Author

U. L. Mallimadugula

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Biophysics· 4 Biochemistry· 1

Signature Assays, Organisms & Methods

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Assay:protein structure· 3 Approach:deep learning· 2 Research Focus:drug response / drug discovery· 2 Research Focus:protein folding & dynamics· 2 Approach:biophysical modeling· 1 Approach:experimental assay· 1 Research Focus:host-pathogen & immune response· 1 Organism:human· 1

Frequent Co-Authors

G. R. Bowman· 4 shared M. I. Zimmerman· 3 shared S. Singh· 3 shared J. R. Porter· 2 shared N. Vithani· 2 shared T. E. Frederick· 2 shared A. M. Harbison· 1 shared A. Meller· 1 shared

Activity by Year

2020-2022 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 31 mutual co-author links

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4 shared papersBiophysics

G. R. Bowman

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Author profile →

5 papers

Recent·Most cited

Apolipoprotein E4 has extensive conformational heterogeneity in lipid free and bound forms

M. D. Stuchell-Brereton, M. I. Zimmerman, J. J. Miller, U. L. Mallimadugula, J. J. Incicco, D. Roy, L. G. Smith, B. Baban, G. T. DeKoster, C. Frieden, G. R. Bowman, A. Soranno

This study uses single-molecule spectroscopy and molecular dynamics simulations to show that ApoE4 has extensive conformational heterogeneity in both lipid-free and lipid-bound states, differing from previous models.

bioRxiv · Feb 2, 2022Biophysics

Opening of a Cryptic Pocket in β-lactamase Increases Penicillinase Activity

C. R. Knoverek, U. L. Mallimadugula, S. Singh, E. Rennella, T. E. Frederick, T. Yuwen, S. Raavicharla, L. E. Kay, G. R. Bowman

The paper investigates how a cryptic pocket in β-lactamase, formed under the Ω-loop, enhances enzyme activity against penicillin, suggesting excited states can improve function.

bioRxiv · Apr 14, 2021Biophysics

A Parallel Ratchet-Stroke Mechanism Leads to an Optimum Force for Molecular Motor Function.

U. L. Mallimadugula, E. Galburt

This paper investigates a hypothetical molecular motor using parallel ratchet and stroke mechanisms, showing how such a system could achieve an optimal force for function and how to detect it experimentally.

bioRxiv · Jun 29, 2020 · PreprintBiophysics

SARS-CoV-2 Simulations Go Exascale to Capture Spike Opening and Reveal Cryptic Pockets Across the Proteome

M. I. Zimmerman, J. R. Porter, M. D. Ward, S. Singh, N. Vithani, A. Meller, U. L. Mallimadugula, C. E. Kuhn, J. H. Borowsky, R. P. Wiewiora, M. F. D. Hurley, A. M. Harbison, C. A. Fogarty, J. E. Coffland, E. Fadda, , G. R. Bowman

The paper uses exascale simulations to study SARS-CoV-2 protein dynamics, revealing cryptic epitopes and conformational changes that inform antiviral target design.

bioRxiv · Jun 27, 2020 · PreprintBiophysics

A cryptic pocket in Ebola VP35 allosterically controls RNA binding

M. A. Cruz, T. E. Frederick, U. L. Mallimadugula, S. Singh, N. Vithani, M. I. Zimmerman, J. R. Porter, K. E. Moeder, G. K. Amarasinghe, G. R. Bowman

This study identifies a cryptic pocket in Ebola VP35 that allosterically controls RNA binding, validated through simulations, experiments, and drug-like modifications.

bioRxiv · Feb 9, 2020Biochemistry