 5-trans isomer of arachidonic acid on model liposomal membranes studied by a combined simulation and experimental approach

Unsaturated fatty acids are found in humans predominantly in the cis configuration. Fatty acids in the trans configuration are primarily the result of human processing (trans fats), but can also be formed endogenously by radical stress. The cis-trans isomerization of fatty acids by free radicals could be connected to several pathologies. Trans fats have been linked to an increased risk of coronary artery disease; however, the reasons for the resulting pathogenesis remain unclear. Here, we investigate the effect of a mono trans isomer of arachidonic acid (C20:4-5trans,8cis,11cis,14cis) produced by free radicals in physiological concentration on a model erythrocyte membrane using a combined experimental and theoretical approach. Molecular Dynamics (MD) simulations of two model lipid bilayers containing arachidonic acid and its 5-trans isomer in 3% mol. were carried out for this purpose. The 5-trans isomer formation in the phospholipids was catalyzed by HOCH2CH2S* radicals, generated from the corresponding thiol by {gamma}-irradiation, in multilamellar vesicles (MLVs) of SAPC. Large unilamellar vesicles were made by the extrusion method (LUVET) as a biomimetic model for cis-trans isomerization. Atomic Force Microscopy and Dynamic Light Scattering were used to measure the average size, morphology, and the z-potential of the liposomes. Both results from MD simulations and experiments are in agreement and indicate that the two model membranes display different physicochemical properties in that the bilayers containing the trans fatty acids were more ordered and more rigid than those containing solely the cis arachidonic acid. Correspondingly, the average size of the liposomes containing trans isomers was smaller than the ones without.

biophysics↗

bioRxiv2018

SESCA: Predicting the Circular Dichroism Spectra of Proteins from Molecular Structure

Circular dichroism spectroscopy is a highly sensitive, but low-resolution technique to study the structure of proteins. Combined with molecular modelling or other complementary techniques, CD spectroscopy can provide essential information at higher resolution. To this end, we introduce a new computational method to calculate the electronic circular dichroism spectra of proteins from a structural model or ensemble using the average secondary structure composition and a pre-calculated set of basis spectra. We compared the predictive power of our method to existing algorithms - namely DichroCalc and PDB2CD - and found that it predicts CD spectra more accurately, with a 50% smaller average deviation from the measured CD spectra. Our results indicate that the derived basis sets are robust to experimental errors in the reference spectra and to the choice of the secondary structure classification algorithm. For over 80% of the globular reference proteins, our basis sets accurately predict the experimental spectrum solely from their secondary structure composition. For the remaining 20%, correcting for intensity normalization considerably improves the prediction power. Additionally, we show that the predictions for short peptides and intrinsically disordered proteins strongly benefit from accounting for side-chain contributions and structural flexibility. Table Of Content Graphics O_TBL View this table: org.highwire.dtl.DTLVardef@1a1d73forg.highwire.dtl.DTLVardef@3aaa8forg.highwire.dtl.DTLVardef@193c090org.highwire.dtl.DTLVardef@1474f92org.highwire.dtl.DTLVardef@b920da_HPS_FORMAT_FIGEXP M_TBL C_TBL

biophysics↗

bioRxiv2018

Pollen Patterns Form from Modulated Phases

Pollen grains are known for their impressive variety of species-specific, microscale surface patterning. Despite having similar biological developmental steps, pollen grain surface features are remarkably geometrically varied. Previous work suggests that a physical process may drive this pattern formation and that the observed diversity of patterns can be explained by viewing pollen pattern development as a phase transition to a spatially modulated phase. Several studies have shown that the polysaccharide material of plant cell walls undergoes phase separation in the absence of cross-linking stabilizers of the mixed phase. Here we show experimental evidence that phase separation of the extracellular polysaccharide material (primexine) during pollen cell development leads to a spatially modulated phase. The spatial pattern of this phase-separated primexine is also mechanically coupled to the undulation of the pollen cell membrane. The resulting patterned pools of denser primexine form the negative template of the ultimate sites of sporopollenin deposition, leading to the final micropattern observed in the mature pollen. We then present a general physical model of pattern formation via modulated phases. Using analytical and numerical techniques, we find that most of the pollen micropatterns observed in biological evolution could result from a physical process of modulated phases. However, an analysis of the relative rates of transitions from states that are equilibrated to or from states that are not equilibrated suggests that while equilibrium states of this process have occurred throughout evolutionary history, there has been no particular evolutionary selection for symmetric, equilibrated states.

biophysics↗

bioRxiv2018

The Dynamics and Energy Landscape of DNA Plectoneme Nucleation

DNA buckling is the fundamental step for plectoneme nucleation and supercoil dynamics that are critical in the processing of genetic information. Here we systematically quantify DNA buckling dynamics using high-speed magnetic tweezers. Buckling times are [~]10-100 ms and depend exponentially on both applied force and twist. By deconvolving measured time traces with the instrument response, we reconstruct full 2D extension-twist energy landscapes of the buckling transition that reveal an asymmetry between the pre- and post-buckling states and suggest a highly bend transition state conformation.

biophysics↗

bioRxiv2018

Radioprotective role of cyanobacterial phycobilisomes

It is now generally accepted that cyanobacteria are responsible for production of oxygen, which led to the so-called \"Great Oxygenation Event\". Appearance of dioxygen in Earths atmosphere resulted in formation of the ozone layer and the ionosphere, which caused significant reduction of ionizing radiation levels at the surface of our planet. This event not only increased biological diversity but also canceled the urgency of previously developed mechanisms of DNA protection, which allowed to survive and develop in harsh environmental conditions including exposure to cosmic rays. In order to test the hypothesis if one of the oldest organisms on Earth retained ancient protection mechanisms, we studied the effect of ionizing radiation (IoR, here: -particles with a kinetic energy of about 30 MeV) and space flight during the mission of the Foton-M4 satellite on cells of Synechocystis sp. PCC6803. By analyzing spectral and functional characteristics of photosynthetic membranes we revealed numerous similarities between cells exposed to IoR and after the space mission. In both cases, we found that excitation energy transfer from phycobilisomes to photosystems was interrupted and the concentration of phycobiliproteins was significantly reduced. Although photosynthetic activity was severely suppressed, the effect was reversible and the cells were able to rapidly recover from stress under normal conditions. Moreover, in vitro experiments demonstrated that the effect of IoR on isolated phycobilisomes was completely different from such in vivo. These observations suggest that the actual existence and the uncoupling of phycobilisomes under irradiation stress could play specific role not only in photo-, but also in radioprotection, which was crucial for early stages of evolution and the development of Life on Earth.

biophysics↗

bioRxiv2018

Predicting three-dimensional genome organization with chromatin states

We introduce a computational model to simulate chromatin structure and dynamics. Starting from one-dimensional genomics and epigenomics data that are available for hundreds of cell types, this model enables de novo prediction of chromatin structures at five-kilo-base resolution. Simulated chromatin structures recapitulate known features of genome organization, including the formation of chromatin loops, topologically associating domains (TADs) and compartments, and are in quantitative agreement with chromosome conformation capture experiments and super-resolution microscopy measurements. Detailed characterization of the predicted structural ensemble reveals the dynamical flexibility of chromatin loops and the presence of cross-talk among neighboring TADs. Analysis of the models energy function uncovers distinct mechanisms for chromatin folding at various length scales.

biophysics↗

bioRxiv2018

Identifying G protein-coupled receptor dimers from crystal packings

Dimers of G protein-coupled receptors are believed to be important for signaling with their associated G proteins. Low resolution electron microscopy shows rhodopsin dimers in native retinal membranes, and CXCR4 dimers are found in several different crystal structures. Evidence for dimers of other GPCRs is more indirect. An alternative to computational modeling studies is to search for parallel dimers in the packing environments of the reported crystal structures of GPCRs. Two major structural types of GPCR dimers exist (as predicted by others), but there is considerable structural variation within each cluster. The different structural variants described here might reflect different functional properties and should provide a range of model structures for computational and experimental examination.\n\nSynopsisAnalysis of intermolecular interactions in G protein-coupled receptor crystal structures shows two major types of dimers.

biophysics↗

bioRxiv2018

ERASE: a novel surface reconditioning strategy for single-molecule experiments

While surface-based single-molecule experiments have revolutionized our understanding of biology and biomolecules, the workflow in preparing for such experiments, especially surface cleaning and functionalization remains labor-intensive and time-consuming. Even worse, meticulously assembled flow channels can be used only once for most experiments. A reusable surface would thus dramatically increase productivity and efficiency of single-molecule experiments. In this paper, we report a novel surface reconditioning strategy termed ERASE (Epitaxial Removal Aided by Strand Exchange) that allows a single flow cell to be used for vast repetition of single-molecule experiments. In this method, biomolecules immobilized to the surface through a nucleic acid duplex are liberated when a competing DNA strand disrupts the duplex via toehold-mediated strand displacement. We demonstrate the wide-range applicability of this method with various common surface preparation techniques, fluorescent dyes, and biomolecules including the bacterial ribosome. Beyond time and cost savings, we also show ERASE can assort molecules based on a nucleic acid barcode sequence, thus allowing experiments on different molecules in parallel. Our method increases the utility of prepared surfaces and is a significant improvement to the current single-use paradigm.

biophysics↗

bioRxiv2018

Structure of the mouse TRPC4 ion channel

Members of the transient receptor potential (TRP) ion channels conduct cations into cells. They mediate functions ranging from neuronally-mediated hot and cold sensation to intracellular organellar and primary ciliary signaling. Structures belonging to the TRPV, TRPM, TRPP, TRPA and TRPML subfamilies have been solved, but to date, none of the founding canonical (TRPC) structures. Here we report an electron cryo-microscopy (cryo-EM) structure of TRPC4 in its apo state to an overall resolution of 3.3 [A]. The structure reveals an unusually complex architecture with a long pore loop stabilized by a disulfide bond. Beyond the shared tetrameric six-transmembrane fold, the TRPC4 structure deviates from other TRP channels with a unique cytosolic domain, this unique cytosolic N-terminal domain forms extensive aromatic contacts with the TRP and the C-terminal domains. The comparison of our structure with other known TRP structures provides molecular insights into TRPC4 ion selectivity and extends our knowledge of the diversity and evolution of the TRP channels.

biophysics↗

bioRxiv2018

Structure of the receptor-activated human TRPC6 ion channel

TRPC6 is a receptor-activated nonselective cation channel that belongs to the family of canonical transient receptor potential (TRPC) channels. It is activated by diacylglycerol, a lipid second messenger. TRPC6 is involved in many physiological processes and implicated in human genetic diseases. Here we present the structure of human TRPC6 homotetramer in complex with a newly identified high affinity inhibitor BTDM solved by single-particle cryo-electron microscopy to 3.8 [A] resolution. The structure shows a two-layer architecture, in which the bell-shaped cytosolic layer holds the transmembrane layer. Extensive inter-subunit interactions of cytosolic domain, including N terminal ankyrin repeats and C terminal coiled-coil, contribute to the tetramer assembly. The high affinity inhibitor BTDM wedges between S5-S6 pore domain and voltage sensor-like domain to inhibit channel opening. Our structure uncovers the molecular architecture of TRPC channels and provides a structural basis for understanding the mechanism of these channels.

biophysics↗

bioRxiv2018

Structural plasticity of CENP-A regulated by H4 influences cellular levels and kinetochore assembly

The Histone variant CENP-ACse4 is a core component of the specialized nucleosome at the centromere in budding yeast. The level of Cse4 in cells is tightly regulated, primarily by ubiquitin-mediated proteolysis. However, the structural transitions in Cse4 that regulate centromere localization and interaction with regulatory components are poorly understood. Using time resolved fluorescence, NMR and molecular dynamics we show for the first time that soluble Cse4 can exist in a closed conformation, inaccessible to various regulatory components. We further determined that binding of its obligate partner H4, alters the inter-domain interaction within Cse4, ensuring an open state that will lend itself to proteolysis. This dynamic model allows kinetochore formation only in presence of H4, as the N-terminus, which is required for interaction with centromeric components will be unavailable in absence of H4. The specific requirement of H4 binding for the conformational regulation of Cse4 suggests a unique structure-based regulatory mechanism for Cse4 localization and prevention of premature kinetochore assembly.

biophysics↗

bioRxiv2018

TOG domain MT polymerases accelerate MT plus end growth via electrostatically-steered diffusion-to-capture and electrostatic templating of GTP-tubulin

TOG domain microtubule polymerases track microtubule plus ends, bind GTP-tubulin and catalyse microtubule growth, by mechanisms that are not yet understood. In this work, we use computational analysis and simulation to probe the detailed mechanism of tubulin capture and exchange by TOG domains. TOG domains display a ridge of 5 surface loops that form the core of the TOG-tubulin interface. Using computational mutagenesis, we confirm that this row of loops, which is positively charged, plays a dominant role in setting the overall electrostatic field on the TOG domain. Brownian dynamics simulations establish that diffusion-to-capture of TOGs by tubulin is very strongly electrostatically steered. Under a range of conditions and in all trajectories examined, TOGs are initially captured and oriented by tubulin at high radius so that their basic loops faced inwards towards the tubulin. Thereafter, the loops continue to face inwards towards the tubulin and to scan its surface until stereospecific docking the crystallographic binding site occurs. We find that the acidic C-terminal tails of tubulin are not required for electrostatic steering, but instead serve to widen the acceptance angles for electrostatically steered diffusion-to-capture. All-atom normal mode analysis indicates that TOGs are remarkably stiff, enabling them to drive free GTP-tubulin into a partially-curved state by conformational selection. Electrostatic free energy calculations show that the complex that each TOG makes with its cognate tubulin is stable. Our work argues that TOGs accelerate microtubule plus end growth by two complementary electrostatic mechanisms, first by electrostatically steered diffusion-to-capture, and second by electrostatic stabilisation of a partially bent conformation of GTP-tubulin that exchanges rapidly into the tip-lattice. To explain this rapid exchange, we propose a model in which simultaneous binding of the GTP-tubulin to the TOG and the microtubule tip-lattice can occur and is required to de-stabilise the crystallographic complex and release and recycle the TOG.\n\nAuthor SummaryTOG domain microtubule polymerases are protein machines that accelerate the growth of microtubule plus ends by capturing tubulin building blocks from solution and feeding them into the growing microtubule tip. Exactly how TOGs manage to do this remains unclear. Several lines of evidence suggest that electrostatic interactions play a key role, but the detailed role of electrostatics in the polymerase mechanism of TOGs is so far little explored. Here using linked computational approaches we analyse the electrostatic fields of TOGs from the TOG polymerase superfamily and simulate their tubulin binding trajectories. We find that each TOG domain has a shaped electrostatic field that is precisely matched to its tubulin binding partner, such that each TOG is electrostatically orientated at high radius and thereafter electrostatically guided to its capture site. Our work shows that electrostatic steering dramatically accelerates the diffusion-to-capture of tubulin by TOGs. The resulting TOG-tubulin complexes are electrostatically stabilized and we suggest that release of the TOG from this complex requires that tubulin first be incorporated into the growing microtubule, thereby being driven into a TOG-incompatible conformation.

biophysics↗

bioRxiv2018

Cochaperones enable Hsp70 to fold proteins like a Maxwell’s demon

The heat shock protein 70 (Hsp70) chaperones, vital to the proper folding of proteins inside cells, consume ATP and require cochaperones in assisting protein folding. It is unclear whether Hsp70 can utilize the free energy from ATP hydrolysis to fold a protein into a native state that is thermodynamically unstable in the chaperone-free equilibrium. Here we present a model of Hsp70-mediated protein folding, which predicts that Hsp70, as a result of differential stimulation of ATP hydrolysis by its Hsp40 cochaperone, dissociates faster from a substrate in fold-competent conformations than from one in misfolding-prone conformations, thus elevating the native concentration above and suppressing the misfolded concentration below their respective equilibrium values. Previous models would not make or imply these predictions, which are experimentally testable. Our model quantitatively reproduces experimental refolding kinetics, predicts how modulations of the Hsp70/Hsp40 chaperone system affect protein folding, and suggests new approaches to regulating cellular protein quality.

biophysics↗

bioRxiv2018

Variability and compensation of cardiomycoyte ionic conductances at the population level

Conductances of ion channels and transporters controlling cardiac excitation may vary in a population of subjects with different cardiac gene expression patterns. However, the amount of variability and its origin are not quantitatively known. We propose a new computational method to predict this variability that consists of finding combinations of conductances generating a normal intracellular Ca2+ transient without any constraint on the action potential. Furthermore, we validate experimentally its predictions using the Hybrid Mouse Diversity Panel, a model system of genetically diverse mouse strains that allows us to quantify inter-subject versus intra-subject variability. The method predicts that conductances of inward Ca2+ and outward K+ currents compensate each other to generate a normal Ca2+ transient in good quantitative agreement with current measurements in ventricular myocytes from hearts of different isogenic strains. Our results suggest that a feedback mechanism sensing the aggregate Ca2+ transient of the heart suffices to regulate ionic conductances.

biophysics↗

bioRxiv2018

Ligand binding and conformational changes of SUR1 subunit in pancreatic ATP-sensitive potassium channels

ATP-sensitive potassium channels (KATP) are energy sensors on the plasma membrane. By sensing the intracellular ADP/ATP ratio of {beta}-cells, pancreatic KATP channels control insulin release and regulate metabolism at the whole body level. They are implicated in many metabolic disorders and diseases and are therefore important drug targets. Here, we present three structures of pancreatic KATP channels solved by cryo-electron microscopy (cryo-EM), at resolutions ranging from 4.1 to 4.5 [A]. These structures depict the binding site of the antidiabetic drug glibenclamide, indicate how Kir6.2 N-terminus participates the coupling between the peripheral SUR1 subunit and the central Kir6.2 channel, reveal the binding mode of activating nucleotides, and suggest the mechanism of how Mg-ADP binding on nucleotide binding domains (NBDs) drives a conformational change of the SUR1 subunit.

biophysics↗

bioRxiv2018

DNA crookedness regulates DNA mechanical properties at short length scales

Sequence-dependent DNA conformation and flexibility play a fundamental role in specificity of DNA-protein interactions. Here we quantify the DNA crookedness: a sequence-dependent deformation of DNA that consists on periodic bends of the base pair centers chain. Using molecular dynamics simulations, we found that DNA crookedness and its associated flexibility are bijective: unveiling a one-to-one relation between DNA structure and dynamics. This allowed us to build a predictive model to compute DNA stretching stiffness from solely its structure. Sequences with very little crookedness show extremely high stiffness and have been previously shown to form unstable nucleosomes and promote gene expression. Interestingly, the crookedness can be tailored by epigenetic modifications, known to affect gene expression. Our results rationalize the idea that the DNA sequence is not only a chemical code, but also a physical one that allows to finely regulate its mechanical properties and, possibly, its 3D arrangement inside the cell.

biophysics↗