Biology subjects

Gosavi, S.

Publications and source records attributed to Gosavi, S..

5 recordsLinked to original sources

bioRxiv2026

SuBMIT: A Software Toolkit for Facilitating Simulations of Coarse-Grained Structure-Based Models of Biomolecules.

Coarse-grained structure-based models (CG-SBMs; or G[o] models) are simplified potential energy functions of biomolecules or biomolecular complexes that encode their structure. Molecular dynamics simulations of such SBMs have been successfully used to study long time-scale dynamics such as protein and RNA folding, and large conformational transitions of biomolecular complexes. SBMs have several advantages: (1) Their MD simulations are computationally inexpensive, making extensive sampling easily accessible to many researchers. (2) They are easy to modify and can be adapted for the specific biomolecular problem that needs to be investigated. However, the force-fields of SBMs are not usually included in commonly used biomolecular simulation packages resulting in a barrier to their use. Here, we present SuBMIT (Structure Based Models Input Toolkit; https://github.com/sglabncbs/submit), a toolkit for generating coarse-grained SBM input files for performing MD simulations with GROMACS and OpenMM/OpenSMOG. Simulations whose input files can be generated using the different flavors of CG-SBMs present in SuBMIT include the folding and conformational ensembles of proteins with intrinsically disordered regions, 3D-domain-swapping in proteins and the dynamics of RNA-protein assemblies (e.g., simple RNA viruses).

biophysics↗

bioRxiv2026

The transmembrane domain regulates the kinetics of the SARS-CoV-2 spike conformational transition

ABSTRACTThe homotrimeric SARS-CoV-2 spike glycoprotein comprises two subunits: S1, which recognizes host-receptors through its receptor-binding domains (RBDs), and S2, anchored to the viral membrane through its transmembrane domain (TMD), which facilitates the fusion of the viral envelope with the host cell membrane. Upon host-receptor engagement and proteolytic activation, S1 dissociates and triggers a large conformational transition in S2, involving structural rearrangements in the S2 ectomembrane-domains and the TMD. While studies have focused on the ectomembrane-domain dynamics, the TMD has typically been modeled as being in a trimeric state. Here, we use molecular dynamics simulations of a coarse-grained structure-based model (SBM) with an implicit membrane to investigate the role of TMD dynamics in modulating S2 conformational conversion. We first recapitulate previous results from an all-atom SBM with a trimeric TMD and re-emphasize that the extended pre-hairpin intermediate state of S2, which brings the two membranes into apposition, is a byproduct of the prefusion-to-postfusion transition. Next, by introducing dynamics into the TMD, we find a late fusion intermediate structurally similar to a recent cryo-EM structure. A dynamic TMD also makes the conformational transition faster. Simulations including the S1/S2 complex reveal coupled RBD-TMD dynamics: when all three RBDs are in the closed state, they can stabilize the TMD in a trimeric configuration, whereas the opening of a single RBD can trigger a transition to a dynamic TMD. So, the dynamics and the conformational preferences of the TMD can be tuned by the presence and conformation of S1. There is some evidence that the TMDs of class I viral fusion proteins, such as spike, contribute to viral fusion by modulating membrane properties. Our simulations indicate an expanded role for the function of the TMD, where it can directly regulate the kinetics of S2 conformational transitions. SIGNIFICANCE STATEMENTThe SARS-CoV-2 fusion protein, spike, undergoes a large conformational transition, which facilitates the fusion of the viral and host-cell membranes and the delivery of the viral genome into the host cell. Despite extensive studies of the spike conformational conversion, its transmembrane domain (TMD) has largely been viewed as a viral membrane anchor. Using coarse-grained structure-based model simulations, we show that TMD dynamics can modulate the timing of the spike-S2 (fusion subunit) prefusion-to-postfusion conformational conversion. The presence of spike-S1 (receptor-recognition subunit) can suppress TMD dynamics, potentially reducing the rate of spike conformational conversion and viral fusion. Thus, the spike TMD regulates the kinetics of spike-mediated membrane fusion, and TMD-targeting strategies can be an additional avenue for antiviral intervention.

biophysics↗

bioRxiv2025

The longer transmembrane helices of class I viral fusion proteins may facilitate viral fusion

The viral envelope-resident viral fusion proteins (VFPs) fuse the envelope with the host cell membrane, which allows virus entry into host cells. The homotrimeric class I VFPs (cI-VFPs) are anchored to the envelope by three single-pass transmembrane helices (spTMHs). It is generally accepted that the hydrophobic length of a TMH matches the thickness of the hydrophobic membrane core, and this reduces TMH dynamics by stabilizing both the TMHs and the membrane. However, to enable fusion, a cI-VFP undergoes a large conformational transition which includes the disassembly of the spTMHs from a pre-fusion trimer and their subsequent reassembly with the cI-VFP fusion peptides into a post-fusion complex. Given the potential functional relevance of the cI-VFP spTMH disassembly-reassembly dynamics, we hypothesized that these spTMH lengths may be mismatched with the thickness of biological membranes. Here, we examine the predicted lengths of a curated dataset of cI-VFP spTMHs and find that they are indeed about 10% longer than the hydrophobic thickness of model membranes. The cI-VFP spTMHs are on average also longer than the spTMHs of human fusion and human non-fusion proteins. Since our dataset contains cI-VFPs from diverse enveloped viruses, and viral proteins are fast evolving, we conclude that the longer spTMHs are functionally relevant and thus, preserved. Our observation that the spTMH lengths of retrovirus-derived human fusogenic proteins, syncytins, are similar to those of cI-VFPs, supports this conclusion. The longer spTMHs may facilitate the cI-VFP conformational change and perturb the fusing membrane, reducing the barrier to fusion.

biochemistry↗

bioRxiv2021

Dynamics and self-assembly of the SARS-CoV-2 spike transmembrane domain

The homotrimeric SARS-CoV-2 spike protein enables viral infection by mediating the fusion of the viral envelope with the host membrane. The spike protein is anchored to the SARS-CoV-2 envelope by its transmembrane domain (TMD), which is composed of three TM helices, each contributed by one of the protomers of the homotrimeric spike. Although the TMD is important for SARS-CoV-2 viral fusion and is well-conserved across the Coronaviridae family, it is unclear whether it is a passive anchor of the spike or actively promotes viral fusion. Specifically, the nature of the TMD dynamics and how these dynamics couple to the large pre- to post-fusion conformational transition of the spike ectomembrane domains remains unknown. Here, we computationally study the SARS-CoV-2 spike TMD in both homogenous POPC and cholesterol containing membranes to characterize its structure, dynamics, and self-assembly. Different tools identify distinct segments of the spike sequence as its TM helix. Atomistic simulations of a spike protomer segment that includes the superset of the TM helix predictions show that the membrane-embedded TM sequence bobs, tilts and gains and loses helicity at the membrane edges. Coarse-grained multimerization simulations using representative TM helix structures from the atomistic simulations exhibit diverse trimer populations whose architecture depends on the structure of the TM helix protomer. Multiple overlapping and conflicting dimerization interfaces stabilized these trimeric populations. An asymmetric conformation is populated in addition to a symmetric conformation and several in-between trimeric conformations. While the symmetric conformation reflects the symmetry of the resting spike, the asymmetric TMD conformation could promote viral membrane fusion through the stabilization of a fusion intermediate. Together, our simulations demonstrate that the SARS-CoV-2 spike TM anchor sequence is inherently dynamic, trimerization does not abrogate these dynamics and the various observed TMD conformations may enable viral fusion.

biophysics↗

bioRxiv2020

Rational design of protein-specific folding modifiers

Protein folding can go wrong in vivo and in vitro, with significant consequences for the living cell and the pharmaceutical industry, respectively. Here we propose a general design principle for constructing small peptide-based protein-specific folding modifiers. We construct a xenonucleus, which is a pre-folded peptide that resembles the folding nucleus of a protein, and demonstrate its activity on the folding of ubiquitin. Using stopped-flow kinetics, NMR spectroscopy, Forster Resonance Energy transfer, single-molecule force measurements, and molecular dynamics simulations, we show that the ubiquitin xenonucleus can act as an effective decoy for the native folding nucleus. It can make the refolding faster by 33 {+/-} 5% at 3 M GdnHCl. In principle, our approach provides a general method for constructing specific, genetically encodable, folding modifiers for any protein which has a well-defined contiguous folding nucleus.

biophysics↗