Article
Chemistry, Multidisciplinary
Jiali Yang, Takahiro Mori, Xingxing Wei, Yudai Matsuda, Ikuro Abe
Summary: The novel isomerase NsrQ from Aspergillus novofumigatus plays a key role in the biosynthesis of fungal tetrahydroxanthones by catalyzing a two-step isomerization reaction. Through biochemical and structural characterizations, it was found that NsrQ and its homologue Dcr3 utilize Glu and His residues as acid-base catalysts and important hydrophobic residues for shaping the active site pocket for substrate binding. The crystal structures of NsrQ and Dcr3 revealed their cone-shaped alpha + beta barrel fold and similarities to the nuclear transport factor 2-like superfamily enzymes.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Multidisciplinary
Gabriela C. Schroder, William B. O'Dell, Simon P. Webb, Pratul K. Agarwal, Flora Meilleur
Summary: Metalloproteins catalyze redox reactions using their metallocofactors. Lytic polysaccharide monooxygenases (LPMOs) are copper-dependent enzymes that degrade recalcitrant polysaccharides. Neutron protein crystallography reveals the initial steps of oxygen activation in Neurospora crassa LPMO9D, with His157 identified as the proton donor. His1 and His161 also display conformational flexibility.
Article
Biochemistry & Molecular Biology
Alfonso Labra-Nunez, Luis Fernando Cofas-Vargas, Gabriel Gutierrez-Magdaleno, Homero Gomez-Velasco, Annia Rodriguez-Hernandez, Adela Rodriguez-Romero, Enrique Garcia-Hernandez
Summary: In this study, the energetic and structural characterization of beta-lactoglobulin molecular recognition at different pH values above and below the Tanford transition zone sheds new light on the interplay between self-association, ligand binding, and conformational states. The combined analysis of crystallographic, calorimetric, and molecular dynamics data reveals novel aspects underlying the molecular recognition mechanism of this enigmatic lipocalin.
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS
(2021)
Article
Biochemistry & Molecular Biology
Gapisha Karunakaran, Yidai Yang, Veronique Tremblay, Zhibin Ning, Jade Martin, Amine Belaouad, Daniel Figeys, Joseph S. Brunzelle, Patrick M. Giguere, Alain Stintzi, Jean-Francois Couture
Summary: Crohn's disease is a chronic inflammation of the gastrointestinal tract associated with dysbiosis of the microbiome and immune system defects. This study characterizes two cysteine desulfurase enzymes in Atopobium parvulum, an H2S producer, and suggests that a better understanding of these enzymes could lead to potential CD treatments.
Article
Biochemistry & Molecular Biology
Zhenzhen Chen, Qiong Guo, Gao Wu, Jie Wen, Shanhui Liao, Chao Xu
Summary: The study examined the crystal structures of PCO2, PCO4, and PCO5 from Arabidopsis thaliana (AtPCOs) and their in vitro activity through Mass spectrometry (MS). By analyzing the Tris-bound AtPCO2 structure and performing mutagenesis experiments, key residues involved in N-Cys recognition and oxidation were identified. This research not only uncovered the substrate recognition and catalytic mode by AtPCOs, but also provides insights for the future design of potent inhibitors for plant cysteine oxidases.
JOURNAL OF STRUCTURAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Malgorzata Magoch, Alastair G. McEwen, Valeria Napolitano, Benedykt Wladyka, Grzegorz Dubin
Summary: Staphylococcus aureus is a common pathogen causing various infections in humans and livestock. This study reveals the three-dimensional structure and active site of staphopain C (ScpA2), a major protease secreted by certain strains of S. aureus. Considering its involvement in a chicken disease, this research lays the groundwork for inhibitor design and potential antimicrobial strategies against this pathogen.
Article
Biochemistry & Molecular Biology
Maximilian K. G. Ehrhardt, Monica L. Gerth, Jodie M. Johnston
Summary: Chemotaxis is the process of bacteria sensing chemical gradients and navigating towards favourable conditions through trans-membrane chemoreceptor proteins. Pseudomonas syringae pv. actinidiae (Psa) has a large number of chemoreceptors encoded in its genome, with many remaining uncharacterized.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2021)
Article
Physics, Applied
Jong Woo Kim, Mathew J. Cherukara, Ashish Tripathi, Zhang Jiang, Jin Wang
Summary: Coherent surface scattering imaging requires a mathematical conversion to visualize specimen structures, which can now be predicted using a deep learning neural network model to instantly obtain results from scattering patterns. This is highly beneficial for both experimental effectiveness and data analysis.
APPLIED PHYSICS LETTERS
(2021)
Article
Chemistry, Multidisciplinary
Cen Chen, Ziyuan Fang, Zhen Huang
Summary: Crystallization phasing and obtaining high-quality crystals are major challenges for X-ray crystallographic analysis of nucleic acids. In this study, the authors addressed these challenges by incorporating selenium atoms into DNA duplexes, which resulted in larger and higher quality crystals compared to standard DNA crystals. These findings provide a simple strategy to overcome crystallization challenges in nucleic acid crystallography.
CRYSTAL GROWTH & DESIGN
(2022)
Article
Medicine, General & Internal
Saeideh Hashemi-Hafshejani, Ahmad Reza Meamar, Maryam Moradi, Nasrin Hemmati, Shahram Solaymani-Mohammadi, Elham Razmjou
Summary: The study identified the genetic diversity of G. duodenalis isolates in Tehran using multilocus sequence typing. Assemblages A and B were the main sources of infection in humans, and dual infections with both assemblages were common. Assemblage A isolates showed low genetic polymorphism, while assemblage B isolates had high genetic variations. Further research is needed to determine the specific multilocus genotypes and the transmission modes in different host populations.
FRONTIERS IN MEDICINE
(2022)
Article
Multidisciplinary Sciences
Akimitsu Higuchi, Wataru Shihoya, Masae Konno, Tatsuya Ikuta, Hideki Kandori, Keiichi Inoue, Osamu Nureki
Summary: SzRs, a newly identified rhodopsin family in Asgard archaea, exhibit unique kinetic behaviors in inward H+ release compared to other H+ pumps. The crystal structure of SzR AM_5_00977 revealed that key residues and structural features are different from other microbial rhodopsins, suggesting a distinct mechanism for inward H+ release.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biology
Hai Li, Chia-Ying Huang, Elena G. Govorunova, Oleg A. Sineshchekov, Adrian Yi, Kenneth J. Rothschild, Meitian Wang, Lei Zheng, John L. Spudich
Summary: The crystal structure of bromide-bound GtACR1 reveals structural changes that relax the constrictions of the channel and involve a novel salt-bridge switch mechanism. These findings suggest that substrate binding induces a transition from an inactivated state to a pre-activated state in the dark, facilitating channel opening.
Review
Crystallography
Nathan Smith, Mark A. Wilson
Summary: This review discusses the use and potential of new time-resolved serial crystallographic methods to study cysteine-dependent enzymes, with a focus on the cysteine proteases of SARS-CoV-2 and other examples. It also explores emerging X-ray techniques, such as time-resolved sulfur X-ray spectroscopy, for detecting changes in sulfur charge states and covalency during catalysis or regulatory modification. In summary, cysteine-dependent enzymes are attractive targets for time-resolved serial crystallography approaches, which can reveal structural and dynamic changes during catalysis in crystalline samples.
Article
Biochemistry & Molecular Biology
Magdalena Masternak, Angela Koch, Saara Laulumaa, Daniel Tapken, Michael Hollmann, Flemming Steen Jorgensen, Jette Sandholm Kastrup
Summary: Ionotropic glutamate receptors play a crucial role in fast excitatory neurotransmission in the brain. This study focuses on the subfamily of delta receptors, GluD1 and GluD2, which bind to glycine/D-serine instead of glutamate. GluD1 is widely expressed in the brain and inner ear, and its dysfunction has been associated with various mental disorders. The X-ray crystal structure of the ligand-binding domain (LBD) of GluD1 (GluD1-LBD) is reported here, revealing that D-serine binds to GluD1-LBD with higher affinity compared to GluD2-LBD. The study also identifies a specific amino acid, Glu822, as a crucial determinant of receptor activation in GluD1 A654T. Differences in structure and dynamics between GluD1 and GluD2 are suggested by molecular dynamics simulations. These findings contribute to our understanding of the role and mechanism of action of GluD1 in neuronal signaling.
Article
Biochemistry & Molecular Biology
Sunbin Deng, Jiaxi Cai, Stephen C. Harrison, Huilin Zhou, Stephen M. Hinshaw
Summary: Successful mitosis relies on the correct attachment of chromosomes to microtubules. The kinetochore plays a crucial role in this process by recognizing specific chromatin and ensuring the formation of only one kinetochore per chromatid at the correct location. The crystal structure of the Cse4 peptide bound to the inner kinetochore Okp1-Ame1 complex provides insights into centromere recognition and the organization of the inner kinetochore.
Article
Biochemistry & Molecular Biology
Cynthia Fernandez-Lainez, Ignacio de la Mora-de La Mora, Sergio Enriquez-Flores, Itzhel Garcia-Torres, Luis A. Flores-Lopez, Pedro Gutierrez-Castrellon, Paul de Vos, Gabriel Lopez-Velazquez
Summary: Understanding the mechanisms of interaction between parasites and the human immune system is important in public health, biology, and medicine. This study focuses on the impact of Giardia lamblia's arginine deiminase on human TLR signaling and highlights the importance of its 3D structure in immunomodulation. Furthermore, it demonstrates the enzyme's influence on specific responses in infant-like dendritic cells.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Oncology
Vanessa Villegas-Ruiz, Isabel Medina-Vera, Paulina Arellano-Perdomo, Adriana Castillo-Villanueva, Cesar A. Galvan-Diaz, Rogelio Paredes-Aguilera, Roberto Rivera-Luna, Sergio Juarez-Mendez
Summary: B-cell acute lymphoblastic leukemia (B-ALL) is the most common childhood hematological malignancy. We found that the overexpression of BRCA1 gene could predict early relapse, while low expression of BRCA1 was associated with B-ALL relapse, suggesting BRCA1 as a potential molecular prognostic marker.
JOURNAL OF PEDIATRIC HEMATOLOGY ONCOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Renan Vergara, Tania Berrocal, Eva Isela Juarez Mejia, Sergio Romero-Romero, Isabel Velazquez-Lopez, Nancy O. Pulido, Haven A. Lopez A. Sanchez, Daniel-Adriano Silva, Miguel Costas, Adela Rodriguez-Romero, Rogelio Rodriguez-Sotres, Alejandro Sosa-Peinado, D. Alejandro Fernandez-Velasco
Summary: This article describes the ligand binding, conformational stability and folding kinetics of the Lysine Arginine Ornithine (LAO) binding protein from Salmonella thiphimurium and constructs corresponding to its two independent domains. The results reveal unexpected behavior of the continuous and discontinuous domains, indicating the crucial role of the continuous domain in nucleating folding.
Article
Biochemistry & Molecular Biology
Jorge Marcos-Viquez, Annia Rodriguez-Hernandez, Laura I. Alvarez-Anorve, Andrea Medina-Garcia, Jacqueline Plumbridge, Mario L. Calcagno, Adela Rodriguez-Romero, Ismael Bustos-Jaimes
Summary: This study describes the regulatory mechanism of Glucosamine-6-phosphate deaminase SdNagBII from Shewanella denitrificans using enzyme kinetics, isothermal titration calorimetry (ITC), and X-ray crystallography. The experiments revealed two different binding sites with distinctive thermodynamic signatures for the allosteric activator GlcNAc6P and the transition-state analog GlcNol6P. Crystallographic data demonstrated the presence of an unusual allosteric site that can bind both GlcNAc6P and GlcNol6P, suggesting that the homotropic activation of this enzyme arises from the occupation of the allosteric site by the substrate. This study unveils a novel mechanism to generate a high degree of homotropic activation in SdNagBII.
Article
Biochemistry & Molecular Biology
Maria G. Teran, Benjamin Garcia-Ramirez, Israel Mares-Mejia, Enrique Ortega, Andrea O'Malley, Maksymilian Chruszcz, Adela Rodriguez-Romero
Summary: Profilins are allergens that can cause IgE-cross-reactivity and the pollen-latex-food syndrome. Two monoclonal antibodies, 1B4 and 2D10, were generated against latex profilin and were found to inhibit the interaction between IgE and IgG4 antibodies in allergic patients. The study also showed that different plant profilins have varying recognition by these antibodies, and identified a specific residue that is essential for the recognition of certain profilins.
Article
Biochemistry & Molecular Biology
Ivan Ignacio-Mejia, Itzel Jatziri Contreras-Garcia, Julieta Griselda Mendoza-Torreblanca, Omar Noel Medina-Campos, Jose Pedraza-Chaverri, Mercedes Edna Garcia-Cruz, Antonio Romo-Mancillas, Saul Gomez-Manzo, Cindy Bandala, Maria Elena Sanchez-Mendoza, Luz Adriana Pichardo-Macias, Noemi Cardenas-Rodriguez
Summary: Epilepsy is a neurological disorder associated with oxidative stress. Some antiseizure drugs, including levetiracetam, have been found to have neuroprotective and antioxidant properties. This study evaluated the effects of levetiracetam on the oxidant-antioxidant status in the hippocampus of rats with temporal lobe epilepsy (TLE). The results showed that levetiracetam increased antioxidant enzyme activity, reduced hydrogen peroxide levels, and demonstrated scavenging activity against hydroxyl radicals.
Review
Biochemistry & Molecular Biology
Beatriz Hernandez-Ochoa, Daniel Ortega-Cuellar, Abigail Gonzalez-Valdez, Victor Martinez-Rosas, Laura Morales-Luna, Miriam Abigail Rojas-Alarcon, Montserrat Vazquez-Bautista, Roberto Arreguin-Espinosa, Veronica Perez de la Cruz, Rosa Angelica Castillo-Rodriguez, Luis Miguel Canseco-avila, Abraham Vidal-Limon, Saul Gomez-Manzo
Summary: Glucose-6-phosphate dehydrogenase (G6PD) deficiency is a genetic disorder that affects around 500 million people worldwide. Different variants of G6PD have been identified to produce varying phenotypes, ranging from mild to severe. Understanding the correlation between G6PD mutation sites and resulting phenotypes is crucial for clinical diagnosis and personalized treatment of G6PD deficiency patients.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Itzhel Garcia-Torres, Ignacio De la Mora-De la Mora, Gabriel Lopez-Velazquez, Nallely Cabrera, Luis Antonio Flores-Lopez, Ingeborg Becker, Juliana Herrera-Lopez, Roberto Hernandez, Ruy Perez-Montfort, Sergio Enriquez-Flores
Summary: This study demonstrates that rabeprazole inhibits cell viability and triosephosphate isomerase activity in Trypanosoma cruzi epimastigotes. The inhibitory effect of rabeprazole is more than 14.5 times greater than that of benznidazole. The inactivation mechanism of rabeprazole on triosephosphate isomerase involves derivatization of three cysteine residues.
JOURNAL OF ENZYME INHIBITION AND MEDICINAL CHEMISTRY
(2023)
Review
Biochemistry & Molecular Biology
Sergio Enriquez-Flores, Ignacio De la Mora-De la Mora, Itzhel Garcia-Torres, Luis A. Flores-Lopez, Yoalli Martinez-Perez, Gabriel Lopez-Velazquez
Summary: Cancer is a group of diseases characterized by uncontrolled cellular growth. It is a major cause of death globally, with a growing incidence and mortality rate, especially in developing countries. Various treatments, such as chemotherapy, immunotherapy, and organ transplantation, are currently used but can lead to severe side effects. Increased glycolytic activity is a hallmark of cancer cells, and post-translational modifications of triosephosphate isomerase, an enzyme involved in glycolysis, offer a potential target for effective cancer treatment.
Review
Cell Biology
Gustavo Ignacio Vazquez Cervantes, Dinora Fabiola Gonzalez Esquivel, Daniela Ramirez Ortega, Tonali Blanco Ayala, Lucio Antonio Ramos Chavez, Humberto Emanuel Lopez-Lopez, Aleli Salazar, Itamar Flores, Benjamin Pineda, Saul Gomez-Manzo, Veronica Perez de la Cruz
Summary: Translation: Arsenic is a metalloid that can be found naturally in the environment and can also be present in food, water, soil, and air. Chronic exposure to even low doses of arsenic can have detrimental effects on public health. The use of arsenic in various applications such as pigments, pesticides, wood preservatives, and medical treatments has decreased due to its toxicity. However, contaminated drinking water remains a major source of human exposure to arsenic, posing a worldwide health problem as millions of people live in areas where arsenic levels exceed safe limits. Chronic exposure to arsenic has been associated with various health issues including cancer, cardiovascular diseases, gastrointestinal problems, and brain dysfunctions. The ability of arsenic to cross the blood-brain barrier makes the brain a target organ for its long-term toxic effects. Mechanisms of arsenic neurotoxicity include oxidative stress, inflammation, DNA damage, and mitochondrial dysfunction, which can all contribute to impaired cellular functions, cell death, and long-term detrimental effects. This article provides an overview of arsenic toxicity, highlights the mechanisms involved in cognitive and behavioral impairment caused by arsenic exposure, and discusses experimental strategies to counter its neurotoxicity.
Review
Engineering, Chemical
Eduardo Rodriguez-Bustamante, Saul Gomez-Manzo, Alvaro De Obeso Fernandez del Valle, Roberto Arreguin-Espinosa, Clara Espitia-Pinzon, Eden Rodriguez-Flores
Summary: Tuberculosis is a global health threat with drug resistance posing a significant challenge. Despite preventive measures and conventional treatments, there is a pressing need to find alternative drugs and novel vaccines to combat this disease.