Sameer Varma
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Explore the profile of Sameer Varma including associated specialties, affiliations and a list of published articles.
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46
Citations
638
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Recent Articles
11.
Kriss C, Duro N, Nadeau O, Guergues J, Chavez-Chiang O, Culver-Cochran A, et al.
J Mass Spectrom
. 2021 May;
56(6):e4713.
PMID: 33942435
Oxidative and nitrative stress have been implicated in the molecular mechanisms underlying a variety of biological processes and disease states including cancer, aging, cardiovascular disease, neurological disorders, diabetes, and alcohol-induced...
12.
Delgado J, Duro N, Rogers D, Tkatchenko A, Pandit S, Varma S
Proteins
. 2021 Apr;
89(9):1134-1144.
PMID: 33864655
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has caused substantially more infections, deaths, and economic disruptions than the 2002-2003 SARS-CoV. The key to understanding SARS-CoV-2's higher infectivity lies partly in its...
13.
Rahman S, Wineman-Fisher V, Al-Hamdani Y, Tkatchenko A, Varma S
J Mol Biol
. 2020 Dec;
433(3):166745.
PMID: 33307090
Lysine methylation is a key regulator of protein-protein binding. The amine group of lysine can accept up to three methyl groups, and experiments show that protein-protein binding free energies are...
14.
Wineman-Fisher V, Delgado J, Nagy P, Jakobsson E, Pandit S, Varma S
J Chem Phys
. 2020 Sep;
153(10):104113.
PMID: 32933310
Therapeutic implications of Li, in many cases, stem from its ability to inhibit certain Mg-dependent enzymes, where it interacts with or substitutes for Mg. The underlying details of its action...
15.
Wineman-Fisher V, Al-Hamdani Y, Nagy P, Tkatchenko A, Varma S
J Chem Phys
. 2020 Sep;
153(9):094115.
PMID: 32891085
The reliability of molecular mechanics (MM) simulations in describing biomolecular ion-driven processes depends on their ability to accurately model interactions of ions simultaneously with water and other biochemical groups. In...
16.
Duro N, Varma S
Structure
. 2019 Aug;
27(10):1601-1611.e2.
PMID: 31402221
Complexity in understanding allosteric stimulation of the hemagglutinin-neuraminidase (HN) protein of paramyxoviruses by host sialic acids (SIAs) stems from (1) unavailability of structure in its SIA-bound state and (2) the...
17.
Kruczek J, Chiu S, Varma S, Jakobsson E, Pandit S
Langmuir
. 2019 Jul;
35(32):10522-10532.
PMID: 31337218
Li is a biologically active and medically important cation. Experiments show that Li modulates some phospholipid bilayer properties in a manner similar to divalent cations, rather than other monovalent cations....
18.
Wineman-Fisher V, Al-Hamdani Y, Addou I, Tkatchenko A, Varma S
J Chem Theory Comput
. 2019 Mar;
15(4):2444-2453.
PMID: 30830778
Ion descriptors in molecular mechanics models are calibrated against reference data on ion-water interactions. It is then typically assumed that these descriptors will also satisfactorily describe interactions of ions with...
19.
Saunders M, Steele M, Lavigne W, Varma S, Pandit S
Biochim Biophys Acta Biomembr
. 2019 Feb;
1861(5):907-915.
PMID: 30742804
A distinguishing feature of Archaeal plasma membranes is that their phospholipids contain ether-links, as opposed to bacterial and eukaryotic plasma membranes where phospholipids primarily contain ester-links. Experiments show that this...
20.
Botlani M, Siddiqui A, Varma S
J Chem Phys
. 2018 Jul;
148(24):241726.
PMID: 29960337
Many proteins are regulated by dynamic allostery wherein regulator-induced changes in structure are comparable with thermal fluctuations. Consequently, understanding their mechanisms requires assessment of relationships between and within conformational ensembles...