Search Results - "Andrew Karplus, P."

Linking Crystallographic Model and Data Quality by Karplus, P. Andrew, Diederichs, Kay

“…In macromolecular x-ray crystallography, refinement R values measure the agreement between observed and calculated data. Analogously, R merge values reporting…”
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Assessing and maximizing data quality in macromolecular crystallography by Karplus, P Andrew, Diederichs, Kay

“…•Common data quality indicators grouped as primary, secondary, or wrong/misleading.•A gedanken experiment reveals shortcomings of some common…”
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Peroxiredoxins: guardians against oxidative stress and modulators of peroxide signaling by Perkins, Arden, Nelson, Kimberly J., Parsonage, Derek, Poole, Leslie B., Karplus, P. Andrew

“…•Prxs are ubiquitous defense enzymes and in some cases signaling regulators.•ROOH orientation and polarization in the active site promotes Prx activity.•The…”
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Tuning of Peroxiredoxin Catalysis for Various Physiological Roles by Perkins, Arden, Poole, Leslie B, Karplus, P. Andrew

“…Peroxiredoxins (Prxs) make up an ancient family of enzymes that are the predominant peroxidases for nearly all organisms and play essential roles in reducing…”
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Differential Kinetics of Two-Cysteine Peroxiredoxin Disulfide Formation Reveal a Novel Model for Peroxide Sensing by Portillo-Ledesma, Stephanie, Randall, Lía M, Parsonage, Derek, Dalla Rizza, Joaquín, Karplus, P. Andrew, Poole, Leslie B, Denicola, Ana, Ferrer-Sueta, Gerardo

“…Two-cysteine peroxiredoxins (Prx) have a three-step catalytic cycle consisting of (1) reduction of peroxide and formation of sulfenic acid on the enzyme, (2)…”
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A complete Fourier‐synthesis‐based backbone‐conformation‐dependent library for proteins by Tronrud, Dale E., Karplus, P. Andrew

“…While broadening the applicability of (ϕ/ψ)‐dependent target values for the bond angles in the peptide backbone, sequence/conformation categories with too few…”
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Structure and role for active site lid of lactate monooxygenase from Mycobacterium smegmatis by Kean, Kelsey M., Karplus, P. Andrew

“…Lactate monooxygenase (LMO) catalyzes the FMN‐dependent “coupled” oxidation of lactate and O2 to acetate, carbon dioxide, and water, involving pyruvate and…”
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The Tumor Suppressor Merlin Controls Growth in Its Open State, and Phosphorylation Converts It to a Less-Active More-Closed State by Sher, Ifat, Hanemann, C. Oliver, Karplus, P. Andrew, Bretscher, Anthony

“…Unlike other ERM family proteins that are activated by phosphorylation, the merlin/NF2 tumor suppressor is inactivated. Sher et al. resolve this apparent…”
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A fresh look at the Ramachandran plot and the occurrence of standard structures in proteins by Hollingsworth Scott A., Karplus P. Andrew

“…The Ramachandran plot is among the most central concepts in structural biology, seen in publications and textbooks alike. However, with the increasing numbers…”
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Peroxiredoxin Evolution and the Regulation of Hydrogen Peroxide Signaling by Wood, Zachary A., Poole, Leslie B., Karplus, P. Andrew

“…Eukaryotic 2-Cys peroxiredoxins (2-Cys Prxs) not only act as antioxidants, but also appear to regulate hydrogen peroxide-mediated signal transduction. We show…”
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The mitotic kinesin-14 KlpA contains a context-dependent directionality switch by Popchock, Andrew R., Tseng, Kuo-Fu, Wang, Pan, Karplus, P. Andrew, Xiang, Xin, Qiu, Weihong

“…Kinesin-14s are commonly known as nonprocessive minus end-directed microtubule motors that function mainly for mitotic spindle assembly. Here we show using…”
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Substrate specificity and redox potential of AhpC, a bacterial peroxiredoxin by Parsonage, Derek, Karplus, P. Andrew, Poole, Leslie B

“…Typical 2-Cys peroxiredoxins (Prxs) are ubiquitous peroxidases that are involved in peroxide scavenging and/or the regulation of peroxide signaling in…”
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De novo synthesis of a sunscreen compound in vertebrates by Osborn, Andrew R, Almabruk, Khaled H, Holzwarth, Garrett, Asamizu, Shumpei, LaDu, Jane, Kean, Kelsey M, Karplus, P Andrew, Tanguay, Robert L, Bakalinsky, Alan T, Mahmud, Taifo

“…Ultraviolet-protective compounds, such as mycosporine-like amino acids (MAAs) and related gadusols produced by some bacteria, fungi, algae, and marine…”
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ChSeq: A database of chameleon sequences by Li, Wenlin, Kinch, Lisa N., Karplus, P. Andrew, Grishin, Nick V.

“…Chameleon sequences (ChSeqs) refer to sequence strings of identical amino acids that can adopt different conformations in protein structures. Researchers have…”
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Automated NMR resonance assignments and structure determination using a minimal set of 4D spectra by Evangelidis, Thomas, Nerli, Santrupti, Nováček, Jiří, Brereton, Andrew E., Karplus, P. Andrew, Dotas, Rochelle R., Venditti, Vincenzo, Sgourakis, Nikolaos G., Tripsianes, Konstantinos

“…Automated methods for NMR structure determination of proteins are continuously becoming more robust. However, current methods addressing larger, more complex…”
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Protein sulfenic acids in redox signaling by POOLE, Leslie B, KARPLUS, P. Andrew, CLAIBORNE, Al

“…Reactive (low pKa) cysteine residues in proteins are critical components in redox signaling. A particularly reactive and versatile reversibly oxidized form of…”
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Thiol dioxygenases: unique families of cupin proteins by Stipanuk, Martha H, Simmons, Chad R, Andrew Karplus, P, Dominy, John E. Jr

“…Proteins in the cupin superfamily have a wide range of biological functions in archaea, bacteria and eukaryotes. Although proteins in the cupin superfamily…”
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A structural foundation for studying chlamydial polymorphic membrane proteins by Debrine, Abigail M, Karplus, P Andrew, Rockey, Daniel D

“…Infections by bacteria in the genus cause a range of widespread and potentially debilitating conditions in humans and other animals. We analyzed predicted…”
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Dissecting Peroxiredoxin Catalysis: Separating Binding, Peroxidation, and Resolution for a Bacterial AhpC by Parsonage, Derek, Nelson, Kimberly J, Ferrer-Sueta, Gerardo, Alley, Samantha, Karplus, P. Andrew, Furdui, Cristina M, Poole, Leslie B

“…Peroxiredoxins make up a ubiquitous family of cysteine-dependent peroxidases that reduce hydroperoxide or peroxynitrite substrates through formation of a…”
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Peroxiredoxin Catalysis at Atomic Resolution by Perkins, Arden, Parsonage, Derek, Nelson, Kimberly J., Ogba, O. Maduka, Cheong, Paul Ha-Yeon, Poole, Leslie B., Karplus, P. Andrew

“…Peroxiredoxins (Prxs) are ubiquitous cysteine-based peroxidases that guard cells against oxidative damage, are virulence factors for pathogens, and are…”
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