Article
Biochemical Research Methods
Alya Hussain, Natasia Paukovich, Morkos A. Henen, Beat Vogeli
Summary: This article introduces the application of the exact nuclear Overhauser enhancement (eNOE) methodology in NMR spectroscopy, which improves the resolution of structure calculation and allows the identification of different conformations of macromolecules. The article reviews the technical development and biological applications in this field.
Article
Chemistry, Physical
Sergei Krivov
Summary: The nonparametric approach accurately determines the slowest relaxation eigenvectors in molecular dynamics without requiring system-specific information or complex functional forms. It uses a simple yet effective validation criterion based on eigenvector time series to assess the results obtained by other methods.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Radiology, Nuclear Medicine & Medical Imaging
Dushyant Kumar, Blake Benyard, Narayan Datt Soni, Anshuman Swain, Neil Wilson, Ravinder Reddy
Summary: This study demonstrates the feasibility of brain lipid mapping using an easily implementable transient NOE (tNOE) approach at 7T.
MAGNETIC RESONANCE IN MEDICINE
(2023)
Article
Chemistry, Multidisciplinary
Peter Kiraly, Nicolas Kern, Mateusz P. Plesniak, Mathias Nilsson, David J. Procter, Gareth A. Morris, Ralph W. Adams
Summary: The article introduces a new approach to selectively excite proton NMR signals using a fast, single-scan method, addressing the issue of signal overlap in traditional methods. Through selective 1D NOESY experiments, the relative configuration can be more effectively determined. This new method has the potential to be widely applied in other experiments.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Materials Science, Ceramics
Rajesh Kumar, Amreen Jan, Mathieu Bauchy, N. M. Anoop Krishnan
Summary: Using molecular dynamics simulations, the study observed that irradiation increases disorder in short- and medium-range order in borosilicate glasses. The volumetric response of borosilicate glasses under irradiation shows a composition-dependent transition, with borate-rich compositions tending to swell and silica-rich glasses tending to densify. The increase in disorder in medium-range order plays a significant role in governing the volumetric changes in the irradiated structure.
JOURNAL OF THE AMERICAN CERAMIC SOCIETY
(2021)
Article
Chemistry, Multidisciplinary
Mattia Negroni, Ertan Turhan, Thomas Kress, Morgan Ceillier, Sami Jannin, Dennis Kurzbach
Summary: Nuclear magnetic resonance (NMR) spectroscopy is a crucial technique for molecular structure determination in solution. Dissolution dynamic nuclear polarization (DDNP) is a versatile approach that can achieve signal enhancements of over 10,000-fold. However, the applicability of DDNP is limited by paramagnetic relaxation enhancements (PREs) caused by co-dissolved radicals. Using potassium nitrosodisulfonate (Fremy's salt) as a polarization agent can solve this problem and has shown promising potential.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Biochemistry & Molecular Biology
Wonjin Yang, Beom Soo Kim, Srinivasan Muniyappan, Young-Ho Lee, Jin Hae Kim, Wookyung Yu
Summary: Monomer dissociation and misfolding of transthyretin (TTR) are crucial factors in TTR amyloidosis, which causes severe human diseases. Studies have shown that stability of the DAGH beta-sheet and conformational perturbations in TTR may lead to aggregation. MD simulation techniques can provide new insights into transient yet important structural states of amyloidogenic proteins.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Multidisciplinary Sciences
Emanuele Scalone, Luca Broggini, Cristina Visentin, Davide Erba, Fran Bacic Toplek, Kaliroi Peqini, Sara Pellegrino, Stefano Ricagno, Cristina Paissoni, Carlo Camilloni
Summary: Understanding the mechanisms of protein aggregation is crucial for treating over 50 incurable diseases. A new hybrid structure model presented in this study effectively captures the essential structural and kinetic aspects of protein aggregation through molecular dynamics simulations. This model can help observe the formation of primary nuclei and the growth of fibrils, providing a structural basis for designing drugs targeting amyloidogenic diseases.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Tobias Gruber, Marc Lewitzky, Lisa Machner, Ulrich Weininger, Stephan M. Feller, Jochen Balbach
Summary: Intrinsically disordered proteins (IDPs) lack tertiary structure elements and play important roles in cellular processes. This study focuses on the C-terminal region of Gab1, an IDP, and investigates its induced structure and binding properties under both non-crowding and crowding conditions. The results show that under crowding conditions, pre-structured motifs are formed in certain regions of Gab1, which are also the binding regions for the protein SHP2. Phosphorylation has no impact on the dynamics and disordered nature of Gab1. Therefore, biological crowders can enhance the binding capacity of SHP2 to Gab1, even in the absence of phosphorylation.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Spectroscopy
Muhammad Haroon, Wissam Iali, Abdulaziz A. Al-Saadi
Summary: Linuron, a commonly used organic herbicide, was studied using NMR and Raman spectroscopic techniques to investigate its conformational behavior and electronic aspects. The SERS technique with gold nanoparticles was implemented for concentration monitoring, successfully enhancing the Raman responses of four vibrational modes. Simulations predicted that the most pronounced binding of linuron with gold nanoclusters occurs at the benzene ring.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2021)
Article
Biochemical Research Methods
Christopher Kolloff, Adam Mazur, Jan K. Marzinek, Peter J. Bond, Simon Olsson, Sebastian Hiller
Summary: This study investigates how dynamics on the supra-tau(c) timescale can influence NOE build-up between methyl groups, showing that supra-tau(c) exchange typically increases NOESY cross-peak intensities. A computational approach is presented to estimate methyl-methyl cross-relaxation rates, contributing to a quantitative estimation of NOE cross-relaxation rates from MD simulations and enhancing precision in structural and functional studies of large proteins.
JOURNAL OF MAGNETIC RESONANCE
(2022)
Article
Radiology, Nuclear Medicine & Medical Imaging
Jing Cui, Yu Zhao, Feng Wang, Daniel F. Gochberg, Zhongliang Zu
Summary: Through in vivo and ex vivo experiments, it is suggested that the NOE(-1.6) is not mainly derived from blood but may be vasculature dependent.
MAGNETIC RESONANCE IN MEDICINE
(2022)
Article
Biochemistry & Molecular Biology
Arup Mondal, Alberto Perez
Summary: The MELD Bayesian approach was found to be the best performing in predicting structures from sparsely labeled NMR data, with improvements noted in an enhanced methodological pipeline. This study highlights the challenges and nature of modeling unassigned sparsely labeled NMR datasets.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Biochemical Research Methods
Thomas C. Terwilliger, Dorothee Liebschner, Tristan I. Croll, Christopher J. Williams, Airlie J. McCoy, Billy K. Poon, Pavel V. Afonine, Robert D. Oeffner, Jane S. Richardson, Randy J. Read, Paul D. Adams
Summary: Artificial intelligence-based protein structure prediction methods, such as AlphaFold, have revolutionized structural biology. While the accuracies of these predictions vary and do not consider environmental factors, AlphaFold predictions can closely match experimental crystallographic maps in many cases. However, there are instances where even high-confidence predictions differ from experimental maps, emphasizing the need for caution and experimental verification when using these predictions.
Article
Biochemistry & Molecular Biology
Luis Guevara, Melissa Gouge, Amanda Ohler, S. Gage Hill, Soham Patel, Adam R. Offenbacher
Summary: Hydrogen tunneling in enzyme reactions plays an important role in connecting protein thermal motions to catalysis. This study investigated the effect of solvent viscosity on protein thermal motions in lipoxygenases (LOXs) and found that viscosity does not affect the catalytic reaction of soybean lipoxygenase (SLO), but inhibits the activity of 15LOX-2. These findings provide insights into the role of water hydration layers in hydrogen tunneling in LOX.
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS
(2023)
Article
Cardiac & Cardiovascular Systems
Tatjana Ruskovska, Aleksandra Konic-Ristic, Andrzej Mazur, Dragan Milenkovic
Summary: This study aimed to investigate the transcriptomic changes in the aorta of rats under different fructose intake conditions. The results showed that fructose intake affected the expression of over 1700 genes related to vascular functions, cell signaling, and cellular metabolism. Partial substitution of fructose with inulin in the diet influenced the expression of over 1300 genes associated with endothelial and vascular functions. Moreover, there was a negative correlation between the gene expression profiles under the two dietary conditions.
NUTRITION METABOLISM AND CARDIOVASCULAR DISEASES
(2023)
Review
Nutrition & Dietetics
Pawel Pludowski, Beata Kos-Kudla, Mieczyslaw Walczak, Andrzej Fal, Dorota Zozulinska-Ziolkiewicz, Piotr Sieroszewski, Jaroslaw Peregud-Pogorzelski, Ryszard Lauterbach, Tomasz Targowski, Andrzej Lewinski, Robert Spaczynski, Miroslaw Wielgos, Jaroslaw Pinkas, Teresa Jackowska, Ewa Helwich, Artur Mazur, Marek Ruchala, Arkadiusz Zygmunt, Mieczyslaw Szalecki, Artur Bossowski, Justyna Czech-Kowalska, Marek Wojcik, Beata Pyrzak, Michal A. Zmijewski, Pawel Abramowicz, Jerzy Konstantynowicz, Ewa Marcinowska-Suchowierska, Andrius Bleizgys, Spirydon N. Karras, William B. Grant, Carsten Carlberg, Stefan Pilz, Michael F. Holick, Waldemar Misiorowski
Summary: It is found that vitamin D deficiency is prevalent among the Polish population based on epidemiological studies. To address this concern, a Polish multidisciplinary group reviewed the evidence and formulated recommendations for prevention and treatment of vitamin D deficiency. The final Polish recommendations included a range of serum vitamin D levels indicating deficiency, guidelines for prophylaxis and treatment, and the importance of improving the overall population's vitamin D status and treating at-risk patient groups.
Article
Environmental Sciences
Justyna Wyszynska, Edyta Luszczki, Grzegorz Sobek, Artur Mazur, Katarzyna Deren
Summary: This study aimed to examine the prevalence and risk factors of hypertension and dyslipidemia in young Polish adults. The prevalence of hypertension was higher in men, while the prevalence of elevated total cholesterol, triglycerides, LDL cholesterol, and low HDL cholesterol was also observed. Spending more than 2 hours per day in front of a computer was associated with hypertension and elevated triglyceride levels. Smoking was also identified as a significant risk factor for hypertension.
INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH
(2023)
Article
Immunology
Pawel Zapolnik, Wojciech Kmiecik, Anna Nowakowska, Lukasz Jerzy Krzych, Henryk Szymanski, Lidia Stopyra, Teresa Jackowska, Dorota Darmochwal-Kolarz, Artur Mazur, Hanna Czajka
Summary: This article presents a study on the relationship between SARS-CoV-2 and tuberculosis vaccines, finding that further research is needed to determine the effect of BCG vaccination on the immune response to SARS-CoV-2.
Article
Public, Environmental & Occupational Health
Krzysztof Kalita, Justyna Leszczak, Ewelina Czenczek-Lewandowska, Artur Mazur
Summary: The study aimed to examine the relationship between the health behaviors and life satisfaction of diocesan priests in Poland. It found that factors such as internal health control, the influence of others, positive mental attitude, preventive behavior, eating habits, and health practices greatly influenced their quality of health and life satisfaction. The survey involved 250 diocesan priests who completed anonymous questionnaires, which were based on tools such as the HBI, MHLC, and SWLS. The priests exhibited moderate levels of health behavior and life satisfaction, placing importance on internal control and the influence of others.
JOURNAL OF RELIGION & HEALTH
(2023)
Review
Biochemistry & Molecular Biology
Pawel Zapolnik, Wojciech Kmiecik, Artur Mazur, Hanna Czajka
Summary: The Bacillus Calmette-Guerin (BCG) vaccine, in use for over 100 years, offers protection against severe, blood-borne forms of tuberculosis and enhances immunity against other diseases. This phenomenon, called trained immunity, is the result of increased response by non-specific immune cells upon repeated contact with a pathogen. In this review, we discuss the molecular mechanisms behind trained immunity and its potential application in managing the SARS-CoV-2 pandemic, while also addressing the challenges faced by the scientific community in this field.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Nutrition & Dietetics
Rafal Podgorski, Sabina Galiniak, Artur Mazur, Agnieszka Domin
Summary: Prenatal alcohol exposure can cause fetal alcohol spectrum disorders (FASDs), leading to growth impairment and various developmental, physical, and cognitive disorders in children. This study aimed to investigate the levels of hormones related to the hypothalamic-pituitary-adrenal axis in FASD patients. Results showed that fasting proopiomelanocortin (POMC) levels were lower in FASD patients compared to controls. However, cortisol concentrations did not differ. The study suggests that hormonal dysregulation may contribute to the negative effects of FASDs on growth, development, and neurological functions.
Article
Nutrition & Dietetics
Marta Suminska, Rafal Podgorski, Piotr Fichna, Artur Mazur, Marta Fichna
Summary: This study aimed to evaluate the differences in steroid metabolism between children with obesity and those with normal weight, especially in relation to sex and puberty progress. Significant differences were found in the excretion of steroid metabolites between normal weight children and children with obesity, particularly in prepubertal children.
Article
Pediatrics
Miguel Vieira Martins, Nora Karara, Lukasz Dembinski, Martine Jacot-Guillarmod, Artur Mazur, Adamos Hadjipanayis, Pierre-Andre Michaud
Summary: Adolescent pregnancy and childbearing are widespread issues with potential consequences for both short and long-term health. Various factors such as social, economic, environmental, structural, and cultural aspects greatly influence adolescents' sexual and reproductive health, as well as early pregnancy. Healthcare professionals have a crucial role in preventing unplanned pregnancies. Strategies such as improved access to family planning, sexuality education in schools, community-based interventions, and policies contribute to reducing the risk of adolescent pregnancy and promoting responsible sexual behavior. Additionally, healthcare professionals can support pregnant adolescents in making informed decisions and provide appropriate healthcare.
FRONTIERS IN PEDIATRICS
(2023)
Article
Nutrition & Dietetics
Rafal Podgorski, Sabina Galiniak, Artur Mazur, Dominika Podgorska, Agnieszka Domin
Summary: This study analyzed the hormone levels in patients with FASD and healthy controls, finding no differences in the hormone levels between affected individuals and controls. However, some associations were found between hormone concentrations and clinical parameters in FASD patients.
Meeting Abstract
Endocrinology & Metabolism
Joanna Baran, Aneta Weres, Justyna Leszczak, Ewelina Czenczek-Lewandowska, Artur Mazur
ANNALS OF NUTRITION AND METABOLISM
(2023)
Review
Biochemistry & Molecular Biology
Jeanette A. M. Maier, Laura Locatelli, Giorgia Fedele, Alessandra Cazzaniga, Andre Mazur
Summary: Magnesium plays a crucial role in regulating metabolism and maintaining tissue homeostasis, including the brain. It is essential for nerve signal transmission and protecting the blood-brain barrier. Deficiency in magnesium can lead to systemic low-grade inflammation, which is common in various diseases, particularly neurodegenerative disorders. This review provides evidence linking magnesium imbalance to multiple sclerosis, Alzheimer's, and Parkinson's diseases.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)