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Ubiquitin Ligase Activities of WWP1 Germline Variants K740N and N745S.

Hanjie Jiang, Daniel R Dempsey, Philip A Cole,

WWP1 is an E3 ubiquitin ligase that has been reported to target the tumor suppressor lipid phosphatase PTEN. K740N and N745S are recently identified germline variants of WWP1 that have been linked to PTEN-associated cancers [Lee, Y. R., et al. (2020) <i>N. Engl. J. Med.</i>]. These WWP1 variants have been ... Read more >>

Biochemistry (Biochemistry)
[2021, :]

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An Engineered Glutamate in Biosynthetic Models of Heme-Copper Oxidases Drives Complete Product Selectivity by Tuning the Hydrogen-Bonding Network.

Igor D Petrik, Roman Davydov, Maximilian Kahle, Braddock Sandoval, Sudharsan Dwaraknath, Pia Ädelroth, Brian Hoffman, Yi Lu,

Efficiently carrying out the oxygen reduction reaction (ORR) is critical for many applications in biology and chemistry, such as bioenergetics and fuel cells, respectively. In biology, this reaction is carried out by large, transmembrane oxidases such as heme-copper oxidases (HCOs) and cytochrome <i>bd</i> oxidases. Common to these oxidases is the ... Read more >>

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Mechanism of Deoxyguanosine Diphosphate Insertion by Human DNA Polymerase β.

Fausto A Varela, Bret D Freudenthal,

DNA polymerases play vital roles in the maintenance and replication of genomic DNA by synthesizing new nucleotide polymers using nucleoside triphosphates as substrates. Deoxynucleoside triphosphates (dNTPs) are the canonical substrates for DNA polymerases; however, some bacterial polymerases have been demonstrated to insert deoxynucleoside diphosphates (dNDPs), which lack a third phosphate ... Read more >>

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[2021, :]

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Retardation of Folding Rates of Substrate Proteins in the Nanocage of GroEL.

Eda Koculi, D Thirumalai,

The <i>Escherichia coli</i> ATP-consuming chaperonin machinery, a complex between GroEL and GroES, has evolved to facilitate folding of substrate proteins (SPs) that cannot do so spontaneously. A series of kinetic experiments show that the SPs are encapsulated in the GroEL/ES nanocage for a short duration. If confinement of the SPs ... Read more >>

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[2021, :]

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Structure, Function, and Thermal Adaptation of the Biotin Carboxylase Domain Dimer from Hydrogenobacter thermophilus 2-Oxoglutarate Carboxylase.

Greg Buhrman, Paul Enríquez, Lucas Dillard, Hayden Baer, Vivian Truong, Amy M Grunden, Robert B Rose,

2-Oxoglutarate carboxylase (OGC), a unique member of the biotin-dependent carboxylase family from the order Aquificales, captures dissolved CO<sub>2</sub> via the reductive tricarboxylic acid (rTCA) cycle. Structure and function studies of OGC may facilitate adaptation of the rTCA cycle to increase the level of carbon fixation for biofuel production. Here we ... Read more >>

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[2021, :]

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Fast Kinetics Reveals Rate-Limiting Oxidation and the Role of the Aromatic Cage in the Mechanism of the Nicotine-Degrading Enzyme NicA2.

Margarita A Tararina, Katie K Dam, Manaswni Dhingra, Kim D Janda, Bruce A Palfey, Karen N Allen,

In <i>Pseudomonas putida</i>, the flavoprotein nicotine oxidoreductase (NicA2) catalyzes the oxidation of (<i>S</i>)-nicotine to <i>N</i>-methyl-myosmine, which is nonenzymatically hydrolyzed to pseudooxynicotine. Structural analysis reveals a monoamine oxidase (MAO)-like fold with a conserved FAD-binding domain and variable substrate-binding domain. The flavoenzyme has a unique variation of the classic aromatic cage with ... Read more >>

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[2021, :]

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Orthogonal Control of DNA Nanoswitches with Mixed Physical and Biochemical Cues.

Nathan T Forrest, Javier Vilcapoma, Kristina Alejos, Ken Halvorsen, Arun Richard Chandrasekaran,

Nanoscale devices that can respond to external stimuli have potential applications in drug delivery, biosensing, and molecular computation. Construction using DNA has provided many such devices that can respond to cues such as nucleic acids, proteins, pH, light, or temperature. However, simultaneous control of molecular devices is still limited. Here, ... Read more >>

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X-ray Crystallographic Snapshots of Substrate Binding in the Active Site of Histone Deacetylase 10.

Corey J Herbst-Gervasoni, David W Christianson,

Histone deacetylase 10 (HDAC10) is a zinc-dependent polyamine deacetylase enriched in the cytosol of eukaryotic cells. The active site of HDAC10 contains catalytic residues conserved in other HDAC isozymes that function as lysine deacetylases: Y307 assists the zinc ion in polarizing the substrate carbonyl for nucleophilic attack, and the H136-H137 ... Read more >>

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Oligomerization of Sticholysins from Förster Resonance Energy Transfer.

Juan Palacios-Ortega, Esperanza Rivera-de-Torre, Sara García-Linares, José G Gavilanes, Álvaro Martínez-Del-Pozo, J Peter Slotte,

Sticholysins are pore-forming toxins produced by sea anemones that are members of the actinoporin family. They exert their activity by forming pores on membranes, provided they have sphingomyelin. To assemble into pores, specific recognition, binding, and oligomerization are required. While recognition and binding have been extensively studied, delving into the ... Read more >>

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[2021, :]

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Optogenetic Analysis of Allosteric Control in Protein Tyrosine Phosphatases.

Akarawin Hongdusit, Jerome M Fox,

Allosteric regulation enables dynamic adjustments to protein function that permit tight control over cellular biochemistry. Discrepancies in the allosteric systems of related proteins can thus reveal important differences in their susceptibilities to influential stimuli (e.g., allosteric ligands, mutations, or post-translational modifications). This study uses an optogenetic actuator as a tool ... Read more >>

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Site-Specific Labeling and 19F NMR Provide Direct Evidence for Dynamic Behavior of the Anthrax Toxin Pore ϕ-Clamp Structure.

Srinivas Gonti, William M Westler, Masaru Miyagi, James G Bann,

The anthrax toxin protective antigen (PA), the membrane binding and pore-forming component of the anthrax toxin, was studied using <sup>19</sup>F NMR. We site-specifically labeled PA with <i>p</i>-fluorophenylalanine (pF-Phe) at Phe427, a critically important residue that comprises the ϕ-clamp that is required for translocation of edema factor (EF) and lethal factor ... Read more >>

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Structural Basis of the Stereochemistry of Inhibition of Tryptophan Synthase by Tryptophan and Derivatives.

Robert S Phillips, Austin P Harris,

We have examined the reaction of <i>Salmonella enterica</i> serovar typhimurium tryptophan (Trp) synthase α<sub>2</sub>β<sub>2</sub> complex with l-Trp, d-Trp, oxindolyl-l-alanine (OIA), and dioxindolyl-l-alanine (DOA) in the presence of disodium (dl)-α-glycerol phosphate (GP), using stopped-flow spectrophotometry and X-ray crystallography. All structures contained the d-isomer of GP bound at the α-active site. (3<i>S</i>)-OIA ... Read more >>

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[2021, :]

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In vitro-Constructed Ribosomes Enable Multi-site Incorporation of Noncanonical Amino Acids into Proteins.

Yi Liu, Roderick G Davis, Paul M Thomas, Neil L Kelleher, Michael C Jewett,

Efforts to expand the scope of ribosome-mediated polymerization to incorporate noncanonical amino acids (ncAAs) into peptides and proteins hold promise for creating new classes of enzymes, therapeutics, and materials. Recently, the integrated synthesis, assembly, and translation (iSAT) system was established to construct functional ribosomes in cell-free systems. However, the iSAT ... Read more >>

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[2021, :]

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Comparison of the Forward and Reverse Photocycle Dynamics of Two Highly Similar Canonical Red/Green Cyanobacteriochromes Reveals Unexpected Differences.

Julia S Kirpich, Che-Wei Chang, Jasper Franse, Qinhong Yu, Francisco Velazquez Escobar, Adam J Jenkins, Shelley S Martin, Rei Narikawa, James B Ames, J Clark Lagarias, Delmar S Larsen,

Cyanobacteriochromes (CBCRs) are cyanobacterial photoreceptors that exhibit photochromism between two states: a thermally stable dark-adapted state and a metastable light-adapted state with bound linear tetrapyrrole (bilin) chromophores possessing 15<i>Z</i> and 15<i>E</i> configurations, respectively. The photodynamics of canonical red/green CBCRs have been extensively studied; however, the time scales of their excited-state ... Read more >>

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[2021, :]

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Asymmetric Roles of Two Histidine Residues in Streptococcus pyogenes Cas9 Catalytic Domains upon Chemical Rescue.

Yuichi Furuhata, Yoshio Kato,

CRISPR-Cas9 technology has been at the forefront of the field of biology. The <i>Streptococcus pyogenes</i> (SpyCas9) protein forms a complex with guide RNA and can recognize and cleave double-stranded DNA through hybridization based on 20 base pairings. SpyCas9 has two nuclease domains, HNH and RuvC, each of which cuts each ... Read more >>

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[2021, :]

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Structural Characterization of the Interaction between the αMI-Domain of the Integrin Mac-1 (αMβ2) and the Cytokine Pleiotrophin.

Wei Feng, Hoa Nguyen, Di Shen, Hanqing Deng, Zhoumai Jiang, Nataly Podolnikova, Tatiana Ugarova, Xu Wang,

Integrin Mac-1 (α<sub>M</sub>β<sub>2</sub>) is an adhesion receptor vital to many functions of myeloid leukocytes. It is also the most promiscuous member of the integrin family capable of recognizing a broad range of ligands. In particular, its ligand-binding α<sub>M</sub>I-domain is known to bind cationic proteins/peptides depleted in acidic residues. This contradicts ... Read more >>

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[2021, :]

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Type II Binders Targeting the "GLR-Out" Conformation of the Pseudokinase STRADα.

Ryan H B Smith, Zaigham M Khan, Peter Man-Un Ung, Alex P Scopton, Lisa Silber, Seshat M Mack, Alexander M Real, Avner Schlessinger, Arvin C Dar,

Pseudokinases play important roles in signal transduction and cellular processes similar to those of catalytically competent kinases. However, pseudokinase pharmacological tractability and conformational space accessibility are poorly understood. Pseudokinases have only recently been suggested to adopt "inactive" conformations or interact with conformation-specific kinase inhibitors (e.g., type II compounds). In this ... Read more >>

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[2021, :]

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Exploring the Evolutionary History of Kinetic Stability in the α-Lytic Protease Family.

Charlotte F Nixon, Shion A Lim, Zachary R Sailer, Ivan N Zheludev, Christine L Gee, Brian A Kelch, Michael J Harms, Susan Marqusee,

In addition to encoding the tertiary fold and stability, the primary sequence of a protein encodes the folding trajectory and kinetic barriers that determine the speed of folding. How these kinetic barriers are encoded is not well understood. Here, we use evolutionary sequence variation in the α-lytic protease (αLP) protein ... Read more >>

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[2021, :]

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Solution Structure and Conformational Dynamics of a Doublet Acyl Carrier Protein from Prodigiosin Biosynthesis.

Thitapa Thongkawphueak, Ashley J Winter, Christopher Williams, Hannah J Maple, Siriwat Soontaranon, Chonthicha Kaewhan, Dominic J Campopiano, Matthew P Crump, Pakorn Wattana-Amorn,

The acyl carrier protein (ACP) is an indispensable component of both fatty acid and polyketide synthases and is primarily responsible for delivering acyl intermediates to enzymatic partners. At present, increasing numbers of multidomain ACPs have been discovered with roles in molecular recognition of trans-acting enzymatic partners as well as increasing ... Read more >>

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[2021, :]

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Protein Mass-Modulated Effects in Alkaline Phosphatase.

Ananda K Ghosh, Vern L Schramm,

Recent experimental studies engaging isotopically substituted protein (heavy protein) have revealed that many, but not all, enzymatic systems exhibit altered chemical steps in response to an altered mass. The results have been interpreted as femtosecond protein dynamics at the active site being linked (or not) to transition-state barrier crossing. An ... Read more >>

Biochemistry (Biochemistry)
[2021, 60(2):118-124]

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Conformational Dynamics of Deubiquitinase A and Functional Implications.

Ashish Kabra, Ying Li,

Deubiquitinase A (DUBA) belongs to the ovarian tumor family of deubiquitinating enzymes and was initially identified as a negative regulator of type I interferons, whose overproduction has been linked to autoimmune diseases. The deubiquitinating activity of DUBA is positively regulated by phosphorylation at a single serine residue, S177, which results ... Read more >>

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[2021, :]

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Conformational Plasticity and DNA-Binding Specificity of the Eukaryotic Transcription Factor Pax5.

Cecilia Perez-Borrajero, Florian Heinkel, Jörg Gsponer, Lawrence P McIntosh,

The eukaryotic transcription factor Pax5 has a DNA-binding Paired domain composed of two independent helical bundle subdomains joined by a flexible linker. Previously, we showed distinct biophysical properties of the N-terminal (NTD) and C-terminal (CTD) subdomains, with implications for how these two regions cooperate to distinguish nonspecific and cognate DNA ... Read more >>

Biochemistry (Biochemistry)
[2021, 60(2):104-117]

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Alternative Sigma Factor of Staphylococcus aureus Interacts with the Cognate Antisigma Factor Primarily Using Its Domain 3.

Debabrata Sinha, Debasmita Sinha, Anindya Dutta, Tushar Chakraborty, Rajkrishna Mondal, Soham Seal, Asim Poddar, Subhrangsu Chatterjee, Subrata Sau,

σ<sup>B</sup>, an alternative sigma factor, is usually employed to tackle the general stress response in <i>Staphylococcus aureus</i> and other Gram-positive bacteria. This protein, involved in <i>S. aureus</i>-mediated pathogenesis, is typically blocked by RsbW, an antisigma factor having serine kinase activity. σ<sup>B</sup>, a σ<sup>70</sup>-like sigma factor, harbors three conserved domains designated ... Read more >>

Biochemistry (Biochemistry)
[2021, 60(2):135-151]

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Dried Protein Structure Revealed at the Residue Level by Liquid-Observed Vapor Exchange NMR.

Candice J Crilly, Julia A Brom, Mark E Kowalewski, Samantha Piszkiewicz, Gary J Pielak,

Water is key to protein structure and stability, yet the relationship between protein-water interactions and structure is poorly understood, in part because there are few techniques that permit the study of dehydrated protein structure at high resolution. Here, we describe liquid-observed vapor exchange (LOVE) NMR, a solution NMR-based method that ... Read more >>

Biochemistry (Biochemistry)
[2021, 60(2):152-159]

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Structure of a Stable Interstrand DNA Cross-Link Involving a β-N-Glycosyl Linkage Between an N6-dA Amino Group and an Abasic Site.

Andrew H Kellum, David Y Qiu, Markus W Voehler, William Martin, Kent S Gates, Michael P Stone,

Abasic (AP) sites are one of the most common forms of DNA damage. The deoxyribose ring of AP sites undergoes anomerization between α and β configurations, via an electrophilic aldehyde intermediate. In sequences where an adenine residue is located on the opposing strand and offset 1 nt to the 3' ... Read more >>

Biochemistry (Biochemistry)
[2021, 60(1):41-52]

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