PaperPlayer biorxiv biophysics

Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.07.25.220962v1?rss=1

Authors: Sannigrahi, A., Chowdhury, S., Das, B., Banerjee, A., Halder, A., Naganathan, A. N., Karmakar, S., Chattopadhyay, K.

Abstract:

Aggregation of Cu-Zn superoxide dismutase (SOD1) is implicated in the motor neuron disease, ALS. Although more than 140 disease mutations of SOD1 are available, their stability or aggregation behaviors in membrane environment are not correlated with disease pathophysiology. Here, we use multiple mutational variants of SOD1 to show that the absence of Zn, and not Cu, significantly impacts membrane attachment of SOD1 through two loop regions facilitating aggregation driven by lipid induced conformational changes. These loop regions influence both the primary (through Cu intake) and the gain of function (through aggregation) of SOD1 presumably through a shared conformational landscape. Combining experimental and theoretical frameworks using representative ALS disease mutants, we develop a co-factor derived membrane association model wherein mutational stress closer to the Zn (but not to the Cu) pocket is responsible for membrane association mediated toxic aggregation and survival time scale after ALS diagnosis.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.07.26.202358v1?rss=1

Authors: Verzini, S., Shah, M., Theillet, F.-X., Belsom, A., Bieschke, J., Wanker, E. E., Rappsilber, J., Binolfi, A., Selenko, P.

Abstract:

Heterogeneous aggregates of the human protein -synuclein (Syn) are abundantly found in Lewy body inclusions of Parkinson's disease patients. While structural information on classical Syn amyloid fibrils is available, little is known about the conformational properties of disease-relevant, non-canonical aggregates. Here, we analyze the structural and dynamic properties of megadalton-sized dityrosine adducts of Syn that form in the presence of reactive oxygen species and cytochrome c, a proapoptotic peroxidase that is released from mitochondria during sustained oxidative stress. In contrast to canonical cross-{beta} amyloids, these aggregates retain high degrees of internal dynamics, which enables their characterization by solution-state NMR spectroscopy. We find that intermolecular dityrosine crosslinks restrict Syn motions only locally whereas large segments of concatenated molecules remain flexible and disordered. Indistinguishable aggregates form in crowded in vitro solutions and in complex environments of mammalian cell lysates, where relative amounts of free reactive oxygen species rather than cytochrome c are rate limiting. We further establish that dityrosine adducts inhibit classical amyloid formation by maintaining Syn in its monomeric form and that they are non-cytotoxic despite retaining basic membrane-binding properties. Our results suggest that oxidative oxidative Syn aggregation scavenges cytochrome c's activity into the formation of amorphous, high molecular-weight structures that may contribute to aggregate diversity in Lewy body deposits.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.07.26.221747v1?rss=1

Authors: Kang, Y., Wu, J.-X., Chen, L.

Abstract:

Resting membrane potential determines the excitability of the cell and is essential for the cellular electrical activities. NALCN channel mediates sodium leak currents, which positively tune the resting membrane potential towards depolarization. NALCN channel is involved in many important neurological processes and is implicated in a spectrum of neurodevelopmental diseases. Despite its functional importance, the mechanisms of ion permeation and voltage-modulation for NALCN channel remain elusive. Here, we report the cryo-EM structure of rat NALCN and mouse FAM155A complex to 2.7 [A] resolution. The structure reveals detailed interactions between NALCN and extracellular cysteine-rich domain of FAM155A. The non-canonical architecture of NALCN selectivity filter dictates its sodium selectivity and calcium block. The asymmetric arrangement of two functional voltage-sensors confers the modulation by membrane potential. Moreover, mutations found in human diseases were mapped to the domain-domain interfaces or the pore domain of NALCN, intuitively suggesting their pathological mechanisms.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.07.25.221416v1?rss=1

Authors: Cobarrubia, A., Tall, J., Crispin-Smith, A., Luque, A.

Abstract:

Mucus is a fluid that protects animals against pathogens while promoting interactions with commensal microbes. Changes in the diffusivity of particles in mucus alter viruses' infectivity, the efficiency of bacterial pathogens to invade a host, and the effectivity of drug delivery. Multiple physicochemical properties modulate the diffusion of microscopic particles in mucus, but their combined effect is unclear. Here, we analyzed the impact of particle size, charge, chemistry, anomalous diffusion exponent, and mucus composition in the diffusivity of particles from 106 published experiments. We used a time window sampling of one second to define a consistent, effective diffusion across experiments. The effective diffusion spanned seven orders of magnitude from 10-5 to 102 {micro}m2/s. The anomalous exponent was the strongest predictor among all variables tested. It displayed an exponential relationship with the effective diffusion that explained 90% of the empirical data variance. We showed that the relationship and dominance of the anomalous diffusion exponent resulted from a general mathematical relationship obtained from first-principles for any subdiffusion mechanism. Our derivation demonstrated that the generalized diffusion coefficient is not a measurable physical quantity and must be replaced by the length and time scales associated with the underlying mobility mechanisms. This led us to a fundamental reformulation of the classic subdiffusion equation, which calls for a reinterpretation of anomalous diffusion in physical systems. We also discussed how our results impact the characterization of microscopic particle diffusion in mucus and other hydrogels.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.07.24.220665v1?rss=1

Authors: Bhopatkar, A. A., Rangachari, V.

Abstract:

Granulins (GRN 1-7) are short (~6 kDa), cysteine-rich proteins that are generated upon the proteolytic processing of progranulin (PGRN). These modules, along with their precursor, have been implicated in multiple pathophysiological roles, especially in neurodegenerative diseases. Our previous investigations into GRN-3 and GRN-5 reveal them to be fully disordered in the reduced form and implicate redox sensitive attributes to the proteins. Such redox-dependent modulation has become associated with proteins involved in oxidative stress regulation and maintaining metal-homeostasis within cells. To probe whether GRNs play a contributory role in such functions, we tested the metal binding potential of the reduced form of GRNs -3 and -5 under neutral and acidic pH mimicking cytosolic and lysosomal conditions, respectively. We found, at neutral pH, both GRNs selectively bind Cu(II) and no other divalent cations. Binding of Cu(II) also partly triggered the oxidative multimerization of GRNs via uncoordinated cystines at both pH conditions. Furthermore, binding did not induce gain in secondary structure and the protein remained disordered. Overall, the results indicate that GRN-3 and -5 have a surprisingly strong affinity for Cu(II) in the pM range, comparable to known copper sequestering proteins. This data also hints at a potential of GRNs to reduce Cu(II) to Cu(I), a process that has significance in mitigating Cu-induced ROS cytotoxicity in cells. Together, this report uncovers a metal-coordinating capability of GRNs for the first time, which could have profound significance in their structure and function.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.07.26.219741v1?rss=1

Authors: Mansbach, R. A., Chakraborty, S., Nguyen, K., Montefiori, D., Korber, B., Gnanakaran, S.

Abstract:

The COVID-19 pandemic underwent a rapid transition with the emergence of a SARS-CoV-2 variant that carried the amino acid substitution D614G in the Spike protein that became globally prevalent. The G-form is both more infectious in vitro and associated with increased viral loads in infected people. To gain insight into the mechanism underlying these distinctive characteristics, we employed multiple replicas of microsecond all-atom simulations to probe the molecular-level impact of this substitution on Spike closed and open states. The open state enables Spike interactions with its human cellular receptor, ACE2. Here we show that changes in the inter-protomer energetics due to the D614G substitution favor a higher population of infection-capable (open) states. The inter-protomer interactions between S1 and S2 subunits in the open state of the D-form are asymmetric. This asymmetry is resolved in the G-form due to the release of tensile hydrogen bonds resulting in an increased population of open conformations. Thus, the increased infectivity of the G-form is likely due to a higher rate of profitable binding encounters with the host receptor. It is also predicted to be more neutralization sensitive due to enhanced exposure of the receptor binding domain, a key target region for neutralizing antibodies.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.07.26.222273v1?rss=1

Authors: Liao, X., Purohit, P. K., Gopinath, A.

Abstract:

Intracellular elastic filaments such as microtubules are subject to thermal Brownian noise and active noise generated by molecular motors that convert chemical energy into mechanical work. Similarly, polymers in living fluids such as bacterial suspensions and swarms suffer bending deformations as they interact with single bacteria or with cell clusters. Often these filaments perform mechanical functions and interact with their networked environment through cross-links, or have other similar constraints placed on them. Here we examine the mechanical properties - under tension - of such constrained active filaments under canonical boundary conditions motivated by experiments. Fluctuations in the filament shape are a consequence of two types of random forces - thermal Brownian forces, and activity derived forces with specified time and space correlation functions. We derive force-extension relationships and expressions for the mean square deflections for tethered filaments under various boundary conditions including hinged and clamped constraints. The expressions for hinged-hinged boundary conditions are reminiscent of the worm-like-chain model and feature effective bending moduli and mode-dependent non-thermodynamic effective temperatures controlled by the imposed force and by the activity. Our results provide methods to estimate the activity by measurements of the force- extension relation of the filaments or their mean-square deflections which can be routinely performed using optical traps, tethered particle experiments, or other single molecule techniques.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.07.24.218958v1?rss=1

Authors: Xie, J., Ke, M., Xu, L., Lin, S., Zhang, J., Yang, F., Wu, J., Yan, Z.

Abstract:

NALCN, a sodium leak channel mainly expressed in the central nervous systems, is responsible for the resting Na+ permeability that controls neuronal excitability. Dysfunctions of the NALCN channelosome, NALCN with several auxiliary subunits, are associated with a variety of human diseases. Here, we reported the cryo-EM structure of human NALCN in complex with FAM155A, at an overall resolution of 3.1 angstrom. FAM155A forms extensive interactions with the extracellular loops of NALCN that help stabilize NALCN in the membrane. A Na+ ion-binding site, reminiscent of a Ca2+ binding site in Cav channels, is identified in the unique EEKE selectivity filter. Despite its 'leaky' nature, the intracellular gate is sealed by S6I, II-III linker and III-IV linker. Our study establishes the molecular basis of Na+ permeation and voltage sensitivity, and provides important clues to the mechanistic understanding of NALCN regulation and NALCN channelosome-related diseases.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.07.22.216952v1?rss=1

Authors: Caruso, I. P., Guimaraes, G. C., Machado, V. B., Fossey, M. A., Willbold, D., Almeida, F. C. L., Souza, F. P.

Abstract:

The human Respiratory Syncytial Virus (hRSV) M2-1 protein functions as a processivity and antitermination factor of the viral polymerase complex. Here it is presented the first evidence that hRSV M2-1 core domain (cdM2-1) alone has an unfolding activity for long RNAs, as well as a biophysical and dynamic characterization of the cdM2-1/RNA complex. The main contact region of cdM2-1 with RNA was the 1-2-5-6 helix bundle, which suffered local conformational changes and promoted the RNA unfolding activity. This activity may be triggered by base-pairing recognition. RNA molecules wrap around the whole cdM2-1, protruding their terminals over the domain. The 2-3 and 3-4 loops of cdM2-1 were marked by an increase in picosecond internal motions upon RNA binding even though they are not directly involved in the interaction. The results revealed that the cdM2-1/RNA complex originates from a fine-tuned binding, contributing to unraveling interaction aspects necessary to M2-1 activity.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.07.23.216341v1?rss=1

Authors: Alavizargar, A., Keller, F., Heuer, A.

Abstract:

Cholesterol and ergosterol are two dominant sterols in the membranes of eukaryotic and yeast cells, respectively. Although their chemical structure is very similar, their impact on the structure and dynamics of membranes differs.In this work, we have explored the effect of these two sterols on binary mixtures with 1,2-dipalnitoyl-sn-glycerol-3-phosphocholine (DPPC) lipid bilayer at various sterol concentration and temperatures, employing molecular dynamics simulations. The simulations revealed that cholesterol has a stronger impact on the ordering of the lipid chains and leads to more condensed membranes with respect to ergosterol. This difference likely arises from a more planar structure of the ring part as well as the better alignment of cholesterol among the DPPC chains with respect to ergosterol. The degree of the planarity of the ring system affects the orientation of the methyl groups on the rough side and distribute the lipid chains on the two sides of the sterols differently. Similar to the structural observations, cholesterol also has a stronger influence on the dynamics, and consistently, establishes stronger DPPC-sterol interactions when compared to ergosterol. Although our findings are consistent with some previous simulations as well as recent experiments, they are at odds with some other studies. Therefore, the presented results may shed new lights on the impact of sterols on the saturated lipids bilayers with implications for binary mixtures of lipids as well as lipid rafts.

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