Article
Chemistry, Multidisciplinary
Vanni Doffini, Haipei Liu, Zhaowei Liu, Michael A. Nash
Summary: This study reports the application of machine learning techniques to classify and analyze protein unfolding trajectories. It demonstrates the potential of machine learning to accelerate data analysis and generate new insights.
Article
Biochemistry & Molecular Biology
Mirva J. Saaranen, Heli Alanen, Kirsi E. H. Salo, Emmanuel Nji, Pekka Karkkainen, Constanze Schmotz, Lloyd W. Ruddock
Summary: Proteins in the thioredoxin superfamily, such as protein disulfide isomerase (PDI) and glutaredoxins, have similar structures and catalytic mechanisms. PDI uses glutathione for oxidation/reduction in vitro, while glutaredoxins have a high affinity for glutathione. Mutating the active site of PDI to a more glutaredoxin-like motif increases its reactivity with glutathione.
Article
Biochemistry & Molecular Biology
Carlos Marcuello, Gifty Animwaa Frempong, Monica Balsera, Milagros Medina, Anabel Lostao
Summary: This study demonstrates that AFM is suitable for evaluating different conformations of ferredoxin-dependent flavin thioredoxin reductase. Results obtained under oxidizing conditions show that only the reduced conformation is observed, highlighting a dynamic disposition of disulfide domains in solution.
Article
Multidisciplinary Sciences
Rita dos Santos Natividade, Melanie Koehler, Priscila S. F. C. Gomes, Joshua D. Simpson, Sydni Caet Smith, Diego E. B. Gomes, Juliette de Lhoneux, Jinsung Yang, Ankita Ray, Terence S. Dermody, Rafael C. Bernardi, Kristen M. Ogden, David Alsteens
Summary: This study investigates the nanomechanical properties of viral attachment proteins and their impact on virus-binding capacity and infectivity. The research reveals that conformational changes in the viral protein a1 significantly increase its affinity for JAM-A, leading to enhanced infectivity. The study also demonstrates how GM2 enhances the a1-JAM-A interaction. These findings provide important insights for the development of antiviral drugs and improved oncolytic vectors.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemistry & Molecular Biology
Mikhail Matveyenka, Stanislav Rizevsky, Jean -Philippe Pellois, Dmitry Kurouski
Summary: Amyloid formation in diseases is related to abnormal aggregation of proteins and lipids. Lipid composition has a unique impact on protein aggregation and the resulting aggregates have different effects on cell viability.
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR AND CELL BIOLOGY OF LIPIDS
(2023)
Review
Biochemistry & Molecular Biology
Carlos Santos-Martin, Geqing Wang, Pramod Subedi, Lilian Hor, Makrina Totsika, Jason John Paxman, Begona Heras
Summary: The DsbA enzyme, as part of the disulfide bond forming system, plays a crucial role in bacterial virulence factor assembly and is a potential target for new virulence blockers. Despite extensive studies on DSB systems in various bacterial species, little is known about how DsbA oxidoreductases recognize and interact with a wide range of substrates.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Multidisciplinary Sciences
Hesam Babahosseini, Inna A. Belyantseva, Rizwan Yousaf, Risa Tona, Shadan Hadi, Sayaka Inagaki, Elizabeth Wilson, Shin-ichiro Kitajiri, Gregory Frolenkov, Thomas B. Friedman, Alexander X. Cartagena-Rivera
Summary: Hearing depends on the morphologies and mechanical properties of inner ear cell types. This study used advanced microscopy techniques to map the stiffness of different cells in the cochlear epithelium and found bidirectional radial stiffness gradients between supporting cells and sensory hair cells. Deficiencies in TRIOBP, a gene associated with deafness, disrupted these stiffness gradients. Ultrastructural changes were also observed in mutant mice, suggesting that the mechanical properties of the sensory epithelium play a role in mammalian hearing.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Biotechnology & Applied Microbiology
M. Artico, C. Roux, F. Peruch, A. -F. Mingotaud, C. Y. Montanier
Summary: This review addresses the challenges and methods of grafting proteins onto synthetic polymer surfaces. The sensitivity of polymers to aqueous media and the differences in chemical functions and physical properties make protein grafting on synthetic polymers a unique process. The review discusses various routes of covalently bonding proteins onto polymeric substrates and highlights the concern of potential loss of function. The characterization methods used to determine grafting efficiency and enzyme behavior are also examined. Furthermore, the review considers the industrial applications and future prospects of protein grafting, emphasizing the importance of sustainable processes based on green chemistry.
BIOTECHNOLOGY ADVANCES
(2023)
Article
Chemistry, Multidisciplinary
Pepijn Gerben Moerman, Momcilo Gavrilov, Taekjip Ha, Rebecca Schulman
Summary: The specific hybridization of DNA can be used as a building block for nanoscale structures and reaction networks. However, the strong binding energy of Watson-Crick base pairing causes the dehybridization rate of DNA to depend on sequence length and temperature. In this study, the ATP-dependent helicase Rep-X is shown to drive specific dehybridization reactions at rates independent of sequence length, removing the constraints of equilibrium on DNA hybridization and dehybridization. Additionally, Rep-X is demonstrated to accelerate the primer exchange reaction in designed DNA reaction networks.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Biotechnology & Applied Microbiology
Lewis W. Francis, Seydou N. Yao, Lydia C. Powell, Sean Griffiths, Alexander Berquand, Thomas Piasecki, William Howe, Andrea S. Gazze, Mary C. Farach-Carson, Pamela Constantinou, Daniel Carson, Lavinia Margarit, Deya Gonzalez, R. Steven Conlan
Summary: This study reveals the important role of MUC1 in the intrinsic and extrinsic adhesive properties of human endometrial epithelial cell surfaces. It demonstrates that an optimal level of MUC1 with highly glycosylated decoration is critical for high affinity L-selectin binding.
JOURNAL OF NANOBIOTECHNOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Peisi Liao, Chunmao He
Summary: This study documents a highly optimized synthesis method for the Sec-to-Cys homologue of human selenoprotein F, and elucidates the disulfide pairing mode of SelF. The research not only lays the foundation for the synthesis of natural selenoproteins, but also provides important insights into the structure of the SelF domain.
FRONTIERS IN CHEMISTRY
(2021)
Article
Immunology
Armand O. Brown, Kavindra Singh, Melissa R. Cruz, Karan Gautam Kaval, Liezl E. Francisco, Barbara E. Murray, Danielle A. Garsin
Summary: Enterococcus faecalis can form cardiac microlesions during severe infection, with DsbA protein playing a key role in virulence and microlesion formation. Additionally, the bacterium promotes cardiomyocyte death and modulates proinflammatory cytokine levels, contributing to the immune response suppression.
JOURNAL OF INFECTIOUS DISEASES
(2021)
Article
Dentistry, Oral Surgery & Medicine
C. Leiva-Sabadini, P. Tiozzo-Lyon, L. Hidalgo-Galleguillos, L. Rivas, A. I. Robles, A. Fierro, N. P. Barrera, L. Bozec, C. M. A. P. Schuh, S. Aguayo
Summary: The adhesion of initial colonizers such as Streptococcus mutans to collagen is affected by the generation of advanced glycation end-products (AGEs) in collagen, particularly those derived from methylglyoxal (MGO). However, the biophysics driving oral streptococcal attachment to MGO-modified collagen remains understudied. This study utilized bacterial cell force spectroscopy to investigate the dynamics of S. mutans adherence to type I collagen in the presence and absence of MGO-derived AGEs, and found that MGO modification increased both the number and adhesion force of detachment events between S. mutans and collagen, without altering the contour or rupture lengths.
JOURNAL OF DENTAL RESEARCH
(2023)
Article
Biochemical Research Methods
Nathan Ponzar, Nicola Pozzi
Summary: Disulfide bonds are essential for protein folding and stability, and dysregulation of this process can lead to various disorders. Thiol-isomerases (TIs) are a family of enzymes that oversee this process in human cells. However, our understanding of how TIs select and interact with their substrates, as well as their response to changes in redox environment, remains limited.
Article
Biotechnology & Applied Microbiology
Cai Guo, Fuyi Chen, Qiang Xiao, Hannah B. Catterall, John H. Robinson, Zhulun Wang, Marissa Mock, Rene Hubert
Summary: This study investigates the challenges and significance of producing multispecific antibodies in the development of biotherapeutics. It reveals that chain mispairing during expression can impact cell growth and protein structure, suggesting potential strategies for improving production processes.
BIOTECHNOLOGY AND BIOENGINEERING
(2021)
Article
Chemistry, Physical
A. Daskalova, Chandra S. R. Nathala, P. Kavatzikidou, A. Ranella, R. Szoszkiewicz, W. Husinsky, C. Fotakis
APPLIED SURFACE SCIENCE
(2016)
Article
Plant Sciences
Izabela Zglobicka, Adrian Chlanda, Michal Wozniak, Maciej Lojkowski, Robert Szoszkiewicz, Marta Mazurkiewicz-Pawlicka, Wojciech Swiezszkowski, Elzbieta Wyroba, Krzysztof J. Kurzydlowski
JOURNAL OF PHYCOLOGY
(2017)
Article
Chemistry, Physical
Wojciech Leon Spychalsid, Marcin Pisarek, Robert Szoszkiewicz
JOURNAL OF PHYSICAL CHEMISTRY C
(2017)
Article
Multidisciplinary Sciences
Izabela Zglobicka, Qiong Li, Juergen Gluch, Magdalena Plocinska, Teresa Noga, Romuald Dobosz, Robert Szoszkiewicz, Andrzej Witkowski, Ehrenfried Zschech, Krzysztof J. Kurzydlowski
SCIENTIFIC REPORTS
(2017)
Article
Chemistry, Physical
Ugonna Ukegbu, Robert Szoszkiewicz
JOURNAL OF PHYSICAL CHEMISTRY C
(2019)
Article
Chemistry, Physical
Robert Szoszkiewicz, Maciej Rogala, Pawel Dabrowski
Article
Chemistry, Physical
Miroslaw Krawczyk, Marcin Pisarek, Robert Szoszkiewicz, Aleksander Jablonski
Article
Biology
Krzysztof Kuczera, Robert Szoszkiewicz, Jinyan He, Gouri S. Jas
Summary: The simulation study on helix folding in ALA peptides revealed an increase in helix populations and relaxation times with longer peptide lengths, while folding free energies decreased linearly. Analysis using the Optimal Dimensionality Reduction method provided insight into the folding process for different peptide lengths. Multiple folding pathways were identified, showing the presence of interesting intermediate states during helix folding.
Article
Chemistry, Multidisciplinary
Maciej Rogala, Stanislaw Sokolowski, Ugonna Ukegbu, Aneta Mierzwa, Robert Szoszkiewicz
Summary: Chemical presence of MoOx species on single microscopic MoS2 flakes has been confirmed, which is of interest for future MoS2-based devices. Experimental results show that thick MoS2 flakes heated in oxidative atmosphere form loose MoOx particles, while flakes heated at 220 degrees Celsius can form a uniform approximately 2 nm thick MoOx layer even at 10% relative humidity.
ADVANCED MATERIALS INTERFACES
(2021)
Review
Chemistry, Physical
Robert Szoszkiewicz
Summary: This review focuses on the local and thermally induced interactions of thin and single MoS2 flakes, particularly in their reactions with atmospheric oxygen. Experimental data and computer simulations are presented to investigate the morphological and chemical changes that occur during thermal oxidation, providing insight into the properties and fate of the resulting Mo oxides.
Correction
Chemistry, Multidisciplinary
Maciej Rogala, Stanislaw Sokolowski, Ugonna Ukegbu, Aneta Mierzwa, Robert Szoszkiewicz
ADVANCED MATERIALS INTERFACES
(2021)
Review
Chemistry, Physical
Saeed Sovizi, Robert Szoszkiewicz
Summary: This review presents the structural changes of MoS2 induced by various single atom dopants and their potential applications in energy storage, catalysis, sensing, etc. High resolution scanning transmission electron microscopy and scanning probe microscopy techniques have been used to study the dopant positions and sub-atomic structural changes in MoS2.
SURFACE SCIENCE REPORTS
(2022)
Article
Biochemistry & Molecular Biology
Krzysztof Kuczera, Robert Szoszkiewicz, Christopher Shaffer, Gouri Jas
Summary: In this study, we used molecular dynamics and replica-exchange simulations to investigate the folding of the GB1 hairpin peptide in aqueous solution. The results supported a cooperative zipper folding model and provided insights into the formation of hydrogen bonds and hydrophobic contacts during the folding process. Additionally, kinetic models constructed using the Optimal Dimensionality Reduction approach revealed the folding and unfolding times, as well as the formation of transition states and off-path intermediates.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Review
Chemistry, Physical
Robert Szoszkiewicz
Summary: This review article summarizes the recent advancements in the research on thermally induced oxidation and oxidative etching of thin and single MoS2 flakes in the field of flexible nanoelectronics, particularly in sensing, optoelectronics, and energy harvesting. It discusses various temperature regimes and their mechanistic insights into respective oxidation and etching processes, as well as the methods used to detect any surface-remaining minute amounts of Mo oxides.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Multidisciplinary
Saeed Sovizi, Sergio Tosoni, Robert Szoszkiewicz
Summary: Sub-nanometer MoOx clusters were found on the basal planes of 2H MoS2 crystals during thermal oxidative etching at 370 degrees C. These clusters were predominantly composed of single MoO3 molecules and their dimers at sulfur vacancies, as observed using high resolution non-contact atomic force microscopy. Additional spectroscopic and microscopy techniques confirmed the sparse coverage of MoO3/MoOx species on the MoS2 surface. The findings support the previously proposed stoichiometry of oxidative etching.
NANOSCALE ADVANCES
(2022)
Article
Biochemistry & Molecular Biology
Hsiao-Chieh Tsai, Ching-Hong Huang, Ling-Hsien Tu
Summary: Islet amyloid polypeptide (IAPP) is a polypeptide hormone co-secreted with insulin by pancreatic beta-cells. It tends to aggregate into soluble oligomers, which are considered one of the hallmarks of type II diabetes. This study successfully grafted the aggregation-induced emission molecule TPE onto IAPP, allowing real-time monitoring of IAPP oligomer formation and potential application in the diagnosis of T2D.
BIOPHYSICAL CHEMISTRY
(2024)
Article
Biochemistry & Molecular Biology
Aristeidis Papagiannopoulos, Aggeliki Sklapani, Nikolaos Spiliopoulos
Summary: This study presents a method for preparing Hb-based nanoparticles (NPs) using a fully biocompatible approach. These NPs have a spherical structure with a diameter ranging from 50 to 100 nm, and can form electrostatic complexes with CS at pH 4. The NPs can be pH-tunable and stable in solutions with high salt content, making them suitable for nanodelivery of nutrients and drugs.
BIOPHYSICAL CHEMISTRY
(2024)
Article
Biochemistry & Molecular Biology
Andrey V. Struts, Alexander V. Barmasov, Steven D. E. Fried, Kushani S. K. Hewage, Suchithranga M. D. C. Perera, Michael F. Brown
Summary: This article summarizes and reviews the osmotic stress studies of G-protein-coupled receptor rhodopsin. It is found that water plays an important role in the activation of the receptor, with at least 80 water molecules entering the receptor in the transition to the active state. If water influx is prevented, the functional transition of the receptor is reversed. These findings reveal the phenomenon of solvent swelling in the activation mechanism of rhodopsin, with water acting as an allosteric modulator of function for rhodopsin-like receptors in lipid membranes.
BIOPHYSICAL CHEMISTRY
(2024)
Article
Biochemistry & Molecular Biology
Maria Chiara Saija, Adela Melcrova, Wojciech Pajerski, Itay Schachter, Matti Javanainen, Marek Cebecauer, Lukasz Cwiklik
Summary: We used molecular dynamics simulations to investigate the effects of palmitoylation on a transmembrane peptide in different lipid environments. The study found that palmitoylation reduces the peptide's impact on membrane thickness, particularly in lipid-ordered and boundary environments. The hydrophobic palmitoyl chains on the peptide did not significantly affect membrane hydration. Interestingly, the boundary membrane environment was found to be highly compatible with the palmitoylated peptide. These findings have important implications for understanding cell signaling, membrane organization, and optimizing lipid membrane-based drug delivery systems.
BIOPHYSICAL CHEMISTRY
(2024)
Article
Biochemistry & Molecular Biology
Achanta Rishisree, Brayer Mallory, Karnaukhova Elena, Jankovic Teodora, Zdunic Gordana, Savikin Katarina, Jeremic Aleksandar
Summary: Pomegranate peel, ironwort, and chokeberry leaf extracts exhibit anti-aggregative and antitoxic properties against human amylin. They can prevent amyloidosis and cell loss in patients with Type 2 Diabetes Mellitus.
BIOPHYSICAL CHEMISTRY
(2024)