Search Results - "Thomas, Leonard M."

Iterative approach to computational enzyme design by Privett, Heidi K, Kiss, Gert, Lee, Toni M, Blomberg, Rebecca, Chica, Roberto A, Thomas, Leonard M, Hilvert, Donald, Houk, Kendall N, Mayo, Stephen L

“…A general approach for the computational design of enzymes to catalyze arbitrary reactions is a goal at the forefront of the field of protein design. Recently,…”
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Kinetic, spectral, and structural studies of the slow-binding inhibition of the Escherichia coli dihydrodipicolinate synthase by 2, 4-oxo-pentanoic acid by Karsten, William, Thomas, Leonard M., Fleming, Christian, Seabourn, Priscilla, Bruxvoort, Christina, Chooback, Lilian

“…Dihydrodipicolinate synthase (DHDPS) catalyzes the first step in the biosynthetic pathway for production of l-lysine in bacteria and plants. The enzyme has…”
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Crystal Structure of Prostate-Specific Membrane Antigen, a Tumor Marker and Peptidase by Davis, Mindy I., Bennett, Melanie J., Thomas, Leonard M., Bjorkman, Pamela J.

“…Prostate-specific membrane antigen (PSMA) is highly expressed in prostate cancer cells and nonprostatic solid tumor neovasculature and is a target for…”
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Crystal structure of HLA-A2 bound to LIR-1, a host and viral major histocompatibility complex receptor by Bjorkman, Pamela J, Willcox, Benjamin E, Thomas, Leonard M

“…Leukocyte immunoglobulin-like receptor 1 (LIR-1), an inhibitory receptor expressed on monocytes, dendritic cells and lymphocytes, regulates cellular function…”
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Distal Pocket Control of Nitrite Binding in Myoglobin by Yi, Jun, Thomas, Leonard M., Richter-Addo, George B.

“…Who is in charge? Nitrite linkage isomerism in the same heme protein occurs as a function of the compound preparation method. An N‐bound nitrite conformation…”
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Structure of a Cofactor-Deficient Nitrogenase MoFe Protein by Schmid, Benedikt, Ribbe, Markus W., Einsle, Oliver, Yoshida, Mika, Thomas, Leonard M., Dean, Dennis R., Rees, Douglas C., Burgess, Barbara K.

“…One of the most complex biosynthetic processes in metallobiochemistry is the assembly of nitrogenase, the key enzyme in biological nitrogen fixation. We…”
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Ternary complexes of isopentenyl phosphate kinase from Thermococcus paralvinellae reveal molecular determinants of non‐natural substrate specificity by Johnson, Bryce P., Mandal, Prashant S., Brown, Sara M., Thomas, Leonard M., Singh, Shanteri

“…Isopentenyl phosphate kinases (IPKs) have recently garnered attention for their central role in biocatalytic “isoprenol pathways,” which seek to reduce the…”
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The nitrosoamphetamine metabolite is accommodated in the active site of human hemoglobin: Spectroscopy and crystal structure by Powell, Samantha M., Thomas, Leonard M., Richter-Addo, George B.

“…Amphetamine-based (Amph) drugs are metabolized in humans to their hydroxylamine (AmphNHOH) and nitroso (AmphNO) derivatives. The latter metabolites are known…”
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Molecular Basis for the Substrate Promiscuity of Isopentenyl Phosphate Kinase from Candidatus methanomethylophilus alvus by Johnson, Bryce P, Kumar, Vikas, Scull, Erin M, Thomas, Leonard M, Bourne, Christina R, Singh, Shanteri

“…Isopentenyl phosphate kinases (IPKs) catalyze the ATP-dependent phosphorylation of isopentenyl monophosphate (IP) to isopentenyl diphosphate (IPP) in the…”
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Insights into Nitrosoalkane Binding to Myoglobin Provided by Crystallography of Wild-Type and Distal Pocket Mutant Derivatives by Herrera, Viridiana E., Charles, Tatyana P., Scott, Tiala G., Prather, Kiana Y., Nguyen, Nancy T., Sohl, Christal D., Thomas, Leonard M., Richter-Addo, George B.

“…Nitrosoalkanes (R–NO; R = alkyl) are biological intermediates that form from the oxidative metabolism of various amine (RNH2) drugs or from the reduction of…”
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Crystal structure of a putative 3‐hydroxypimelyl‐CoA dehydrogenase, Hcd1, from Syntrophus aciditrophicus strain SB at 1.78 Å resolution by Dinh, David M., Thomas, Leonard M., Karr, Elizabeth A.

“…Syntrophus aciditrophicus strain SB is a model syntroph that degrades benzoate and alicyclic acids. The structure of a putative 3‐hydroxypimelyl‐CoA…”
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Nitrosyl Myoglobins and Their Nitrite Precursors: Crystal Structural and Quantum Mechanics and Molecular Mechanics Theoretical Investigations of Preferred Fe–NO Ligand Orientations in Myoglobin Distal Pockets by Wang, Bing, Shi, Yelu, Tejero, Jesús, Powell, Samantha M, Thomas, Leonard M, Gladwin, Mark T, Shiva, Sruti, Zhang, Yong, Richter-Addo, George B

“…The globular dioxygen binding heme protein myoglobin (Mb) is present in several species. Its interactions with the simple nitrogen oxides, namely, nitric oxide…”
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Crystal structural investigations of heme protein derivatives resulting from reactions of aryl- and alkylhydroxylamines with human hemoglobin by Powell, Samantha M., Wang, Bing, Herrera, Viridiana E., Prather, Kiana Y., Nguyen, Nancy T., Abucayon, Erwin G., Thomas, Leonard M., Safo, Martin K., Richter-Addo, George B.

“…Phenylhydroxylamine (PhNHOH) and nitrosobenzene (PhNO) interact with human tetrameric hemoglobin (Hb) to form the nitrosobenzene adduct Hb(PhNO). These…”
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Inhibitor design to target a unique feature in the folate pocket of Staphylococcus aureus dihydrofolate reductase by Muddala, N. Prasad, White, John C., Nammalwar, Baskar, Pratt, Ian, Thomas, Leonard M., Bunce, Richard A., Berlin, K. Darrell, Bourne, Christina R.

“…Staphylococcus aureus (Sa) is a serious concern due to increasing resistance to antibiotics. The bacterial dihydrofolate reductase enzyme is effectively…”
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Organometallic myoglobins: Formation of Fe–carbon bonds and distal pocket effects on aryl ligand conformations by Wang, Bing, Thomas, Leonard M., Richter-Addo, George B.

“…Bioorganometallic Fe–C bonds are biologically relevant species that may result from the metabolism of natural or synthetic hydrazines. The molecular structures…”
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Using Molecular Dynamics Simulations as an Aid in the Prediction of Domain Swapping of Computationally Designed Protein Variants by Mou, Yun, Huang, Po-Ssu, Thomas, Leonard M., Mayo, Stephen L.

“…In standard implementations of computational protein design, a positive-design approach is used to predict sequences that will be stable on a given backbone…”
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Degradation of human hemoglobin by organic C-nitroso compounds by Yi, Jun, Ye, Guan, Thomas, Leonard M, Richter-Addo, George B

“…The crystal structure of the nitrosomethane adduct of human Hb shows N-binding of the MeNO ligands to heme Fe. The structure of the EtNO adduct reveals a…”
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Structures and Energetics of Four Adjacent G·U Pairs That Stabilize an RNA Helix by Gu, Xiaobo, Mooers, Blaine H. M, Thomas, Leonard M, Malone, Joshua, Harris, Steven, Schroeder, Susan J

“…Consecutive G·U base pairs inside RNA helices can be destabilizing, while those at the ends of helices are thermodynamically stabilizing. To determine if this…”
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Nitrosoamphetamine binding to myoglobin and hemoglobin: Crystal structure of the H64A myoglobin-nitrosoamphetamine adduct by Wang, Bing, Powell, Samantha M., Guan, Ye, Xu, Nan, Thomas, Leonard M., Richter-Addo, George B.

“…N-hydroxyamphetamine (AmphNHOH) is an oxidative metabolite of amphetamine and methamphetamine. It is known to form inhibitory complexes upon binding to heme…”
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Crystal structure and DNA binding activity of a PadR family transcription regulator from hypervirulent Clostridium difficile R20291 by Isom, Catherine E, Menon, Smita K, Thomas, Leonard M, West, Ann H, Richter-Addo, George B, Karr, Elizabeth A

“…Clostridium difficile is a spore-forming obligate anaerobe that can remain viable for extended periods, even in the presence of antibiotics, which contributes…”
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