Biochemistry

[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] Instantaneous Iodine-Assisted DNAzyme Cleavage of Phosphorothioate RNA

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

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

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

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

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

[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] 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

Next-Generation Photodynamic Therapy: New Probes for Cancer Imaging and Treatment

Posted on Oct 26th, 2017 - By Andrew A. Beharry

Sequence-Based Prediction of Cysteine Reactivity Using Machine Learning

Posted on Oct 26th, 2017 - By Haobo Wang, Xuemin Chen, Can Li, Yuan Liu, Fan Yang and Chu Wang

Bacterial Branched-Chain Amino Acid Biosynthesis: Structures, Mechanisms, and Drugability

Posted on Oct 23rd, 2017 - By Tathyana M. Amorim Franco and John S. Blanchard

Exploring the Untapped Biosynthetic Potential of Apicomplexan Parasites

Posted on Oct 18th, 2017 - By Jack G. Ganley, Maria Toro-Moreno and Emily R. Derbyshire

Hop to It

Posted on Oct 13th, 2017 - By Jillian L. Dempsey and Matthew R. Hartings

Fluorotryptophan Incorporation Modulates the Structure and Stability of Transthyretin in a Site-Specific Manner

Posted on Sep 28th, 2017 - By Xun Sun, H. Jane Dyson and Peter E. Wright

Transfer Hydrogenation Catalyzed by Organometallic Complexes Using NADH as a Reductant in a Biochemical Context

Posted on Sep 27th, 2017 - By Yasunori Okamoto and Thomas R. Ward

Cation−π Lights Up “Halo”

Posted on Sep 20th, 2017 - By Jianmin Gao

Detecting Activity at Different Length Scales: From Subdiffraction to Whole-Animal Activity

Posted on Sep 15th, 2017 - By Tsz-Leung To and Xiaokun Shu

A New Nucleoside Antibiotic Chokes Bacterial RNA Polymerase

Posted on Sep 8th, 2017 - By Eric P. Trautman and Jason M. Crawford

Staphylococcus aureus CidC Is a Pyruvate:Menaquinone Oxidoreductase

Posted on Aug 25th, 2017 - By Xinyan Zhang, Kenneth W. Bayles and Sorin Luca

Lysine Deacetylases Exhibit Distinct Changes in Activity Profiles Due to Fluorophore Conjugation of Substrates

Posted on Aug 16th, 2017 - By Tasha B. Toro, Jenae R. Bryant and Terry J. Watt

Functional Complementation Studies Reveal Different Interaction Partners of Escherichia coli IscS and Human NFS1

Posted on Aug 16th, 2017 - By Martin Bühning, Martin Friemel and Silke Leimkühler

Engineering Aromatic–Aromatic Interactions To Nucleate Folding in Intrinsically Disordered Regions of Proteins

Posted on Aug 11th, 2017 - By Swati Balakrishnan and Siddhartha P. Sarma

Fibronectin Conformation and Assembly: Analysis of Fibronectin Deletion Mutants and Fibronectin Glomerulopathy (GFND) Mutants

Posted on Aug 10th, 2017 - By Tomoo Ohashi, Christopher A. Lemmon and Harold P. Erickson

Mapping Functionally Important Residues in the Na+/Dicarboxylate Cotransporter, NaDC1

Posted on Aug 10th, 2017 - By Claire Colas, Avner Schlessinger and Ana M. Pajor

Two Dynamical Regimes of the Substrate Radical Rearrangement Reaction in B12-Dependent Ethanolamine Ammonia-Lyase Resolve Contributions of Native Protein Configurations and Collective Configurational Fluctuations to Catalysis

Posted on Jun 15th, 2017 - By Meghan Kohne, Chen Zhu and Kurt Warncke

Remote Perturbations in Tertiary Contacts Trigger Ligation of Lysine to the Heme Iron in Cytochrome c

Posted on May 31st, 2017 - By Jie Gu, Dong-Woo Shin and Ekaterina V. Pletneva

Deamidation Slows Curli Amyloid-Protein Aggregation

Posted on May 26th, 2017 - By Hanliu Wang, Qin Shu, Carl Frieden and Michael L. Gross

Induced Fit Is a Special Case of Conformational Selection

Posted on May 22nd, 2017 - By Pradipta Chakraborty and Enrico Di Cera

Redox-Sensitive MarR Homologue BifR from Burkholderia thailandensis Regulates Biofilm Formation

Posted on Apr 21st, 2017 - By Ashish Gupta, Stanley M. Fuentes and Anne Grove

Two Distinct Assembly States of the Cysteine Regulatory Complex of Salmonella typhimurium Are Regulated by Enzyme–Substrate Cognate Pairs

Posted on Apr 21st, 2017 - By Abhishek Kaushik, Mary Krishna Ekka and Sangaralingam Kumaran

The Role of SufS Is Restricted to Fe–S Cluster Biosynthesis in Escherichia coli

Posted on Mar 30th, 2017 - By Martin Bühning, Angelo Valleriani and Silke Leimkühler

Simultaneous Measurement of Glucose-6-phosphate 3-Dehydrogenase (NtdC) Catalysis and the Nonenzymatic Reaction of Its Product: Kinetics and Isotope Effects on the First Step in Kanosamine Biosynthesis

Posted on Mar 29th, 2017 - By Natasha D. Vetter and David R. J. Palmer

Through the Lipopolysaccharide Glass: A Potent Antimicrobial Peptide Induces Phase Changes in Membranes

Posted on Mar 7th, 2017 - By Damien Jefferies, Pin-Chia Hsu and Syma Khalid

Synthetic Riboswitches: From Plug and Pray toward Plug and Play

Posted on Feb 24th, 2017 - By Maja Etzel and Mario Mörl

Cyclotide Structure and Function: The Role of Membrane Binding and Permeation

Posted on Jan 27th, 2017 - By Sónia Troeira Henriques and David J. Craik

Biochemical Validation of a Third Guanidine Riboswitch Class in Bacteria

Posted on Jan 6th, 2017 - By Madeline E. Sherlock and Ronald R. Breaker

Can Reduction of NO to N2O in Cytochrome c Dependent Nitric Oxide Reductase Proceed through a Trans-Mechanism?

Posted on Dec 21st, 2016 - By Margareta R. A. Blomberg

A Comparison between the Photoactivation Kinetics of Human and Bovine Rhodopsins

Posted on Dec 9th, 2016 - By Chie Funatogawa, Istvan Szundi and David S. Kliger

Sequential and Coupled Proton and Electron Transfer Events in the S2 → S3 Transition of Photosynthetic Water Oxidation Revealed by Time-Resolved X-ray Absorption Spectroscopy

Posted on Dec 5th, 2016 - By Ivelina Zaharieva, Holger Dau and Michael Haumann

Mechanisms of Protein Translocation on DNA Are Differentially Responsive to Water Activity

Posted on Dec 5th, 2016 - By Brigitte S. Naughton and Norbert O. Reich

Identification of a Novel Activator of Mammalian Glutamate Dehydrogenase

Posted on Nov 14th, 2016 - By Hong Q. Smith and Thomas J. Smith

Mn4Ca Cluster of Photosynthetic Oxygen-Evolving Center: Structure, Function and Evolution

Posted on Oct 14th, 2016 - By James Barber

Crotonic Acid Blocks the Gloeobacter Ligand-Gated Ion Channel (GLIC) via the Extracellular Domain

Posted on Oct 14th, 2016 - By Mona A. Alqazzaz, Kerry L. Price and Sarah C. R. Lummis

The AAA+ FtsH Protease Degrades an ssrA-Tagged Model Protein in the Inner Membrane of Escherichia coli

Posted on Sep 30th, 2016 - By Sanjay B. Hari and Robert T. Sauer

The Influenza M2 Ectodomain Regulates the Conformational Equilibria of the Transmembrane Proton Channel: Insights from Solid-State Nuclear Magnetic Resonance

Posted on Sep 12th, 2016 - By Byungsu Kwon and Mei Hong

Nuclear Magnetic Resonance Observation of α-Synuclein Membrane Interaction by Monitoring the Acetylation Reactivity of Its Lysine Side Chains

Posted on Aug 23rd, 2016 - By Jung Ho Lee, Jinfa Ying and Ad Bax

Apolipoprotein C-III Nanodiscs Studied by Site-Specific Tryptophan Fluorescence

Posted on Aug 23rd, 2016 - By Chase A. Brisbois and Jennifer C. Lee

Nitric Oxide Regulation of H-NOX Signaling Pathways in Bacteria

Posted on Aug 19th, 2016 - By Lisa-Marie Nisbett and Elizabeth M. Boon

DFT Study on Enzyme Turnover Including Proton and Electron Transfers of Copper-Containing Nitrite Reductase

Posted on Aug 9th, 2016 - By Masami Lintuluoto and Juha M. Lintuluoto

Enhanced Nitrite Reductase Activity and Its Correlation with Oxygen Affinity in Hemoglobin Bis-Tetramers

Posted on Aug 5th, 2016 - By Aizhou Wang and Ronald Kluger

Identification of Cyanobacteriochromes Detecting Far-Red Light

Posted on Jul 2nd, 2016 - By Nathan C. Rockwell, Shelley S. Martin and J. Clark Lagarias

Preincubation of t-SNAREs with Complexin I Increases Content-Mixing Efficiency

Posted on Jun 24th, 2016 - By Jaewook Kim, Yicheng Zhu and Yeon-Kyun Shin

Effects of Macromolecular Crowding on Alcohol Dehydrogenase Activity Are Substrate-Dependent

Posted on Jun 17th, 2016 - By A. E. Wilcox, Micaela A. LoConte and Kristin M. Slade

Role of Ca2+ in the Stability and Function of TMEM16F and 16K

Posted on Jun 3rd, 2016 - By Kenji Ishihara, Jun Suzuki and Shigekazu Nagata

The Involvement of His50 during Protein Disulfide Isomerase Binding Is Essential for Inhibiting α-Syn Fibril Formation

Posted on May 6th, 2016 - By Priyatosh Ranjan and Ashutosh Kumar

Effect of Different Divalent Cations on the Kinetics and Fidelity of RB69 DNA Polymerase

Posted on Apr 28th, 2016 - By Ashwani Kumar Vashishtha and William H. Konigsberg

Role of Electrostatic Interactions in Binding of Peptides and Intrinsically Disordered Proteins to Their Folded Targets: 2. The Model of Encounter Complex Involving the Double Mutant of the c-Crk N-SH3 Domain and Peptide Sos

Posted on Mar 14th, 2016 - By Tairan Yuwen, Yi Xue and Nikolai R. Skrynnikov