Review
Plant Sciences
Damien Caubriere, Anna Moseler, Nicolas Rouhier, Jeremy Couturier
Summary: This review focuses on the biochemical, structural, and physiological roles of cysteine desulfurases in sulfur-dependent biosynthetic pathways in photosynthetic organisms, with particular emphasis on Arabidopsis isoforms. Cysteine desulfurases are highly conserved enzymes that catalyze the extraction of sulfur from cysteine, leading to the formation of persulfide groups on catalytic cysteine residues. The sulfur is then transferred to various targets, including iron-sulfur clusters and molybdenum cofactors. While there is extensive knowledge about cysteine desulfurases in some pathways, such as iron-sulfur cluster synthesis, our understanding of their involvement in other pathways, especially in photosynthetic organisms, is limited. This review summarizes the current knowledge of cysteine desulfurases and highlights gaps in understanding, emphasizing the need for future research in this area.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Biochemistry & Molecular Biology
Ryosuke Nakamura, Shoko Ogawa, Yasuhiro Takahashi, Takashi Fujishiro
Summary: This study investigated the inhibition mechanisms of SufS by D-cycloserine (DCS) and L-cycloserine (LCS), and found that they act through different mechanisms and result in different products. The study also identified the importance of key residues in the inhibition mechanisms through the investigation of SufS variants. These findings provide valuable insights for the structure-based design of new drugs targeting SufS.
Article
Chemistry, Medicinal
Juan P. Rincon Pabon, Brent A. Kochert, Yan-Hui Liu, Douglas D. Richardson, David D. Weis
Summary: Affinity chromatography is widely used for antibody purification in biopharmaceutical production, and here we used hydrogen exchange-mass spectrometry to study the conformational changes in the NIST mAb upon binding with a protein A matrix. The results showed increased protection in certain regions of the antibody structure when bound to ProA, but this effect was not observed with lower ProA concentration or when ProA resin was used.
JOURNAL OF PHARMACEUTICAL SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Ingie Elchennawi, Philippe Carpentier, Christelle Caux, Marine Ponge, Sandrine Ollagnier de Choudens
Summary: Iron-sulfur (Fe-S) clusters are essential for cellular pathways and require proteins to mobilize sulfur and iron for their assembly. The SUF system in Mycobacterium tuberculosis is the primary Fe-S biogenesis system and a potential target for fighting tuberculosis. In this study, two proteins of the Mtb SUF system, Rv1464(sufS) and Rv1465(sufU), were characterized and their interaction and activities in Fe-S biogenesis were investigated.
Article
Chemistry, Analytical
Ramin Ekhteiari Salmas, Antoni James Borysik
Summary: The quantification of hydrogen deuterium exchange (HDX) kinetics provides information on the stability of individual amino acids in proteins. The new programming tool HDXmodeller allows for optimization of low-resolution HDX-mass spectrometry (MS) data to understand exchange rates of individual amino acids. The tool also has a unique autovalidation method based on a covariance matrix for quantifying the accuracy of modeled exchange rates.
ANALYTICAL CHEMISTRY
(2021)
Article
Multidisciplinary Sciences
Sven-A Freibert, Michal T. Boniecki, Claudia Stuempfig, Vinzent Schulz, Nils Krapoth, Dennis R. Winge, Ulrich Muehlenhoff, Oliver Stehling, Miroslaw Cygler, Roland Lill
Summary: The conserved N-terminal Tyr35 of ISCU2 plays a crucial mechanistic role in de novo mitochondrial [2Fe-2S] cluster synthesis, with ionic forces replacing Tyr-Tyr interactions during dimerization-induced [2Fe-2S] cluster formation. Hydrophobic interaction of two conserved N-terminal tyrosines induces ISCU2 dimerization and concomitant [2Fe-2S] cluster synthesis.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Daniele Peterle, Elena S. Klimtchuk, Thomas E. Wales, Florian Georgescauld, Lawreen H. Connors, John R. Engen, Olga Gursky
Summary: This study identifies the N32T substitution in the CRD1 of lambda 6 LC as a driver of amyloid formation, which increases the amyloidogenic propensity of the CDR1 loop and accelerates amyloid growth. The destabilizing effects of N32T propagate across the molecule and impact regions up to 30 angstrom away from the substitution site, suggesting long-range effects of a conservative point substitution in a dynamic surface loop relevant to Ig function. Comparisons between patient-derived and engineered proteins indicate that interactions between N32T and other substitution sites contribute to amyloidosis, highlighting the critical role of CDR1 in amyloid formation by lambda 6 LCs.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Chemistry, Analytical
Joseph Anacleto, Cristina Lento, Vladimir Sarpe, Ayesha Maqsood, Banafsheh Mehrazma, David Schriemer, Derek J. Wilson
Summary: Hydrogen deuterium exchange mass spectrometry (HDX-MS) is a rapidly growing technique that provides information about the dynamic structural changes in proteins during biological function. The continuous flow injection setup for time-resolved HDX-MS (CFI-TRESI-HDX) introduced in this work allows for automated, continuous or discrete labeling time measurements from milliseconds to hours, with substantially reduced runtimes compared to conventional systems.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Eric Largy, Matthieu Ranz
Summary: Hydrogen-deuterium exchange mass spectrometry (HDX/MS) is used for studying protein conformation dynamics and characterizing oligonucleotide conformations and their interactions with cations, small molecules, and proteins. OligoR is a web-based application that provides dedicated solutions for processing and visualizing native HDX/MS data of oligonucleotides. It offers a simple and robust approach to deconvoluting bimodal isotope distributions and can be extended to various analytes. The results are presented in interactive data tables and can be exported as publication-quality figures.
ANALYTICAL CHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Rohit Jain, Khaja Muneeruddin, Jeremy Anderson, Michael J. Harms, Scott A. Shaffer, C. Robert Matthews
Summary: The study revealed the folding mechanisms of bacterial IGPS TIM barrel enzyme using HDX-MS, identifying protected sites and stable cores, and emphasizing the key role of hydrophobicity in stabilizing high-energy folding intermediates.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemical Research Methods
Kellye A. Cupp-Sutton, Thomas Welborn, Mulin Fang, Joel B. Langford, Zhe Wang, Kenneth Smith, Si Wu
Summary: Hydrogen-deuterium exchange mass spectrometry (HDX-MS) is a powerful technique to study protein dynamics and binding, but its data analysis can be challenging and time-consuming. Therefore, there is a need for a simple, open-source software package to analyze large and highly complex protein systems. In this regard, The Deuterium Calculator, a Python-based software package for HDX-MS data analysis, has been developed. It allows for differential and nondifferential HDX-MS analysis, generates standardized data files for increased transparency, and provides statistical analysis and data visualization through Woods' plots.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Vinzent Schulz, Somsuvro Basu, Sven-A Freibert, Holger Webert, Linda Boss, Ulrich Muehlenhoff, Fabien Pierrel, Lars-O Essen, Douglas M. Warui, Squire J. Booker, Oliver Stehling, Roland Lill
Summary: This study identifies new biochemical functions of mitochondrial ferredoxins and provides structural insights into their functional specificity.
NATURE CHEMICAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Jasmin Duelfer, Hao Yan, Maxim N. Brodmerkel, Robert Creutznacher, Alvaro Mallagaray, Thomas Peters, Carl Caleman, Erik G. Marklund, Charlotte Uetrecht
Summary: Noroviruses are the main cause of viral gastroenteritis, with different strains showing strain-dependent glycan-induced protein dynamics, influenced by the prevalence in humans. Deamidation of N373 also plays a role in modulating glycan-mediated cell attachment in GII.4 strains, indicating a complex relationship between deamidation and glycan binding dynamics.
Article
Biochemical Research Methods
Clint Vorauer, Michael S. Wrigley, Juan P. Rincon Pabon, Michael J. Watson, Charlie C. Mundorff, David D. Weis, Miklos Guttman
Summary: This study presents a simple method using common peptide cocktails as substrates to serve as a rapid check of pepsin column activity, helping to improve data quality in HDX-MS studies.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2021)
Article
Chemistry, Multidisciplinary
Mariia A. Beliaeva, Florian P. Seebeck
Summary: The physiological function of Ergothioneine is still unclear, but it may play a fundamental role in cellular life. Different types of bacteria and fungi produce Ergothioneine through sulfur transfer reactions catalyzed by different enzymes. A metallopterin-dependent Ergothioneine synthase has been identified in Caldithrix abyssi, which contains multiple domains for Ergothioneine synthesis.
Article
Biochemistry & Molecular Biology
Yuyuan Dai, Dokyong Kim, Guangchao Dong, Laura S. Busenlehner, Patrick A. Frantom, F. Wayne Outten
Review
Biochemistry & Molecular Biology
F. Wayne Outten
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH
(2015)
Article
Biochemistry & Molecular Biology
Kei Hirabayashi, Eiki Yuda, Naoyuki Tanaka, Sumie Katayama, Kenji Iwasaki, Takashi Matsumoto, Genji Kurisu, F. Wayne Outten, Keiichi Fukuyama, Yasuhiro Takahashi, Kei Wada
JOURNAL OF BIOLOGICAL CHEMISTRY
(2015)
Article
Multidisciplinary Sciences
David A. Hanna, Raven M. Harvey, Osiris Martinez-Guzman, Xiaojing Yuan, Bindu Chandrasekharan, Gheevarghese Raju, F. Wayne Outten, Iqbal Hamza, Amit R. Reddi
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2016)
Article
Biochemistry & Molecular Biology
Dokyong Kim, Harsimran Singh, Yuyuan Dai, Guangchao Dong, Laura S. Busenlehner, F. Wayne Outten, Patrick A. Frantom
Article
Biochemistry & Molecular Biology
Matthew Blahut, Stephen Dzul, Suning Wang, Ashoka Kandegedara, Nicholas E. Grossoehme, Timothy Stemmler, F. Wayne Outten
JOURNAL OF INORGANIC BIOCHEMISTRY
(2018)
Article
Microbiology
Clorissa L. Washington-Hughes, Geoffrey T. Ford, Alsten D. Jones, Kimberly McRae, F. Wayne Outten
Article
Biochemistry & Molecular Biology
Jack A. Dunkle, Michael R. Bruno, F. Wayne Outten, Patrick A. Frantom
Article
Biochemistry & Molecular Biology
Joshua D. Wofford, Naimah Bolaji, Nathaniel Dziuba, F. Wayne Outten, Paul A. Lindahl
JOURNAL OF BIOLOGICAL CHEMISTRY
(2019)
Article
Biochemistry & Molecular Biology
Claudia Montllor-Albalate, Alyson E. Colin, Bindu Chandrasekharan, Naimah Bolaji, Joshua L. Andersen, F. Wayne Outten, Amit R. Reddi
Article
Biochemistry & Molecular Biology
Matthew Blahut, Courtney E. Wise, Michael R. Bruno, Guangchao Dong, Thomas M. Makris, Patrick A. Frantom, Jack A. Dunkle, F. Wayne Outten
JOURNAL OF BIOLOGICAL CHEMISTRY
(2019)
Article
Engineering, Biomedical
Leman Buzoglu Kurnaz, Swagatam Barman, Xiaoming Yang, Claire Fisher, F. Wayne Outten, Prakash Nagarkatti, Mitzi Nagarkatti, Chuanbing Tang
Summary: Inspired by the facial amphiphilic nature and antimicrobial efficacy of antimicrobial peptides, this study developed a new class of facial amphiphilic bicyclic naphthoic acid derivatives that were attached to poly(glycidyl methacrylate). These polymers exhibited potent antibacterial activity against multi-drug resistant gram-negative pathogens and showed low hemolysis and high antimicrobial selectivity. They were also effective in eradicating biofilms and killing dormant cells, suggesting a mechanism of action through membrane disruption. Overall, these facial amphiphiles have the potential to address antimicrobial resistance in both planktonic and biofilm-related infections.
Review
Biochemistry & Molecular Biology
Matthew Blahut, Enis Sanchez, Claire E. Fisher, F. Wayne Outten
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH
(2020)
Meeting Abstract
Biochemistry & Molecular Biology
F. Wayne Outten, Naimah Bolaji, Joshua Wofford, Paul Lindahl
Meeting Abstract
Chemistry, Multidisciplinary
F. Wayne Outten
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY
(2016)