Biology subjects

Sowlati-Hashjin, S.

Publications and source records attributed to Sowlati-Hashjin, S..

6 recordsLinked to original sources

bioRxiv2023

ProteinVAE: Variational AutoEncoder forTranslational Protein Design

There have recently been rapid advances in deep learning models for protein design. To demonstrate proof-of-concept, these advancements have focused on small proteins with lots of data for training. This means that they are often not suitable for generating proteins with the most potential for high clinical impact -due to the additional challenges of sparse data and large size many therapeutically relevant proteins have. One major application that fits this category is gene therapy delivery. Viral vectors such as Adenoviruses and AAVs are a common delivery vehicle for gene therapy. However, environmental exposure means that most people exhibit potent pre-existing immune responses to many serotypes. This response, primarily driven by neutralizing antibodies, also precludes repeated administration with the same serotype. Rare serotypes, serotypes targeting other species, and capsid engineering, have all been deployed in the service of reducing neutralization by pre-existing antibodies. However, progress has been very limited using conventional methods and a new approach is urgently needed. To address this, we developed a variational autoencoder that can generate synthetic viral vector serotypes without epitopes for pre-existing neutralizing antibodies. A compact generative computational model was constructed, with only 12.4 million parameters that could be efficiently trained on the limited natural sequences (e.g., 711 natural Adenovirus hexon sequences with average length of 938 amino acids). In contrast to the current state-of-the-art, the model was able to generate high-quality Adenovirus hexon sequences that were folded with high confidence by Alphafold2 to produce structures essentially identical to natural hexon structures. Molecular dynamics simulations confirmed that the structures are stable and protein-protein interfaces are intact. Local secondary structure and local mobility is also comparable with natural serotype behavior. Our model could be used to generate a broad range of synthetic adenovirus serotype sequences without epitopes for pre-existing neutralizing antibodies in the human population. It could be used more broadly to generate different types of viral vector, and any large, therapeutically valuable proteins, where available data is sparse.

synthetic biology↗

bioRxiv2023

Systematically testing human HMBS missense variants to reveal mechanism and pathogenic variation

Defects in hydroxymethylbilane synthase (HMBS) can cause Acute Intermittent Porphyria (AIP), an acute neurological disease. Although sequencing-based diagnosis can be definitive, ~[1/3] of clinical HMBS variants are missense variants, and most clinically-reported HMBS missense variants are designated as "variants of uncertain significance" (VUS). Using saturation mutagenesis, en masse selection, and sequencing, we applied a multiplexed validated assay to both the erythroid-specific and ubiquitous isoforms of HMBS, obtaining confident functional impact scores for >84% of all possible amino-acid substitutions. The resulting variant effect maps generally agreed with biochemical expectation. However, the maps showed variants at the dimerization interface to be unexpectedly well tolerated, and suggested residue roles in active site dynamics that were supported by molecular dynamics simulations. Most importantly, these HMBS variant effect maps can help discriminate pathogenic from benign variants, proactively providing evidence even for yet-to-be-observed clinical missense variants.

molecular biology↗

bioRxiv2022

Identification of Catechins Binding Pockets in Monomeric Aβ42 Through Ensemble Docking and MD Simulations

The assembly of the Amyloid-{beta} peptide (A{beta}) into toxic oligomers and fibrils is associated with Alzheimers disease and dementia. Therefore, disrupting amyloid assembly by direct targeting of the A{beta} monomeric form with small molecules or antibodies is a promising therapeutic strategy. However, given the dynamic nature of A{beta}, standard computational tools cannot be easily applied for high-throughput structure-based virtual screening in drug discovery projects. In the current study, we propose a computational pipeline - in the framework of the ensemble docking strategy - to identify catechins binding pockets in monomeric A{beta}42. It is shown that both hydrophobic aromatic interactions and hydrogen bonding are crucial for the binding of catechins to A{beta}42. Also, it has been found that all the studied ligands, especially the EGCG, can act as potent inhibitors against amyloid aggregation by blocking the central hydrophobic region of the A{beta}. Our findings are evaluated and confirmed with multi-microsecond MD simulations. Finally, it is suggested that our proposed pipeline, with low computational cost in comparison with MD simulations, is a suitable approach for the virtual screening of ligand libraries against A{beta}.

biophysics↗

bioRxiv2021

Free energy and stacking of eumelaninnanoaggregates

Eumelanin, a member of the melanin family, is a black-brown insoluble pigment. It possesses a broad range of properties such as antioxidation, free radical scavenging, photo-protection, and charge carrier transportation. Surprisingly, the exact molecular structure of eumelanin remains undefined. It is, however, generally considered to consist of two main building blocks, 5,6-dihydroxyindole (DHI) and 5,6-dihydroxyindole carboxylic acid (DHICA). We focus on DHI and report, for the first time, a computational investigation of structural properties of DHI eumelanin aggregates in aqueous solutions. First, multi-microsecond molecular dynamics (MD) simulations at different concentrations were performed to investigate aggregation and ordering of tetrameric DHI-eumelanin protomolecules. This was followed by umbrella sampling (US) and density functional theory (DFT) calculations to study the physical mechanisms of stacking. Aggregation occurs through formation of nanoscale stacks and was observed in all systems. Further analyses showed that aggregation and coarsening of the domains is due to decrease in hydrogen bonds between the eumelanins and water; while domains exist, there is no long-range order. The results show non-covalent stacks with and interlayer distance between eumelanin protomolecules being less than 3.5 [A]. This is in good agreement with transmission electron microscopy data. Both free energy calculations and DFT revealed strong stacking interactions. The electrostatic potential map provides an explanation and a rationale for the slightly sheared relative orientations and, consequently, for the curved shapes of the nanoscale domains.

biophysics↗

bioRxiv2020

Insights into the Polyhexamethylene Biguanide (PHMB) Mechanism of Action on Bacterial Membrane and DNA: A Molecular Dynamics Study

Polyhexamethylene biguanide (PHMB) is a cationic polymer with antimicrobial and antiviral properties. It has been commonly accepted that the antimicrobial activity is due the ability of PHMB to perforate the bacterial phospholipid membrane leading ultimately to its death. In this study we show by the means of atomistic molecular dynamics (MD) simulations that while the PHMB molecules attach to the surface of the phospholipid bilayer and partially penetrate it, they do not cause any pore formation at least within the microsecond simulation times. The polymers initially adsorb onto the membrane surface via the favourable electrostatic interactions between the phospholipid headgroups and the biguanide groups, and then partially penetrate the membrane slightly disrupting its structure. This, however, does not lead to the formation of any pores. The microsecond-scale simulations reveal that it is unlikely for PHMB to spontaneously pass through the phospholipid membrane. Our findings suggest that PHMB translocation across the bilayer may take place through binding to the phospholipids. Once inside the cell, the polymer can effectively bind to DNA through extensive interactions with DNA phosphate backbone, which can potentially block the DNA replication process or activate DNA repair pathways. TOC Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=161 SRC="FIGDIR/small/007732v1_ufig1.gif" ALT="Figure 1"> View larger version (93K): org.highwire.dtl.DTLVardef@17c8c69org.highwire.dtl.DTLVardef@1e65ceeorg.highwire.dtl.DTLVardef@df0f42org.highwire.dtl.DTLVardef@62ba9a_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2018

The role of matrix-oriented salt-bridge on the proton transport in a multimeric uncoupling protein 2

Uncoupling proteins (UCPs) are members of the mitochondrial carrier family (MCF) that transport protons across the inner mitochondrial membrane, thereby uncoupling electron transport from ATP synthesis. The stoichiometry of UCPs, and the possibility of co-existence of this protein as mono-meric and associated forms in lipid membranes remain an intriguing open question. In the current study, the tertiary structure of UCP2 was analyzed both experimentally and through molecular dynamics (MD) simulations. After recombinant expression of UCP2 in the inner membrane of E. coli, the protein was directly extracted from the bacterial membranes with a non-denaturing detergent and purified both as a pure monomer and as a mixture of monomers, dimers and tetramers. Both protein preparations were re-constituted in egg yolk lipid vesicles. Gel electrophoresis, circular dichroism spectroscopy and fluorescence methods were used to characterize the structure and the proton transport function of protein. UCP2 showed unique stable tetrameric forms in lipid bilayers. MD simulations using membrane lipids and principal component analysis support the experimental results and provided new molecular insights into the nature of noncovalent interactions in oligomeric UCP2. MD simulations indicate that UCP2 tetramers are asymmetric dimers of dimers, in which the interactions between the monomers forming the dimer are stronger than the interactions between the dimers within the tetramer. It is also shown that UCP2 has a specific tendency to form functional tetramers in lipid bilayers, capable of proton transport. The asymmetric nature of the UCP2 tetramer could act as a scaffold for regulating the activity of the monomeric units through cooperative intercommunication between these subunits. Under similar experimental conditions, the structurally comparable ADP/ATP carrier protein did not form tetramers in vesicles, implying that spontaneous tetramerization cannot be generalized to all MCF members.\n\nSTATEMENT OF SIGNIFICANCESelf-assembly of membrane proteins plays a significant role in their biological function. In this article, both experimental and computational evidence are provided for spontaneous tetramerization of one of the mitochondrial uncoupling proteins (UCP2) in model lipid membranes. It is also shown that the tetrameric form of UCP2 is capable of proton transport, which leads to regulation of ATP synthesis in mitochondrion. Molecular dynamics simulations confirm the presence of asymmetric UCP2 tetramers as a potential scaffold for regulating the activity of the monomeric units through mutual intercommunication. The outcome of this study provides a solid ground for potential co-existence of monomeric and multimeric functional forms of UCPs that contributes to a deeper molecular insight into their structure and function.

biophysics↗