Article
Chemistry, Physical
Christina Felbek, Federica Arrigoni, David de Sancho, Aurore Jacq-Bailly, Robert B. Best, Vincent Fourmond, Luca Bertini, Christophe Leger
Summary: The study investigates the inhibitory mechanism of hydrogen sulfide on FeFe hydrogenase through a combination of various experimental and theoretical methods, revealing the underlying mechanisms and providing insights into the oxidation and reduction of the enzyme. Additionally, it was observed that the inhibition by sulfide may lead to irreversible inactivation of the hydrogenase.
Article
Nuclear Science & Technology
O. Lindblom, T. Ahlgren, K. Heinola
Summary: This study utilizes molecular dynamics simulations to explain the exchange process of hydrogen isotopes in metals, finding that lattice mono-vacancies and small vacancy clusters produced in irradiation experiments exhibit isotope exchange at low temperatures. Additionally, the isotope exchange process may occur in other hydrogen trapping defects with similar properties as vacancies.
NUCLEAR MATERIALS AND ENERGY
(2021)
Article
Multidisciplinary Sciences
Rhiannon M. Evans, Natalie Krahn, Bonnie J. Murphy, Harrison Lee, Fraser A. Armstrong, Dieter Soll
Summary: The study investigates the impact of substituting cysteine with selenocysteine on the function of [NiFe]-hydrogenases, revealing that while the activity of the enzymes is reduced after substitution, variants with selenocysteine show significant differences in O-2 tolerance and electrocatalytic properties.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Andrew E. Huckleby, Jhawn G. Saul, Hyunshun Shin, Staci Desmarais, Apparao Bokka, Junha Jeon, Sung-Kun Kim
Summary: This study demonstrated the inhibitory effect of two compounds with two hydroxamate functional groups on MBL from Bacillus anthracis. The inhibition was found to be competitive and the compounds showed potential as inhibitors to overcome bacterial resistance.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Harmandeep Kaur Gulati, Sushil Choudhary, Nitish Kumar, Ajaz Ahmed, Kavita Bhagat, Jatinder Vir Singh, Atamjit Singh, Ajay Kumar, Preet Mohinder Singh Bedi, Harbinder Singh, Debaraj Mukherjee
Summary: This study successfully reduced the hepatotoxicity of Tacrine by synthesizing Tacrine-linked sugar conjugates, and identified one compound with good AChE inhibition activity, which can be further explored for its mechanism of action in Alzheimer's disease treatment.
BIOORGANIC CHEMISTRY
(2022)
Article
Geochemistry & Geophysics
Andrew C. Turner, Nicholas J. Pester, Markus Bill, Mark E. Conrad, Kevin G. Knauss
Summary: The hydrogen isotopic composition of methane can serve as an indicator of gas origins. This study presents experimental constraints on the kinetics of hydrogen isotope exchange between methane and supercritical water, showing that exchange rates vary with temperature and suggesting the influence of life activity and thermogenic natural gas systems. The findings have implications for understanding the signatures of methane and water on Earth and other planetary bodies.
GEOCHIMICA ET COSMOCHIMICA ACTA
(2022)
Article
Polymer Science
Sarah C. Seeger, Kevin D. Dorfman, Timothy P. Lodge
Summary: The combination of umbrella sampling and dissipative particle dynamics simulations reveals that the core block A of the expelled chain remains partially stretched at the transition state. The free energy barrier linearly increases with the Flory-Huggins interaction parameter chi, and the spherical core structure deforms near the transition state at large interaction energies.
Article
Biochemistry & Molecular Biology
Victoria J. Laye, Shahlo Solieva, Vincent A. Voelz, Shiladitya DasSarma
Summary: In this study, the polyextremophilic activity of the beta-galactosidase enzyme in the haloarchaeon Halorubrum lacusprofundi was investigated. The results showed that the catalytic efficiency of the enzyme improved with increasing temperature and salinity, while the substrate binding capacity decreased with decreasing temperatures and increasing salinity. Molecular dynamics simulations revealed that the enzyme's flexibility played a crucial role in its function, and regions distant from the active site were found to be important in adapting to extreme conditions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Benjamin P. Brown, Yun-Kai Zhang, Soyeon Kim, Patrick Finneran, Yingjun Yan, Zhenfang Du, Jiyoon Kim, Abigail Leigh Hartzler, Michele L. LeNoue-Newton, Adam W. Smith, Jens Meiler, Christine M. Lovly
Summary: Oncogenic mutations in EGFR are common in non-small-cell lung carcinomas. Among the different EGFR mutations, exon 19 deletion (ex19del) is the most common subtype. This study investigates the functional differences among ex19del variants and how they affect protein structure and function. The findings demonstrate that these variants can alter cell growth, dimerization, enzyme kinetics, and sensitivity to tyrosine kinase inhibitors.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Chemistry, Physical
Xudong Mao, Xiaojun Hu, Weiyu Cui, Hiroyuki Matsuura, Fumitaka Tsukihashi, Kuochih Chou
Summary: A novel isotope exchange method is developed for measuring the rate constant of hydrogen production from water and steelmaking slag. The apparent rate constant of the reaction increases with temperature and the probable rate controlling steps of reaction are biased towards interfacial chemical reaction.
INTERNATIONAL JOURNAL OF HYDROGEN ENERGY
(2023)
Article
Chemistry, Multidisciplinary
Claudia Brocks, Chandan K. Das, Jifu Duan, Shanika Yadav, Ulf-Peter Apfel, Subhasri Ghosh, Eckhard Hofmann, Martin Winkler, Vera Engelbrecht, Lars V. Schaefer, Thomas Happe
Summary: This study proposes a new strategy to improve the O-2 stability of [FeFe]-hydrogenases by blocking the O-2 diffusion pathway and protecting the catalytic cofactor.
Article
Chemistry, Physical
Ion Mitxelena, Xabier Lopez, David de Sancho
Summary: Markov state models (MSMs) are a preferred method for analyzing and interpreting molecular dynamics simulations of conformational transitions in biopolymers. By utilizing hierarchical density-based clustering, it is possible to define slow dynamics more effectively and consistently with the assumption of Markovianity.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Polymer Science
Sarah C. Seeger, Timothy P. Lodge, Kevin D. Dorfman
Summary: By using dissipative particle dynamics simulations and umbrella sampling, we investigated the dependence of the free energy trajectory for chain expulsion from a diblock copolymer micelle in a selective solvent on the core chain length. It was found that the free energy barrier scales linearly with the core block length of the expelled tracer chain, and the simulations revealed the mechanism of chain expulsion.
Article
Biochemistry & Molecular Biology
Rafael de Almeida Barros, Yaremis Merino-Cabrera, Jose Severiche Castro, Neilier Rodrigues da Silva Junior, Joao Vitor Aguilar de Oliveira, Halina Schultz, Rafael Junior de Andrade, Humberto Josue de Oliveira Ramos, Maria Goreti de Almeida Oliveira
Summary: This study aimed to investigate the feasibility of using inhibitory proteins as potential inhibitors of digestive enzymes in pests. The results showed that the protein extracted from mammals can competitively interact with the pest's digestive enzymes, effectively reducing their activity and causing a decrease in larval survival rate and pupal weight.
PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY
(2022)
Article
Chemistry, Physical
Andreas Rutz, Chandan K. Das, Andrea Fasano, Jan Jaenecke, Shanika Yadav, Ulf-Peter Apfel, Vera Engelbrecht, Vincent Fourmond, Christophe Leger, Lars Schaefer, Thomas Happe
Summary: The active site of [FeFe]-hydrogenases degrades upon contact with oxygen, but the protein structure of a certain hydrogenase (CbA5H) allows its active site to be protected, reducing degradation caused by oxygen. By modifying the surface residue, the hydrogenase's resistance to oxygen can be increased.
Article
Multidisciplinary Sciences
Delfim Ferreira, Ana C. C. Barbosa, Goncalo P. Oliveira, Teresa Catarino, Sofia S. Venceslau, Ines A. C. Pereira
Summary: Dissimilatory sulfur metabolism is widespread among bacteria and archaea, with DsrAB and other Dsr proteins playing key roles. DsrD acts as an activator of DsrAB and its function is still debated.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Chemistry, Multidisciplinary
Filippo Carboni, Annabel Kitowski, Charlotte Sorieul, Daniele Veggi, Marta C. Marques, Davide Oldrini, Evita Balducci, Barbara Brogioni, Linda Del Bino, Alessio Corrado, Francesca Angiolini, Lucia Dello Iacono, Immaculada Margarit, Maria Rosaria Romano, Goncalo J. L. Bernardes, Roberto Adamo
Summary: The introduction of glycoconjugate vaccines has improved the immune response against infectious diseases. However, the conjugation site and strategy greatly affect the immunogenic properties of the vaccine, and more research is needed to fully understand this relationship.
Article
Biochemistry & Molecular Biology
Marta C. Marques, Diana Lousa, Patricia M. Silva, Andre F. Faustino, Claudio M. Soares, Nuno C. Santos
Summary: Nipah virus is an emerging zoonotic virus with a high mortality rate and no available antiviral drugs. This study evaluated the properties of lipid-tagged peptides and their interaction with biomembranes, with the goal of developing effective antiviral therapies. The results suggest that these peptides, with specific lipid tags, show potential as inhibitors of Nipah virus fusion.
Article
Chemistry, Multidisciplinary
Alena Istrate, Michael B. Geeson, Claudio D. Navo, Barbara B. Sousa, Marta C. Marques, Ross J. Taylor, Toby Journeaux, Sebastian R. Oehler, Michael R. Mortensen, Michael J. Deery, Andrew D. Bond, Francisco Corzana, Gonzalo Jimenez-Oses, Goncalo J. L. Bernardes
Summary: In this study, a new protein conjugation strategy using CPO-based reagents for selective modification of N-terminal cysteine residues was reported. The method achieved stable linkage under mild conditions and was compatible with common reducing agent DTT.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Multidisciplinary
Claudia F. Afonso, Marta C. Marques, Joao P. M. Antonio, Carlos Cordeiro, Pedro M. P. Gois, Pedro M. S. D. Cal, Goncalo J. L. Bernardes
Summary: Post-translational modifications of histones, such as lysine acetylation, play a crucial role in regulating chromatin structure and function. However, studying the individual contribution of single acetylation events has been challenging due to the difficulty in obtaining homogeneous samples of histones with a single acetylation. In this study, the authors developed a click-to-acetylate approach that allows for controlled, site-specific acetylation of a single lysine residue, enabling easier access to and study of acetylated histones.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Meeting Abstract
Biochemistry & Molecular Biology
Ines A. C. Pereira
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS
(2022)
Meeting Abstract
Biochemistry & Molecular Biology
Julien Maillard, Lorenzo Cimmino, Babatunde Ekundayo, Dongchun Ni, Americo G. Duarte, Ines A. C. Pereira, Christof Holliger
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS
(2022)
Article
Microbiology
Delfim Ferreira, Sofia S. S. Venceslau, Raquel Bernardino, Andre Preto, Lichun Zhang, Jacob R. R. Waldbauer, William D. D. Leavitt, Ines A. C. Pereira
Summary: DsrC is a crucial protein in dissimilatory sulfur metabolism, serving as a co-substrate of the dissimilatory sulfite reductase DsrAB. It has been found to have additional functions beyond sulfite reduction. In this study, the role of DsrC in fermentative growth of Desulfovibrio vulgaris Hildenborough was investigated, and it was found that impairment of DsrC function led to reduced growth and a shift towards more fermentative metabolism.
ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Chemistry, Physical
Jose M. Abad, Marcos Pita, Antonio L. De Lacey
Summary: Monolayer-Protected Gold Clusters (AuMPCs) have attracted great interest as nanoscale capacitors in aqueous media for various nanobiotechnological applications. However, achieving subattofarad double-layer capacitance and single-electron charging has been challenging. In this study, we successfully synthesized Thioctic Acid Monolayer-Protected Au Clusters (TA-AuMPCs) that exhibited electrochemical single electron quantized capacitance charging in both organic and aqueous solutions. The functional carboxylic groups present in TA-AuMPCs provide a simple strategy for interfacing nanoparticles with biomolecules for biological electron transfer reactions.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Chemistry, Multidisciplinary
Vladimir Pelmenschikov, Delfim Ferreira, Sofia S. Venceslau, Peter Hildebrandt, Ines A. . C. Pereira, Smilja Todorovic, Smilja Todorovic
Summary: In this study, resonance Raman spectroscopy and density functional theory calculations were used to investigate the structural, electronic, and vibrational properties of the noncubane [4Fe-4S] cluster in heterodisulfide reductase (HdrB). Homology modeling was employed to predict the protein environment of the neighboring clusters in DvHdrB. The results showed that the oxidized [4Fe-4S](3+) cluster adopts a closed conformation in the absence of substrate, but transitions to an open structure upon substrate coordination, accompanied by a ligand switch. This study provides valuable insights for future research on enzymes with this unconventional cofactor.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Ecology
Sinje Neukirchen, Ines A. C. Pereira, Filipa L. Sousa
Summary: Microbial dissimilatory sulfur metabolism plays a significant role in Earth's biochemical sulfur cycle. Comparative genomics and phylogenetic analyses indicate an archaeal origin of the minimal DsrABCMK(N) protein set, with sulfite reduction as its primordial function. The acquisition of additional Dsr proteins increased the complexity of the Dsr pathway. Further discoveries of two types of Qmo complexes allowed microorganisms to use sulfate as an electron acceptor. Chlorobi and Proteobacteria evolved the ability to use the Dsr pathway for sulfur oxidation independently.
Article
Nanoscience & Nanotechnology
Keyvan Jodeiri, Aleksandra Foerster, Gustavo F. Trindade, Jisun Im, Diego Carballares, Roberto Fernandez-Lafuente, Marcos Pita, Antonio L. De Lacey, Christopher Parmenter, Christopher Tuck
Summary: The drive for miniaturization in enzyme-based bioelectronics has led to the development of 3D microstructured electrodes. Additive manufacturing combined with electroless metal plating allows the production of these electrodes with high surface area. The challenge lies in ensuring strong adhesion between the metal layer and polymer structure, which has been achieved in this study through the introduction of an interfacial adhesion layer.
ACS APPLIED MATERIALS & INTERFACES
(2023)
Meeting Abstract
Biochemistry & Molecular Biology
M. Saramago, V. G. Costa, C. S. Souza, C. Barria, S. Domingues, S. C. Viegas, D. Lousa, C. M. Soares, C. M. Arraiano, R. G. Matos
Meeting Abstract
Biochemistry & Molecular Biology
R. Teixeira, M. Valerio, L. Borges-Araujo, M. N. Melo, J. B. Vicente, D. Lousa, C. M. Soares
Meeting Abstract
Biochemistry & Molecular Biology
M. Valerio, L. Borges-Araujo, M. Nuno Melo, D. Lousa, C. Manuel Soares