Biology subjects

Jawaid, M. Z.

Publications and source records attributed to Jawaid, M. Z..

5 recordsLinked to original sources

bioRxiv2026

Computational Study of Antibody Binding to SARS-CoV-2 Variants

Background/ObjectivesThe unprecedented structural and binding data for antibodies to the SARS-COV2 virus taken together with the mutations for the spike protein allows for a broad simulation study of antibody-spike protein binding. This provides an understanding of the co-evolution of human immunity and viral immunity escape. MethodsWe utilized the YASARA molecular dynamics program to generate initial antibody-spike structures and simulate to equilibration for six SARS-COV2 variants and 10 different antibodies sampling two different binding regions to the receptor binding domain of the spike (especially for the Class I antibodies in the same part of the spike which attaches to the ACE2 receptor protein) and one to the N-terminal of the spike. Starting structures for antibody binding to variant spike proteins are perturbatively achieved through point mutations and insertions/deletions in the YASARA program. We employed YASARA to measure interfacial hydrogen bound counts between antibodies and variant spike proteins, and the HawkDock MMGBSA program to characterize trends in binding energies with mutation for four of the antibodies. We utilized the VMD program to analyze the time course of hydrogen bond populations. ResultsAs seen in previous studies, interfacial hydrogen bond counts serve as an excellent proxy for binding energies without the large systematic error inherent in the latter. We find that there is generally a decline in antibody binding strength, as measured by interfacial hydrogen bond counts, with viral evolution, but that a modest re-entrance of binding strength is present for most antibodies studied. Generically, the antibody heavy chain binds more strongly to the spike protein, through for approximately half the antibodies the light chain binding strength converges to the heavy chain strength with viral evolution. ConclusionsThe key conclusion is that the identified re-entrant immunity, speculatively arising from a balancing of maintenance of ACE2-spike binding while escaping antibodies through mutation, allows for some maintenance and even strengthening of immunity for later viral strains from early infection or vaccination.

biophysics↗

bioRxiv2023

Four-dimensional quantitative analysis of cell plate development using lattice light sheet microscopy identifies robust transition points between growth phases

Cell plate formation during cytokinesis entails multiple stages occurring concurrently and requiring orchestrated vesicle delivery, membrane remodeling, and timely polysaccharide deposition, such as callose. Such a dynamic process requires dissection in time and space; hence this has been a major hurdle in studying cytokinesis. Using lattice light sheet microscopy (LLSM) we studied cell plate development in four dimensions, monitored by the behavior of the cytokinesis specific GTPase RABA2a. We monitored the entire length of cell plate development, from its first emergence, with the aid of RABA2a, both in the presence and absence of cytokinetic callose. By developing a robust cytokinetic vesicle volume analysis, we identified distinct behavioral patterns allowing for the identification of three easily trackable, cell plate developmental phases. Notably, the phase transition between phase I and phase II is striking, indicating a switch from membrane accumulation to the recycling of excess membrane material. We interrogated the role of callose using pharmacological inhibition with LLSM and electron microscopy. Loss of callose inhibited phase transition, establishing quantitatively the critical role and timing of the polysaccharide in cell plate expansion and maturation. This study exemplifies the power of LLSM, combined with quantitative analysis to decode and untangle such a complex process. HighlightWe employed lattice light sheet 4D microscopy in plants to dissect cytokinesis, a multistage process involving orchestrating delivery of membranes and timely polysaccharide deposition. Robust quantitative analysis revealed distinct phase shifts, while inhibition of callose deposition abolished the phase transition.

plant biology↗

bioRxiv2023

Improving few-shot learning-based protein engineering with evolutionary sampling

Designing novel functional proteins remains a slow and expensive process due to a variety of protein engineering challenges; in particular, the number of protein variants that can be experimentally tested in a given assay pales in comparison to the vastness of the overall sequence space, resulting in low hit rates and expensive wet lab testing cycles. In this paper, we propose a few-shot learning approach to novel protein design that aims to accelerate the expensive wet lab testing cycle and is capable of leveraging a training dataset that is both small and skewed ({approx} 105 datapoints, < 1% positive hits). Our approach is composed of two parts: a semi-supervised transfer learning approach to generate a discrete fitness landscape for a desired protein function and a novel evolutionary Monte Carlo Markov Chain sampling algorithm to more efficiently explore the fitness landscape. We demonstrate the performance of our approach by experimentally screening predicted high fitness gene activators, resulting in a dramatically improved hit rate compared to existing methods. Our method can be easily adapted to other protein engineering and design problems, particularly where the cost associated with obtaining labeled data is significantly high. We have provided open source code for our method at https://github.com/SuperSecretBioTech/evolutionary_monte_carlo_search.

bioinformatics↗

bioRxiv2022

Computational study of the furin cleavage domain of SARS-CoV-2: delta binds strongest of extant variants

We demonstrate that AlphaFold and AlphaFold Multimer, implemented within the ColabFold suite, can accurately predict the structures of the furin enzyme with known six residue inhibitory peptides. Noting the similarity of the peptide inhibitors to polybasic furin cleavage domain insertion region of the SARS-CoV-2, which begins at P681, we implement this approach to study the wild type furin cleavage domain for the virus and several mutants. We introduce mutations in silico for alpha, omicron, and delta variants, for several sequences which have been rarely observed, for sequences which have not yet been observed, for other coronaviruses (NL63, OC43, HUK1a, HUK1b, MERS, and 229E), and for the H5N1 flu. We show that interfacial hydrogen bonds between the furin cleavage domain and furin are a good measure of binding strength that correlate well with endpoint binding free energy estimates, and conclude that among all candidate viral sequences studied, delta is near the very top binding strength within statistical accuracy. However, the binding strength of several rare sequences match delta within statistical accuracy. We find that the furin S1 pocket is optimized for binding arginine as opposed to lysine. This residue, typically at sequence position five, contains the most hydrogen bonds to the furin, and hydrogen bond count for just this residue shows a strong positive correlation with the overall hydrogen bond count. We demonstrate that the root mean square backbone C-alpha fluctuation of the first residue in the furin cleavage domain has a strong negative correlation with the interfacial hydrogen bond count. We show by considering the variation with the number of basic residues that the maximum mean number of interfacial hydrogen bonds expected is 15.7 at 4 basic residues.

biophysics↗

bioRxiv2020

A Biophysical Model for Plant Cell Plate Development

Plant cytokinesis, a fundamental process of plant life, involves de novo formation of a cell plate that partitions the cytoplasm of the dividing cell. Cell plate formation is directed by orchestrated delivery, fusion of cytokinetic vesicles, and membrane maturation to the form the nascent cell wall by the timely deposition of polysaccharides such as callose, cellulose, and crosslinking glycans. In contrast to the role of endomembrane protein regulators the role of polysaccharides, in cell plate development is poorly understood. Callose, a {beta}-1-3 glucan polymer, is transiently accumulated during cell plate expansion to be replaced by cellulose in mature stages. Based on the severity of cytokinesis defects in the absence of callose, it has been proposed that it stabilizes this membrane network structure. However, there is currently no theory to understand its role in cytokinesis. Here we extend the Helfrich free energy model for membranes including a phenomenological spreading force as an "areal pressure" generated by callose and/or other polysaccharides. Regular cell plate development in the model is possible, with suitable bending modulus, for a two-dimensional late stage spreading force parameter of between 2-6pN/nm, an osmotic pressure difference of 2-10kPa, and spontaneous curvature between 0-0.04nm-1. With these conditions, stable membrane conformation sizes and morphologies emerge in concordance with stages of cell plate development. With no spreading force, the cell plate fails to mature properly, corroborating experimental observations of cytokinesis arrest in the absence of callose. To reach a nearly mature cell plate, our model requires the late stage onset that the spreading force coupled with a concurrent loss of spontaneous curvature. A simple model based upon production of callose as a quasi-two-dimensional self-avoiding polymer produces the correct phenomenological form of the spreading force, which will be further refined, since matching to our numbers requires an exceptionally high callose synthesis rate. Significance StatementPlant cell division features the development of a unique membrane network called the cell plate that matures to a cell wall which separates the two daughter cells. During cell plate development, callose, a {beta}-1-3 glucan polymer, is transiently synthesized at the cell plate only to be replaced by cellulose in mature stages. The role for this transient callose accumulation at the cell plate is unknown. It has been suggested that callose provides mechanical stability, as well as a spreading force that widens and expands tubular and fenestrated cell plate structures to aid the maturation of the cell plate. Chemical inhibition of callose deposition results in the failure of cell plate development supporting this hypothesis. This publication establishes the need for a spreading force in cell plate development using a biophysical model that predicts cell plate development in the presence and the absence of this force. Such models can potentially be used to decipher for the transition/maturation of membrane networks upon the deposition of polysaccharide polymers.

biophysics↗