PaperPlayer biorxiv biophysics

Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.09.06.285080v1?rss=1

Authors: Fleig, P., Kramar, M., Wilczek, M., Alim, K.

Abstract:

What is the origin of behavior? Although typically associated with a nervous system, simple life forms also show complex behavior - thus serving as a model to study how behaviors emerge. Among them, the slime mold Physarum polycephalum, growing as a single giant cell, is renowned for its sophisticated behavior. Here, we show how locomotion and morphological adaptation behavior emerge from self-organized patterns of rhythmic contractions of the actomyosin lining of the tubes making up the network-shaped organism. We quantify the spatio-temporal contraction dynamics by decomposing experimentally recorded contraction patterns into spatial contraction modes. Surprisingly, we find a continuous spectrum of modes, as opposed to few dominant modes. Over time, activation of modes along this continuous spectrum is highly dynamic, resulting in contraction patterns of varying regularity. We show that regular patterns are associated with stereotyped behavior by triggering a behavioral response with a food stimulus. Furthermore, we demonstrate that the continuous spectrum of modes and the existence of irregular contraction patterns persist in specimens with a morphology as simple as a single tube. Our data suggests that the continuous spectrum of modes allows for dynamic transitions between a plethora of specific behaviors with transitions marked by highly irregular contraction states. By mapping specific behaviors to states of active contractions, we provide the basis to understand behavior's complexity as a function of biomechanical dynamics. This perspective will likely stimulate bio-inspired design of soft robots with a similarly rich behavioral repertoire as P. polycephalum.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.09.07.284703v1?rss=1

Authors: Hanrahan, N., Lane, S. I. R., JOHNSON, P. B., Bourdakos, K. N., Brereton, C. J., Ridley, R. A., Davies, E. R., Hosny, N. A., Spickermann, G., Forster, R., Malcolm, G., Davies, D. E., Jones, M. G., Mahajan, S.

Abstract:

Light sheet microscopy (LSM) has emerged as one of most profound three dimensional (3D) imaging tools in the life sciences over the last decade. However, LSM is currently performed with fluorescence detection on one- or multi-photon excitation. Label-free LSM imaging approaches have been rather limited. Second Harmonic Generation (SHG) imaging is a label-free technique that has enabled detailed investigation of collagenous structures, including its distribution and remodelling in cancers and respiratory tissue, and how these link to disease. SHG is generally regarded as having only forward- and back-scattering components, apparently precluding the orthogonal detection geometry used in Light Sheet Microscopy. In this work we demonstrate SHG imaging on a light sheet microscope (SHG-LSM) using a rotated Airy beam configuration that demonstrates a powerful new approach to direct (without any further processing or deconvolution) 3D imaging of harmonophores such as collagen fibres in biological samples. We provide unambiguous identification of SHG signals on the LSM through its wavelength and polarisation sensitivity. In a multimodal LSM setup we demonstrate that SHG and two-photon signals can be acquired on multiple types of different biological samples. We further show that SHG-LSM is sensitive to changes in collagen synthesis within lung fibroblast 3D cell cultures. This work expands on the existing optical methods available for use with light sheet microscopy, adding a further label-free imaging technique which can be combined with other detection modalities to realise a powerful multi-modal microscope for 3D bioimaging.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.09.06.285353v1?rss=1

Authors: Li, X., Song, X., Li, Y., Li, M., Wang, H.

Abstract:

Optical tweezers is a powerful tool in the study of membrane tension. Comparing to pulling out an entire membrane tether at one time, the step-like method is more efficient because multiple relaxation curves can be obtained from one membrane tether. However, there is few proper models that describe relaxation curves to characterize mechanical properties of cell membrane. Here we established a model to describe the relaxation curve of HeLa cells based on the relationship between membrane tether diameter and tensions. We obtained effective viscosities and static tensions by fitting relaxation curves to our model. We noticed the delicate structure of relaxation curves contains information of cell skeleton changes and protein diffusion. Our study paved a novel pathway to characterize the dynamics and mechanics of cell membrane.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.09.06.285312v1?rss=1

Authors: Banerjee, S., Hashemi, M., Zagorski, K., Lyubchenko, Y. L.

Abstract:

The formation of amyloid {beta} (1-42) (A{beta}42) oligomers is considered to be a critical step in the development of Alzheimer's disease (AD). However, the mechanism underlying this process at physiologically low concentrations of A{beta}42 remains unclear. We have previously shown that oligomers assemble at such low A{beta}42 monomer concentrations in vitro on phospholipid membranes. We hypothesized that membrane composition is the factor controlling the aggregation process. Accumulation of cholesterol in membranes is associated with AD development, suggesting that insertion of cholesterol into membranes may initiate the A{beta}42 aggregation, regardless of a low monomer concentration. We used atomic force microscopy (AFM) to directly visualize the aggregation process of A{beta}42 on the surface of a lipid bilayer containing cholesterol. Time-lapse AFM imaging unambiguously demonstrates that cholesterol in the lipid bilayer significantly enhances the aggregation process of A{beta}42 at nanomolar monomer concentration. Quantitative analysis of the AFM data shows that both the number of A{beta}42 oligomers and their sizes grow when cholesterol is present. Importantly, the aggregation process is dynamic, so the aggregates assembled on the membrane can dissociate from the bilayer surface into the bulk solution. Computational modeling demonstrated that the lipid bilayer containing cholesterol had an elevated affinity to A{beta}42. Moreover, monomers adopted the aggregation-prone conformations present in amyloid fibrils. The low energy barriers between these conformations facilitate the transition between monomer states and is another factor promoting the self- association of the monomers.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.09.06.285239v1?rss=1

Authors: Park, H., Zhou, G., Baek, M., Baker, D., DiMaio, F.

Abstract:

Accurate and rapid calculation of protein-small molecule interaction energies is critical for computational drug discovery. Because of the large chemical space spanned by drug-like molecules, classical force fields contain thousands of parameters describing atom-pair distance and torsional preferences; each parameter is typically optimized independently on simple representative molecules. Here we describe a new approach in which small-molecule force field parameters are jointly optimized guided by the rich source of information contained within thousands of available small molecule crystal structures. We optimize parameters by requiring that the experimentally determined molecular lattice arrangements have lower energy than all alternative lattice arrangements. Thousands of independent crystal lattice-prediction simulations were run on each of 1,386 small molecule crystal structures, and energy function parameters of an implicit solvent energy model were optimized so native crystal lattice arrangements had lowest energy. The resulting energy model was implemented in Rosetta, together with a rapid genetic algorithm docking method employing grid based scoring and receptor flexibility. The success rate of bound structure recapitulation in cross-docking on 1,112 complexes was improved by more than 10% over previously published methods, with solutions within <1 [A] in over half of the cases. Our results demonstrate that small molecule crystal structures are a rich source of information for systematically improving computational drug discovery.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.09.06.284901v1?rss=1

Authors: Bhattacharjee, S., Bhattacharyya, R., Sengupta, J.

Abstract:

The pathogenesis of novel SARS-CoV-2 virus initiates through recognition of ACE2 receptor (Angiotensin-converting enzyme 2) of the host cells by the receptor-binding domain (RBD) located at spikes of the virus. Following receptor-recognition, proteolytic cleavage between S1 and S2 subunits of the spike protein occurs with subsequent release of fusion peptide. Here, we report our study on allosteric communication within RBD that propagates the signal from ACE2-binding site towards allosteric site for the post-binding activation of proteolytic cleavage. Using MD simulations, we have demonstrated allosteric crosstalk within RBD in apo- and receptor-bound states where dynamic correlated motions and electrostatic energy perturbations contribute. While allostery, based on correlated motions, dominates inherent distal communication in apo-RBD, electrostatic energy perturbations determine favorable crosstalk within RBD upon binding to ACE2. Notably, allosteric path is constituted with evolutionarily conserved residues pointing towards their biological relevance. As revealed from recent structures, in the trimeric arrangement of spike, RBD of one copy interacts with S2 domain of another copy. Interestingly, the allosteric site identified is in direct contact (H-bonded) with a region in RBD that corresponds to the interacting region of RBD of one copy with S2 of another copy in trimeric constitution. Apparently, inter-monomer allosteric communication orchestrates concerted action of the trimer. Based on our results, we propose the allosteric loop of RBD as a potential drug target.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.09.07.286831v1?rss=1

Authors: Cheng, R. C., Krishnamoorti, A., Berka, V., Durham, R. J., Jayaraman, V., Maduke, M.

Abstract:

CLC transporters catalyze the exchange of chloride ions for protons across cellular membranes. As secondary active transporters, CLCs must alternately allow ion permeation to the extracellular and intracellular sides of the membrane, adopting outward-facing and inward-facing conformational states. Here, we use single-molecule Forster resonance energy transfer (smFRET) to monitor the conformational state of CLC-ec1, an E. coli homolog for which high-resolution structures of occluded and outward-facing states are known. Since each subunit within the CLC homodimer contains its own transport pathways for chloride and protons, we developed a labeling strategy to follow conformational change within a subunit, without crosstalk from the second subunit of the dimer. Using this strategy, we evaluated smFRET efficiencies for labels positioned on the extracellular side of the protein, to monitor the status of the outer permeation pathway. When [H+] is increased to enrich the outward-facing state, the smFRET efficiencies for this pair decrease. In a triple-mutant CLC-ec1 that mimics the protonated state of the protein and is known to favor the outward-facing conformation, the lower smFRET efficiency is observed at both low and high [H+]. These results confirm that the smFRET assay is following the transition to the outward-facing state and demonstrate the feasibility of using smFRET to monitor the relatively small (~1 Angstrom) motions involved in CLC transporter conformational change. Using the smFRET assay, we show that the conformation of the partner subunit does not influence the conformation of the subunit being monitored by smFRET, thus providing evidence for the independence of the two subunits in the transport process.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.09.07.285783v1?rss=1

Authors: Kosoglu, K., Omur, M. E., Jang, H., Nussinov, R., Keskin, O., Gursoy, A.

Abstract:

Ras proteins activate their effectors through physical interactions in response to the various extracellular stimuli at the plasma membrane. Oncogenic Ras forms dimer and nanoclusters at the plasma membrane, boosting the downstream MAPK signal. It was reported that K-Ras4B can dimerize through two major interfaces: (i) the effector lobe interface, mapped to Switch I and effector binding regions; (ii) the allosteric lobe interface involving 3 and 4 helices. Recent experiments showed that constitutively active, oncogenic mutant K-Ras4B G12D dimers are enriched in the plasma membrane. Here, we perform molecular dynamics simulations of K-Ras4B G12D homodimers aiming to quantify the two major interfaces in atomic level. To examine the effect of mutations on dimerization, two double mutations, K101D/R102E on the allosteric lobe and R41E/K42D on the effector lobe interfaces were added to the K-Ras4B G12D dimer simulations. We observed that the effector lobe K-Ras4B G12D dimer is stable, while the allosteric lobe dimer alters its helical interface during the simulations, presenting multiple conformations. The K101D/R102E mutations slightly weakens the allosteric lobe interface. However, the R41E/K42D mutations disrupt the effector lobe interface. Using the homo-oligomers prediction server, we obtained trimeric, tetrameric, and pentameric complexes with the allosteric lobe K-Ras4B G12D dimers. However, the allosteric lobe dimer with the K101D/R102E mutations is not capable of generating multiple higher order structures. Our detailed interface analysis may help to develop inhibitor design targeting functional Ras dimerization and high order oligomerization at the membrane signaling platform.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.09.07.286484v1?rss=1

Authors: Lovely, G. A., Braikia, F.-Z., Singh, A. K., Schatz, D., Murre, C., Liu, Z., Sen, R.

Abstract:

The RAG1 and RAG2 proteins introduce double-strand DNA breaks at antigen-receptor loci in developing lymphocytes to initiate V(D)J recombination. How RAG proteins find the correct target locus in a vast excess of non-specific chromatin is not known. Here we measured dynamics of RAG1/RAG2 interactions with chromatin in living pro-B cells. We found that the majority of RAG1 or RAG1/RAG2 complex is in a fast 3D diffusive state, and the residual slow diffusive (bound) fraction was determined by a non-core portion of RAG1, and the PHD domain of RAG2. The RAG proteins exhibited distinct dynamics at the IgH locus. In particular, RAG2 increased the probability of RAG1 binding to IgH, a property that likely explains its non-catalytic role in V(D)J recombination. Our observations reveal how RAG finds its targets in developing B cells.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.09.04.283341v1?rss=1

Authors: Clemens, L., Kutuzov, M., Bayer, K. V., Goyette, J., Allard, J., Dushek, O.

Abstract:

Immune receptor signalling proceeds by the binding of enzymes to their cytoplasmic tails before they catalyse reactions on substrates within reach. Studies of binding and catalysis have led to a binding- induced allosteric activation model for enzymes, such as SHP-1, whose catalytic activity increases upon recruitment to inhibitory receptors, such as PD-1. However, the impact of molecular reach is poorly understood. Here, we use surface plasmon resonance to measure binding, catalysis, and molecular reach for tethered SHP-1 reactions. We find a molecular reach for SHP-1 (13.0 nm) that is smaller than a maximum stretch estimate (20.4 nm) but larger than an estimate from crystal structure of the active conformation (5.3 nm), suggesting that SHP-1 explores a spectrum of active conformations. The molecular reach confines SHP-1 to a small membrane-proximal volume near its substrates leading membrane recruitment to increase its activity by a 1000-fold increase in concentration with a smaller 2-fold activity increase by PD-1 binding-induced allostery. Lastly, we use mathematical modelling to quantify the degree of co-clustering required for PD-1-SHP-1 complexes to reach their substrates.

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