Sudeep Sarma

Works (7)

Updated: August 20th, 2024 05:01

2024 journal article

Design of parallel β-sheet nanofibrils using Monte Carlo search, coarse-grained simulations, and experimental testing

PROTEIN SCIENCE, 33(8).

By: S. Sarma n, T. Sudarshan*, V. Nguyen n, A. Robang *, X. Xiao n, J. Le*, M. Helmicki*, A. Paravastu *, C. Hall n 

author keywords: amyloid beta-sheet fibrils; DMD/PRIME20 simulations; peptide assembly design; peptide self-assembly
topics (OpenAlex): Supramolecular Self-Assembly in Materials; Polydiacetylene-based materials and applications; Lipid Membrane Structure and Behavior
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Sources: Web Of Science, NC State University Libraries
Added: August 14, 2024

2023 journal article

Design of 8-mer peptides that block <i>Clostridioides difficile</i> toxin A in intestinal cells

COMMUNICATIONS BIOLOGY, 6(1).

By: S. Sarma n, C. Catella n, E. San Pedro*, X. Xiao n, D. Durmusoglu n, S. Menegatti n , N. Crook n , S. Magness*, C. Hall n 

topics (OpenAlex): Clostridium difficile and Clostridium perfringens research; Microscopic Colitis; Toxin Mechanisms and Immunotoxins
TL;DR: An approach that combines a Pep tide B inding D esign (PepBD) algorithm, molecular-level simulations, a rapid screening assay, and surface plasmon resonance (SPR) measurements to develop peptide inhibitors that block Toxin A in colon epithelial cells is described. (via Semantic Scholar)
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Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 27, 2023

2022 journal article

<p>De novo discovery of peptide-based affinity ligands for the fab fragment of human immunoglobulin G</p>

JOURNAL OF CHROMATOGRAPHY A, 1669.

By: X. Xiao n, R. Kilgore n, S. Sarma n, W. Chu n, S. Menegatti n  & C. Hall n 

author keywords: Affinity ligands; Ligand design; Biorecognition; Protein chromatography; Fragment antigen binding
MeSH headings : Humans; Immunoglobulin Fab Fragments / chemistry; Immunoglobulin G; Ligands; Peptides; Tissue Distribution
topics (OpenAlex): Monoclonal and Polyclonal Antibodies Research; Protein purification and stability; Glycosylation and Glycoproteins Research
TL;DR: An integrated computational and experimental scheme is described to de novo design 9-mer peptides that bind to Fab fragments that lay the groundwork for future development of these ligands towards biomanufacturing translation. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: May 2, 2022

2022 journal article

Computational Design and Experimental Validation of ACE2-Derived Peptides as SARS-CoV-2 Receptor Binding Domain Inhibitors

JOURNAL OF PHYSICAL CHEMISTRY B, 126(41), 8129–8139.

By: S. Sarma, S. Herrera, X. Xiao, G. Hudalla & C. Hall 

topics (OpenAlex):
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Sources: Web Of Science, NC State University Libraries
Added: November 7, 2022

2022 article

Computational Design and Experimental Validation of ACE2-Derived Peptides as SARS-CoV-2 Receptor Binding Domain Inhibitors

Sarma, S., Herrera, S. M., Xiao, X., Hudalla, G. A., & Hall, C. K. (2022, October 11). JOURNAL OF PHYSICAL CHEMISTRY B, Vol. 10.

By: S. Sarma n, S. Herrera*, X. Xiao  n, G. Hudalla * & C. Hall n 

MeSH headings : Humans; Angiotensin-Converting Enzyme 2; SARS-CoV-2; Spike Glycoprotein, Coronavirus / chemistry; Pandemics; Tryptophan / metabolism; COVID-19; Protein Binding; Peptides / metabolism
topics (OpenAlex): SARS-CoV-2 and COVID-19 Research; Computational Drug Discovery Methods; vaccines and immunoinformatics approaches
TL;DR: Data show that while relatively short unstructured peptides can bind to SARS-CoV-2 RBD with moderate affinity, they are incapable of outcompeting the strong interactions between RBD and ACE2. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: November 7, 2022

2022 journal article

Sequence patterns and signatures: Computational and experimental discovery of amyloid-forming peptides

PNAS NEXUS, 1(5).

By: X. Xiao n, A. Robang *, S. Sarma n, J. Le*, M. Helmicki*, M. Lambert*, R. Guerrero-Ferreira *, J. Arboleda-Echavarria*, A. Paravastu *, C. Hall n 

author keywords: peptide assembly design; discontinuous molecular dynamics; amyloid-forming peptides; fourier-transform infrared spectroscopy; transmission electron microscopy
topics (OpenAlex): Supramolecular Self-Assembly in Materials; Polydiacetylene-based materials and applications; Chemical Synthesis and Analysis
TL;DR: Experimental results from Fourier transform infrared spectroscopy, thioflavin T (ThT) fluorescence, circular dichroism (CD), and transmission electron microscopy, indicate that all the peptides predicted to assemble in silico assemble into antiparallel β-sheet nanofibers in a concentration-dependent manner. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: October 23, 2023

2021 article

In Silico Identification and Experimental Validation of Peptide-Based Inhibitors Targeting Clostridium difficile Toxin A

Xiao, X., Sarma, S., Menegatti, S., Crook, N., Magness, S. T., & Hall, C. K. (2021, December 29). ACS CHEMICAL BIOLOGY, Vol. 17.

By: X. Xiao n, S. Sarma n, S. Menegatti n , N. Crook n , S. Magness* & C. Hall n 

MeSH headings : Bacterial Toxins / antagonists & inhibitors; Bacterial Toxins / chemistry; Computer Simulation; Drug Design; Enterotoxins / antagonists & inhibitors; Enterotoxins / chemistry; Models, Molecular; Peptides / chemistry; Peptides / pharmacology; Protein Binding; Protein Conformation; Protein Domains; Reproducibility of Results
topics (OpenAlex): Clostridium difficile and Clostridium perfringens research; Viral gastroenteritis research and epidemiology; Toxin Mechanisms and Immunotoxins
TL;DR: This work used a computational strategy that integrates a peptide binding design algorithm and explicit-solvent atomistic molecular dynamics simulation to determine promising toxin A-targeting peptides that can recognize and bind to the catalytic site of the TcdA glucosyltransferase domain (GTD). (via Semantic Scholar)
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Sources: Web Of Science, ORCID, NC State University Libraries
Added: December 30, 2021

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