Biochemistry

[ASAP] Examining the Mechanism of Phosphite Dehydrogenase with Quantum Mechanical/Molecular Mechanical Free Energy Simulations

Posted on Feb 14th, 2020 - By David R. Stevens and Sharon Hammes-Schiffer*

[ASAP] Depurination of Colibactin-Derived Interstrand Cross-Links

Posted on Feb 13th, 2020 - By Mengzhao Xue†, Kevin M. Wernke†, and Seth B. Herzon*†‡

[ASAP] Substitutions of Amino Acid Residues in the Substrate Binding Site of Horse Liver Alcohol Dehydrogenase Have Small Effects on the Structures but Significantly Affect Catalysis of Hydrogen Transfer

Posted on Feb 10th, 2020 - By Keehyuk Kim† and Bryce V. Plapp*

[ASAP] Ferroptosis Suppressor Protein 1 (FSP1) and Coenzyme Q<sub>10</sub> Cooperatively Suppress Ferroptosis

Posted on Jan 31st, 2020 - By Kamyar Hadian*

[ASAP] Avian MRP126 Restricts Microbial Growth through Ca(II)-Dependent Zn(II) Sequestration

Posted on Jan 21st, 2020 - By Aaron T. Bozzi and Elizabeth M. Nolan*

[ASAP] Early Metastable Assembly during the Stress-Induced Formation of Worm-like Amyloid Fibrils of Nucleic Acid Binding Domains of TDP-43

Posted on Jan 9th, 2020 - By Meenakshi Pillai†‡ and Santosh Kumar Jha*†‡

[ASAP] Molecular Dynamics Simulations of the Hypoxia-Inducible Factor PAS-B Domain Confirm That Internally Bound Water Molecules Function To Stabilize the Protein Core for Ligand Binding

Posted on Jan 6th, 2020 - By Andrew S. Chong and Peter C. Anderson*

[ASAP] Evolution of Substrates and Components of the Pro/N-Degron Pathway

Posted on Jan 2nd, 2020 - By Shun-Jia Chen, Artem Melnykov†, and Alexander Varshavsky*

[ASAP] Determination of a Structural Ensemble Representing the Dynamics of a G-Quadruplex DNA

Posted on Dec 23rd, 2019 - By pthomas2

[ASAP] Correction to “Orchestration of Enzymatic Processing by Thiazole/Oxazole-Modified Microcin Dehydrogenases”

Posted on Dec 19th, 2019 - By Joel O. Melby, Xiangpo Li, and Douglas A. Mitchell*

[ASAP] Coupling Computational and Intracellular Screening and Selection Toward Co-compatible cJun and cFos Antagonists

Posted on Dec 19th, 2019 - By pthomas2

[ASAP] Harnessing Human Neural Networks for Protein Design

Posted on Dec 13th, 2019 - By Po-Ssu Huang* and Kirsten A. Thompson

[ASAP] Structural and Biochemical Investigations of the [4Fe-4S] Cluster-Containing Fumarate Hydratase from <italic toggle=”yes”>Leishmania major</italic>

Posted on Nov 27th, 2019 - By pthomas2

[ASAP] Measurement of Net Rate Constants from Enzyme Progress Curves without Curve Fitting

Posted on Nov 22nd, 2019 - By Mark W. Ruszczycky*† and Hung-wen Liu†‡

[ASAP] Single-Cell CRISPR-Based Lineage Tracing in Mice

Posted on Nov 15th, 2019 - By Kian Kalhor† and George M. Church*‡

[ASAP] The Expanding Role of Methyl-Coenzyme M Reductase in the Anaerobic Functionalization of Alkanes

Posted on Oct 10th, 2019 - By Danielle V. Miller† and Squire J. Booker*†‡§

[ASAP] Not All Quiet on the Sugar Front: Glycan Combatants in Host–Pathogen Interactions

Posted on Oct 6th, 2019 - By Atossa C. Ghorashi and Jennifer J. Kohler*

[ASAP] A Transient Intermediate Populated in Prion Folding Leads to Domain Swapping

Posted on Sep 26th, 2019 - By Balaka Mondal and Govardhan Reddy*

[ASAP] Decoding Principles of Selective GPCR-Ga Coupling

Posted on Sep 25th, 2019 - By Sang Min Lim*

[ASAP] Anti-CD3 Antibody for the Prevention of Type 1 Diabetes: A Story of Perseverance

Posted on Sep 23rd, 2019 - By Jason Gaglia†‡ and Stephan Kissler*†‡

[ASAP] Scalable Chemoenzymatic Synthesis of Inositol Pyrophosphates

Posted on Sep 13th, 2019 - By pthomas2

[ASAP] Replication of the Enzymatic Temperature Dependency of the Primary Hydride Kinetic Isotope Effects in Solution: Caused by the Protein-Controlled Rigidity of the Donor–Acceptor Centers?

Posted on Sep 12th, 2019 - By Yun Lu*, Samantha Wilhelm†, Mingxuan Bai†, Peter Maness, and Li Ma

[ASAP] Biosynthesis of GDP-<sc>d</sc>-<italic toggle=”yes”>glycero</italic>-a-<sc>d</sc>-<italic toggle=”yes”>manno</italic>-heptose for the Capsular Polysaccharide of <italic toggle=”yes”>Campylobacter jejuni</italic>

Posted on Aug 28th, 2019 - By Jamison P. Huddleston and Frank M. Raushel*

[ASAP] Functional Characterization of YdjH, a Sugar Kinase of Unknown Specificity in <italic toggle=”yes”>Escherichia coli</italic> K12

Posted on Jul 23rd, 2019 - By Jamison P. Huddleston and Frank M. Raushel*

[ASAP] Effects of Refolding on Large-Scale RNA Structure

Posted on Jul 2nd, 2019 - By Elizabeth A. Dethoff and Kevin M. Weeks*

[ASAP] Helical Behavior of the Interdomain Linker of the <italic toggle=”yes”>Escherichia coli</italic> AraC Protein

Posted on Jun 21st, 2019 - By Matthew J. Brown and Robert Schleif*

[ASAP] <italic toggle=”yes”>Vibrio natriegens</italic>: An Alternative Expression System for the High-Yield Production of Isotopically Labeled Proteins

Posted on Jun 13th, 2019 - By Walter Becker*, Florian Wimberger, and Klaus Zangger*

[ASAP] Design of a Protein Motif Responsive to Tyrosine Nitration and an Encoded Turn-Off Sensor of Tyrosine Nitration

Posted on Jun 11th, 2019 - By Andrew R. Urmey and Neal J. Zondlo*

[ASAP] Characterization of Acyl Carrier Protein-Dependent Glycosyltransferase in Mitomycin C Biosynthesis

Posted on Jun 11th, 2019 - By Hai P. Nguyen† and Kenichi Yokoyama*†‡

[ASAP] Thermally versus Chemically Denatured Protein States

Posted on May 15th, 2019 - By Abhishek Narayan, Kabita Bhattacharjee, Athi N. Naganathan

[ASAP] An Intermediate Conformational State of Cytochrome P450cam-CN in Complex with Putidaredoxin

Posted on Apr 25th, 2019 - By Shih-Wei Chuo, Lee-Ping Wang, R. David Britt, David B. Goodin

[ASAP] Thrombin Exosite Maturation and Ligand Binding at ABE II Help Stabilize PAR-Binding Competent Conformation at ABE I

Posted on Feb 11th, 2019 - By Ramya Billur, T. Michael Sabo, Muriel C. Maurer

[ASAP] Cas14: Big Advances from Small CRISPR Proteins

Posted on Feb 11th, 2019 - By David F. Savage

[ASAP] Shaping the Future of Protein Engineering

Posted on Feb 6th, 2019 - By Dominic J. Glover, Dawei Xu, Douglas S. Clark

[ASAP] Retro Styles for Vesicle Coats

Posted on Jan 17th, 2019 - By James H. Hurley, Ludger Johannes

[ASAP] Targeting Type 1 Diabetes: Selective Approaches for New Therapies

Posted on Jan 17th, 2019 - By Daniel F. Sheehy, Sean P. Quinnell, Arturo J. Vegas

[ASAP] Effector-Binding-Directed Dimerization and Dynamic Communication between Allosteric Sites of Ribonucleotide Reductase

Posted on Jan 8th, 2019 - By Bill Pham, Richard J. Lindsay, Tongye Shen

[ASAP] Tuning Protein Diffusivity with Membrane Tethers

Posted on Dec 24th, 2018 - By David Mörsdorf, Patrick Müller

[ASAP] The Polycystin Complex Reveals Its Complexity

Posted on Dec 12th, 2018 - By Valeria Padovano, Michael J. Caplan

[ASAP] Genome, Epigenome, and Transcriptome Editing via Chemical Modification of Nucleobases in Living Cells

Posted on Dec 12th, 2018 - By Brodie L. Ranzau, Alexis C. Komor

[ASAP] Mechanistic Characterization of Long Residence Time Inhibitors of Diacylglycerol Acyltransferase 2 (DGAT2)

Posted on Dec 7th, 2018 - By Brandon Pabst, Kentaro Futatsugi, Qifang Li, Kay Ahn

[ASAP] Endoplasmic Reticulum–Endosome Contact Sites: Specialized Interfaces for Orchestrating Endosomal Tubule Fission?

Posted on Nov 30th, 2018 - By James L. Daly, Peter J. Cullen

[ASAP] Investigation of Human Neutrophil Elastase Inhibition by <italic toggle=”yes”>Staphylococcus aureus</italic> EapH1: The Key Role Played by Arginine 89

Posted on Nov 30th, 2018 - By Timothy J. Herdendorf, Brian V. Geisbrecht

[ASAP] Ancient Family of Retinal Proteins Brought to Light “Sight-Unseen”

Posted on Nov 30th, 2018 - By Thomas P. Sakmar, Thomas Huber

[ASAP] Discovery and Characterization of a Naturally Occurring, Turn-On Yellow Fluorescent Protein Sensor for Chloride

Posted on Nov 21st, 2018 - By Jasmine N. Tutol, Weicheng Peng, Sheel C. Dodani

[ASAP] Understanding and Engineering Distributed Biochemical Pathways in Microbial Communities

Posted on Nov 20th, 2018 - By Xinyun Cao, Joshua J. Hamilton, Ophelia S. Venturelli

[ASAP] Hinge–Linker Elements in the AAA+ Protein Unfoldase ClpX Mediate Intersubunit Communication, Assembly, and Mechanical Activity

Posted on Nov 20th, 2018 - By Tristan A. Bell, Tania A. Baker, Robert T. Sauer

[ASAP] Binding Affinity and Function of the Extremely Disordered Protein Complex Containing Human Linker Histone H1.0 and Its Chaperone ProTa

Posted on Nov 19th, 2018 - By Hanqiao Feng, Bing-Rui Zhou, Yawen Bai

[ASAP] In Situ Photoregulation of Carbonic Anhydrase Activity Using Azobenzenesulfonamides

Posted on Oct 31st, 2018 - By Kanchan Aggarwal, Mandira Banik, Brenda Medellin, Emily L. Que

[ASAP] Instantaneous Iodine-Assisted DNAzyme Cleavage of Phosphorothioate RNA

Posted on Oct 14th, 2018 - By Po-Jung Jimmy Huang, Woohyun J. Moon, Juewen Liu

[ASAP] High-Throughput Explorations of RNA Structural Modularity

Posted on Oct 14th, 2018 - By Mark A. Boerneke, Kevin M. Weeks

[ASAP] Analysis of the Ub to Ub-CR Transition in Ubiquitin

Posted on Oct 14th, 2018 - By Konstantin Röder, David J. Wales

[ASAP] Crystal Structures of Wild-Type and F448A Mutant <italic toggle=”yes”>Citrobacter freundii</italic> Tyrosine Phenol-Lyase Complexed with a Substrate and Inhibitors: Implications for the Reaction Mechanism

Posted on Oct 11th, 2018 - By Robert S. Phillips, Steven Craig

[ASAP] Characterization of Interactions and Phospholipid Transfer between Substrate Binding Proteins of the OmpC-Mla System

Posted on Oct 7th, 2018 - By Bilge Ercan, Wen-Yi Low, Xuejun Liu, Shu-Sin Chng

[ASAP] Distinct Differences in Structural States of Conserved Histidines in Two Related Proteins: NMR Studies of the Chemokines CXCL1 and CXCL8 in the Free Form and Macromolecular Complexes

Posted on Oct 1st, 2018 - By Krishna Mohan Sepuru, Krishna Rajarathnam

[ASAP] Three-Step Isomerization of the Retinal Chromophore during the Anion Pumping Cycle of Halorhodopsin

Posted on Oct 1st, 2018 - By Tsutomu Kouyama, Kunio Ihara, Kosuke Maki, Siu Kit Chan

[ASAP] Reduced Occupancy of the Oxygen-Evolving Complex of Photosystem II Detected in Cryo-Electron Microscopy Maps

Posted on Sep 30th, 2018 - By Jimin Wang, Krystle Reiss, Gary W. Brudvig, Victor S. Batista

[ASAP] Light at the End of the Amyloid Tunnel<subtitle>Published as part of the <italic toggle=”yes”>Biochemistry</italic> series “Biochemistry to Bedside”</subtitle>

Posted on Sep 30th, 2018 - By Dennis J. Selkoe

[ASAP] <italic toggle=”yes”>In Silico</italic> Protein Design Promotes the Rapid Evolution of Industrial Enzymes

Posted on Sep 20th, 2018 - By Yang Wang, Jian Chen, Zhen Kang

[ASAP] Caught in the Act? Quantifying Biochemistry Inside and Outside of Biomolecular Condensates

Posted on Sep 20th, 2018 - By Johannes H. Wilbertz, Jeffrey A. Chao

[ASAP] Interactions of the DNA Repair Enzyme Human Thymine DNA Glycosylase with Cognate and Noncognate DNA

Posted on Sep 19th, 2018 - By Natalia Kanaan, Petra Imhof

[ASAP] New Crystallographic Snapshots of Large Domain Movements in Bacterial 3-Hydroxy-3-methylglutaryl Coenzyme A Reductase

Posted on Sep 18th, 2018 - By Edwin R. Ragwan, Eri Arai, Yan Kung

[ASAP] Kinetic Mechanism of Nicotinamide <italic toggle=”yes”>N</italic>-Methyltransferase

Posted on Sep 9th, 2018 - By Heather S. Loring, Paul R. Thompson

[ASAP] Variant Bacterial Riboswitches Associated with Nucleotide Hydrolase Genes Sense Nucleoside Diphosphates

Posted on Aug 23rd, 2018 - By Madeline E. Sherlock, Harini Sadeeshkumar, Ronald R. Breaker

[ASAP] Generation and Comparative Kinetic Analysis of New Glycosynthase Mutants from <italic toggle=”yes”>Streptococcus pyogenes</italic> Endoglycosidases for Antibody Glycoengineering

Posted on Aug 21st, 2018 - By Xin Tong, Tiezheng Li, Chao Li, Lai-Xi Wang

[ASAP] A New Class of EutT ATP:Co(I)rrinoid Adenosyltransferases Found in <italic toggle=”yes”>Listeria monocytogenes</italic> and Other <italic toggle=”yes”>Firmicutes</italic> Does Not Require a Metal Ion for Activity

Posted on Aug 15th, 2018 - By Flavia G. Costa, Jorge C. Escalante-Semerena

[ASAP] Investigation of Solvent Hydron Exchange in the Reaction Catalyzed by the Antibiotic Resistance Protein Cfr

Posted on Jul 22nd, 2018 - By Matthew R. Bauerle, Tyler L. Grove, Squire J. Booker

[ASAP] Engineering a Protein Binder Specific for p38a with Interface Expansion

Posted on Jul 18th, 2018 - By Mahmud Hussain, Steven P. Angus, Brian Kuhlman

[ASAP] Kinetics and Degradation Mechanism of Adrenaline Derivative CpQ in Diluted Aqueous Solutions

Posted on Jul 18th, 2018 - By Andrei Blasko, James Tam, Sajeevi Gunasekera, Ale Eboreime

[ASAP] Complete Coupled Binding–Folding Pathway of the Intrinsically Disordered Transcription Factor Protein Brinker Revealed by Molecular Dynamics Simulations and Markov State Modeling

Posted on Jul 18th, 2018 - By Andrew P. Collins, Peter C. Anderson

[ASAP] Proton Transfer and Tautomerism in 2-Aminopurine–Thymine and Pyrrolocytosine–Guanine Base Pairs

Posted on Jul 18th, 2018 - By Graham D. Bull, Katherine C. Thompson

[ASAP] Functional Evaluation of the p-Helix in the NAD(P)H:FMN Reductase of the Alkanesulfonate Monooxygenase System

Posted on Jul 18th, 2018 - By Jonathan M. Musila, Dianna L. Forbes, Holly R. Ellis

[ASAP] Extracellular Electron Transfer by the Gram-Positive Bacterium <italic toggle=”yes”>Enterococcus faecalis</italic>

Posted on Jul 18th, 2018 - By Galina Pankratova, Dónal Leech, Lo Gorton, Lars Hederstedt

[ASAP] A Bifunctional Noncanonical Amino Acid: Synthesis, Expression, and Residue-Specific Proteome-wide Incorporation

Posted on Jun 21st, 2018 - By Jan-Erik Hoffmann, Dmytro Dziuba, Frank Stein, Carsten Schultz

[ASAP] So Close, yet Sulfur Away: Opening the Nitrogenase Cofactor Structure Creates a Binding Site

Posted on Jun 20th, 2018 - By Kazimer L. Skubi, Patrick L. Holland

[ASAP] Charge Dispersion and Its Effects on the Reactivity of Thiamin-Derived Breslow Intermediates

Posted on Jun 14th, 2018 - By Michael Bielecki, Graeme W. Howe, Ronald Kluger

[ASAP] Catalytic Bases and Stereocontrol in Lamiaceae Class II Diterpene Cyclases

Posted on May 30th, 2018 - By Samuel Schulte, Kevin C. Potter, Cody Lemke, Reuben J. Peters

[ASAP] Sulfonium Ion Condensation: The Burden Borne by SAM Synthetase

Posted on May 30th, 2018 - By Charles A. Lewis , Jr., Richard Wolfenden

[ASAP] Understanding Which Residues of the Active Site and Loop Structure of a Tyrosine Aminomutase Define Its Mutase and Lyase Activities

Posted on May 29th, 2018 - By Gayanthi Attanayake, Tyler Walter, Kevin D. Walker

[ASAP] Molecular Mechanism for Folding Cooperativity of Functional RNAs in Living Organisms

Posted on May 6th, 2018 - By Kathleen A. Leamy, Neela H. Yennawar, Philip C. Bevilacqua

[ASAP] Second-Shell Hydrogen Bond Impacts Transition-State Structure in <italic toggle=”yes”>Bacillus subtilis</italic> Oxalate Decarboxylase

Posted on Apr 11th, 2018 - By Wen Zhu, Laurie A. Reinhardt, Nigel G. J. Richards

[ASAP] Structural Determinants for the Interactions of Chemically Modified Nucleic Acids with the Stabilin-2 Clearance Receptor

Posted on Mar 29th, 2018 - By Hans Gaus, Colton M. Miller, Punit P. Seth, Edward N. Harris

[ASAP] Structures of the Catalytic Domain of Bacterial Primase DnaG in Complexes with DNA Provide Insight into Key Priming Events

Posted on Mar 22nd, 2018 - By Caixia Hou, Tapan Biswas, Oleg V. Tsodikov

Relationship of Sequence and Phase Separation in Protein Low-Complexity Regions

Posted on Mar 16th, 2018 - By Erik W. Martin and Tanja Mittag

Characterization of 1,2-Propanediol Dehydratases Reveals Distinct Mechanisms for B12-Dependent and Glycyl Radical Enzymes

Posted on Mar 16th, 2018 - By Benjamin J. Levin and Emily P. Balskus

Sequential Protein Expression and Capsid Assembly in Cell: Toward the Study of Multiprotein Viral Capsids Using Solid-State Nuclear Magnetic Resonance Techniques

Posted on Feb 23rd, 2018 - By Sébastien Alphonse, Boris Itin, Reza Khayat and Ranajeet Ghose

Protein Plasticity and Peptide Editing in the MHC I Antigen Processing Pathway

Posted on Feb 22nd, 2018 - By Tim Elliott and Andy van Hateren

Prediction of Hot Spots at Myeloid Cell Leukemia-1–Inhibitor Interface Using Energy Estimation and Alanine Scanning Mutagenesis

Posted on Feb 1st, 2018 - By Parthiban Marimuthu and Kalaimathy Singaravelu

Kinetic Characterization of Prenyl-Flavin Synthase from Saccharomyces cerevisiae

Posted on Dec 27th, 2017 - By Nattapol Arunrattanamook and E. Neil G. Marsh

Complexity in pH-Dependent Ribozyme Kinetics: Dark pKa Shifts and Wavy Rate–pH Profiles

Posted on Dec 22nd, 2017 - By Erica A. Frankel and Philip C. Bevilacqua

Where Informatics Lags Chemistry Leads

Posted on Dec 22nd, 2017 - By Rahul Kaushik, Ankita Singh and B. Jayaram

Structural Features and Domain Movements Controlling Substrate Binding and Cofactor Specificity in Class II HMG-CoA Reductase

Posted on Dec 21st, 2017 - By Bradley R. Miller and Yan Kung

Tuning the Flexibility of Glycine-Serine Linkers To Allow Rational Design of Multidomain Proteins

Posted on Dec 7th, 2017 - By Martijn van Rosmalen, Mike Krom and Maarten Merkx

Novel Biology and Druggable Targets via Chemoproteomics

Posted on Dec 7th, 2017 - By Alan Saghatelian

Biochemical Basis of Vosevi, a New Treatment for Hepatitis C

Posted on Nov 29th, 2017 - By Ronald Besandre and Hung-wen Liu

Ragtime Regulation: Mechanism of TORC1 Activation in Nutrient Sensing

Posted on Nov 29th, 2017 - By Roger L. Williams and Madhanagopal Anandapadamanaban

Biosynthesis of an Opine Metallophore by Pseudomonas aeruginosa

Posted on Nov 3rd, 2017 - By Jeffrey S. McFarlane and Audrey L. Lamb

The Conformational Change in Elongation Factor Tu Involves Separation of Its Domains

Posted on Oct 27th, 2017 - By Jonathan Lai, Zhaleh Ghaemi and Zaida Luthey-Schulten

Correction to Probing the Binding Mechanism of Mnk Inhibitors by Docking and Molecular Dynamics Simulations

Posted on Oct 27th, 2017 - By Srinivasaraghavan Kannan, Anders Poulsen, Hai Yan Yang, Melvyn Ho, Shi Hua Ang, Tan Sum Wai Eldwin, Duraiswamy Athisayamani Jeyaraj, Lohitha Rao Chennamaneni, Boping Liu, Jeffrey Hill, Chandra S. Verma and Kassoum Nacro

The G126V Mutation in the Mouse Prion Protein Hinders Nucleation-Dependent Fibril Formation by Slowing Initial Fibril Growth and by Increasing the Critical Concentration

Posted on Oct 26th, 2017 - By Ambadi Thody Sabareesan and Jayant B. Udgaonkar