Biochemistry

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

[NiFe]-Hydrogenase Maturation

Posted on Mar 13th, 2016 - By Michael J. Lacasse and Deborah B. Zamble

Enzyme Architecture: A Startling Role for Asn270 in Glycerol 3-Phosphate Dehydrogenase-Catalyzed Hydride Transfer

Posted on Mar 3rd, 2016 - By Archie C. Reyes, Tina L. Amyes and John P. Richard

Role of Calcium in Secondary Structure Stabilization during Maturation of Nitrous Oxide Reductase

Posted on Feb 29th, 2016 - By Lisa K. Schneider and Oliver Einsle

Molecular Modeling of the Structural and Dynamical Changes in Calcium Channel TRPV5 Induced by the African-Specific A563T Variation

Posted on Feb 15th, 2016 - By Lingyun Wang, Ross P. Holmes and Ji-Bin Peng

HosA, a MarR Family Transcriptional Regulator, Represses Nonoxidative Hydroxyarylic Acid Decarboxylase Operon and Is Modulated by 4-Hydroxybenzoic Acid

Posted on Feb 11th, 2016 - By Ajit Roy and Akash Ranjan

Structural Insights into Mycobacterium tuberculosis Rv2671 Protein as a Dihydrofolate Reductase Functional Analogue Contributing to para-Aminosalicylic Acid Resistance

Posted on Feb 5th, 2016 - By Yu-Shan Cheng and James C. Sacchettini

Real-Time Observation of Backtracking by Bacterial RNA Polymerase

Posted on Jan 21st, 2016 - By Agnieszka Lass-Napiorkowska and Tomasz Heyduk

Protein Arginine Methyltransferase 8: Tetrameric Structure and Protein Substrate Specificity

Posted on Dec 15th, 2015 - By pthomas2

Active Site Structure and Peroxidase Activity of Oxidatively Modified Cytochrome c Species in Complexes with Cardiolipin

Posted on Dec 15th, 2015 - By pthomas2

Mutagenic Bypass of an Oxidized Abasic Lesion-Induced DNA Interstrand Cross-Link Analogue by Human Translesion Synthesis DNA Polymerases

Posted on Dec 14th, 2015 - By pthomas2

Activation of Phosphorylase Kinase by Physiological Temperature

Posted on Dec 14th, 2015 - By pthomas2

Binding of DNA-Intercalating Agents to Oxidized and Reduced Quinone Reductase 2

Posted on Dec 14th, 2015 - By Kevin K. K. Leung and Brian H. Shilton

A New Covalent Inhibitor of Class C β-Lactamases Reveals Extended Active Site Specificity

Posted on Dec 11th, 2015 - By pthomas2

Correction to Interaction of Doxorubicin with Polynucleotides. A Spectroscopic Study

Posted on Dec 10th, 2015 - By Marta Airoldi, Giampaolo Barone, Giuseppe Gennaro, Anna Maria Giuliani and Mauro Giustini

Neuropathy Target Esterase Is Degraded by the Ubiquitin–Proteasome Pathway with ARA54 as the Ubiquitin Ligase

Posted on Dec 10th, 2015 - By pthomas2

Multiple Src Homology 3 Binding to the Ubiquitin Ligase Itch Conserved Proline-Rich Region

Posted on Dec 10th, 2015 - By pthomas2

Structural Basis for Dimerization and DNA Binding of Transcription Factor FLI1

Posted on Dec 10th, 2015 - By Caixia Hou and Oleg V. Tsodikov

Universal Stress Protein Regulates Electron Transfer and Superoxide Generation Activities of the Cytochrome bc1 Complex from Rhodobacter sphaeroides

Posted on Dec 9th, 2015 - By Ting Su, Qiyu Wang, Linda Yu and Chang-An Yu

Mechanisms of Very Long Abortive Transcript Release during Promoter Escape

Posted on Dec 8th, 2015 - By pthomas2

Ion Channel Formation by Tau Protein: Implications for Alzheimer’s Disease and Tauopathies

Posted on Dec 7th, 2015 - By pthomas2

Pulsed Dipolar Spectroscopy Reveals That Tyrosyl Radicals Are Generated in Both Monomers of the Cyclooxygenase-2 Dimer

Posted on Dec 7th, 2015 - By pthomas2

Evaluating Sense Codon Reassignment with a Simple Fluorescence Screen

Posted on Dec 5th, 2015 - By Wil Biddle, Margaret A. Schmitt and John D. Fisk

Conservation and Covariance in Small Bacterial Phosphoglycosyltransferases Identify the Functional Catalytic Core

Posted on Dec 4th, 2015 - By pthomas2

Promotion or Inhibition of Islet Amyloid Polypeptide Aggregation by Zinc Coordination Depends on Its Relative Concentration

Posted on Dec 4th, 2015 - By pthomas2

Design, Synthesis, and Investigation of Novel Nitric Oxide (NO)-Releasing Prodrugs as Drug Candidates for the Treatment of Ischemic Disorders: Insights into NO-Releasing Prodrug Biotransformation and Hemoglobin–NO Biochemistry

Posted on Dec 3rd, 2015 - By pthomas2

“Bind and Crawl” Association Mechanism of Leishmania major Peroxidase and Cytochrome c Revealed by Brownian and Molecular Dynamics Simulations

Posted on Dec 3rd, 2015 - By pthomas2

Crystal Structure of Recoverin with Calcium Ions Bound to Both Functional EF Hands

Posted on Dec 3rd, 2015 - By pthomas2

Characterization of Heme–DNA Complexes Composed of Some Chemically Modified Hemes and Parallel G-Quadruplex DNAs

Posted on Dec 3rd, 2015 - By pthomas2

Heterogeneity and Turnover of Intermediates during Amyloid-β (Aβ) Peptide Aggregation Studied by Fluorescence Correlation Spectroscopy

Posted on Dec 3rd, 2015 - By pthomas2

Top-Down Mass Spectrometry Analysis of Membrane-Bound Light-Harvesting Complex 2 from Rhodobacter sphaeroides

Posted on Dec 2nd, 2015 - By pthomas2

Imidazole as a Small Molecule Analogue in Two-Component Signal Transduction

Posted on Dec 2nd, 2015 - By pthomas2

Dimethyl Sulfoxide Induced Destabilization and Disassembly of Various Structural Variants of Insulin Fibrils Monitored by Vibrational Circular Dichroism

Posted on Dec 2nd, 2015 - By pthomas2

Processivity, Substrate Positioning, and Binding: The Role of Polar Residues in a Family 18 Glycoside Hydrolase

Posted on Dec 2nd, 2015 - By pthomas2

Correction to The Semiquinone at the Qi Site of the bc1 Complex Explored Using HYSCORE Spectroscopy and Specific Isotopic Labeling of Ubiquinone in Rhodobacter sphaeroides via 13C Methionine and Construction of a Methionine Auxotroph

Posted on Dec 1st, 2015 - By Sangjin Hong, Wagner B. de Almeida, Alexander T. Taguchi, Rimma I. Samoilova, Robert B. Gennis, Patrick J. O’Malley, Sergei A. Dikanov and Antony R. Crofts

Mechanistic Investigation of cPMP Synthase in Molybdenum Cofactor Biosynthesis Using an Uncleavable Substrate Analogue

Posted on Dec 1st, 2015 - By pthomas2

Phenotypic Screening Identifies Protein Synthesis Inhibitors as H-Ras-Nanocluster-Increasing Tumor Growth Inducers

Posted on Nov 30th, 2015 - By pthomas2

Cholesterol-Dependent Conformational Exchange of the C-Terminal Domain of the Influenza A M2 Protein

Posted on Nov 30th, 2015 - By pthomas2

Molecular Basis of Hydroperoxide Specificity in Peroxiredoxins: The Case of AhpE from Mycobacterium tuberculosis

Posted on Nov 30th, 2015 - By pthomas2

Specific Binding of Tetratricopeptide Repeat Proteins to Heat Shock Protein 70 (Hsp70) and Heat Shock Protein 90 (Hsp90) Is Regulated by Affinity and Phosphorylation

Posted on Nov 25th, 2015 - By pthomas2

H-NOX from Clostridium botulinum, like H-NOX from Thermoanaerobacter tengcongensis, Binds Oxygen but with a Less Stable Oxyferrous Heme Intermediate

Posted on Nov 25th, 2015 - By Gang Wu, Wen Liu, Vladimir Berka and Ah-lim Tsai

Dissecting Proton Delocalization in an Enzyme’s Hydrogen Bond Network with Unnatural Amino Acids

Posted on Nov 25th, 2015 - By Yufan Wu, Stephen D. Fried and Steven G. Boxer

Evidence That Compound I Is the Active Species in Both the Hydroxylase and Lyase Steps by Which P450scc Converts Cholesterol to Pregnenolone: EPR/ENDOR/Cryoreduction/Annealing Studies

Posted on Nov 25th, 2015 - By pthomas2

Proteorhodopsin Activation Is Modulated by Dynamic Changes in Internal Hydration

Posted on Nov 25th, 2015 - By Jun Feng and Blake Mertz

Correction to Formation of a Stacked Dimeric G-Quadruplex Containing Bulges by the 5′-Terminal Region of Human Telomerase RNA (hTERC)

Posted on Nov 25th, 2015 - By Herry Martadinata and Anh Tuân Phan

Structural Studies of Geosmin Synthase, a Bifunctional Sesquiterpene Synthase with αα Domain Architecture That Catalyzes a Unique Cyclization–Fragmentation Reaction Sequence

Posted on Nov 24th, 2015 - By pthomas2

Nucleosomes Inhibit Cas9 Endonuclease Activity in Vitro

Posted on Nov 24th, 2015 - By John M. Hinz, Marian F. Laughery and John J. Wyrick

Skp Trimer Formation Is Insensitive to Salts in the Physiological Range

Posted on Nov 24th, 2015 - By pthomas2

Long-Range Communication Network in the Type 1B Bone Morphogenetic Protein Receptor

Posted on Nov 20th, 2015 - By pthomas2

Origin of the Enigmatic Stepwise Tight-Binding Inhibition of Cyclooxygenase-1

Posted on Nov 20th, 2015 - By pthomas2

The RNA Stem–Loop to G-Quadruplex Equilibrium Controls Mature MicroRNA Production inside the Cell

Posted on Nov 19th, 2015 - By pthomas2

A Ferredoxin Disulfide Reductase Delivers Electrons to the Methanosarcina barkeri Class III Ribonucleotide Reductase

Posted on Nov 19th, 2015 - By pthomas2

Sequence Variation in the Response Element Determines Binding by the Transcription Factor p73

Posted on Nov 18th, 2015 - By pthomas2

Differential Large-Amplitude Breathing Motions in the Interface of FKBP12–Drug Complexes

Posted on Nov 18th, 2015 - By pthomas2

CD/MCD/VTVH-MCD Studies of Escherichia coli Bacterioferritin Support a Binuclear Iron Cofactor Site

Posted on Nov 18th, 2015 - By pthomas2

Streptomyces wadayamensis MppP Is a Pyridoxal 5′-Phosphate-Dependent l-Arginine α-Deaminase, γ-Hydroxylase in the Enduracididine Biosynthetic Pathway

Posted on Nov 17th, 2015 - By pthomas2

A Novel Role of Salt-Inducible Kinase 1 (SIK1) in the Post-Translational Regulation of Scavenger Receptor Class B Type 1 Activity

Posted on Nov 16th, 2015 - By pthomas2

Key Role of the Adenylate Moiety and Integrity of the Adenylate-Binding Site for the NAD+/H Binding to Mitochondrial Apoptosis-Inducing Factor

Posted on Nov 16th, 2015 - By pthomas2

The N- and C-Terminal Domains Differentially Contribute to the Structure and Function of Dystrophin and Utrophin Tandem Calponin-Homology Domains

Posted on Nov 13th, 2015 - By pthomas2

Mass Spectrometric Analysis of Surface-Exposed Regions in the Hexadecameric Phosphorylase Kinase Complex

Posted on Nov 13th, 2015 - By pthomas2

A Phosphotyrosine Switch Controls the Association of Histone Mark Readers with Methylated Proteins

Posted on Nov 13th, 2015 - By Bronwyn Kate Irving-Hooper and Olivier Binda

Disulfide-Linked Dinitroxides for Monitoring Cellular Thiol Redox Status through Electron Paramagnetic Resonance Spectroscopy

Posted on Nov 13th, 2015 - By pthomas2

Long-Range Effects of Na+ Binding in Na,K-ATPase Reported by ATP

Posted on Nov 12th, 2015 - By pthomas2

Transition State Charge Stabilization and Acid–Base Catalysis of mRNA Cleavage by the Endoribonuclease RelE

Posted on Nov 12th, 2015 - By Brian F. Dunican, David A. Hiller and Scott A. Strobel

Helix-Capping Histidines: Diversity of N–H···N Hydrogen Bond Strength Revealed by 2hJNN Scalar Couplings

Posted on Nov 12th, 2015 - By pthomas2

A Rigid Hinge Region Is Necessary for High-Affinity Binding of Dimannose to Cyanovirin and Associated Constructs

Posted on Nov 12th, 2015 - By pthomas2

Bidirectional Transformation of a Metamorphic Protein between the Water-Soluble and Transmembrane Native States

Posted on Nov 11th, 2015 - By Koji Tanaka, Jose M. M. Caaveiro and Kouhei Tsumoto

Detection of RNA–Protein Interactions in Living Cells with SHAPE

Posted on Nov 11th, 2015 - By pthomas2