Article
Multidisciplinary Sciences
Hai Lei, Quan Ma, Wenfei Li, Jing Wen, Haibo Ma, Meng Qin, Wei Wang, Yi Cao
Summary: Bacterial surface adhesion proteins exhibit unique mechanical properties, with ester bonds found to withstand considerable mechanical forces and prevent complete protein unfolding. The study demonstrates that an ester-bond containing stalk domain of Cpe0147 remains inextensible even at forces > 2 nN by locking the structure to a partially unfolded conformation. This design principle could inspire engineering approaches to create protein mutants resistant to mechanical unfolding.
NATURE COMMUNICATIONS
(2021)
Article
Biophysics
Tobias Dahlberg, Joseph L. Baker, Esther Bullitt, Magnus Andersson
Summary: This study investigates the biophysical function and structural interactions of adhesion pili on the surface of bacteria. Optical tweezers are used to measure the interaction dynamics of pilus subunits, and steered molecular dynamics simulations reveal atomic details of subunit interactions under tension. The results indicate that the compliance and stability of the helical filament structure are dependent on their length and the presence of the N-terminal "staple" region. This study contributes to our understanding of the essential features of adhesion pili and their importance in bacterial attachment.
BIOPHYSICAL JOURNAL
(2022)
Article
Multidisciplinary Sciences
Scott A. McConnell, Rachel A. McAllister, Brendan R. Amer, Brendan J. Mahoney, Christopher K. Sue, Chungyu Chang, Hung Ton-That, Robert T. Clubb
Summary: This research reveals how Gram-positive bacteria assemble pili on their surfaces to adhere to host tissues and promote interactions, with a focus on the specific mechanisms involved in crosslinking pilins by sortase enzymes. The study proposes a latch mechanism in which a conserved loop in SpaA facilitates the crosslinking reaction and stabilizes the isopeptide bond, shedding light on the biogenesis of pili. General features of this structure and mechanism are likely conserved in Gram-positive bacteria.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Matthew C. Gaines, Michail N. Isupov, Shamphavi Sivabalasarma, Risat Ul Haque, Mathew McLaren, Clara L. Mollat, Patrick Tripp, Alexander Neuhaus, Vicki A. M. Gold, Sonja-Verena Albers, Bertram Daum
Summary: This study describes the structure of a new type of pilus, named 'thread', from the model archaeaon Sulfolobus acidocaldarius. The thread is highly glycosylated and composed of subunits of the protein Saci_0406, showing structural similarity to certain bacterial pili but likely assembled by a distinct mechanism.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Rajnesh Kumari Yadav, Vengadesan Krishnan
Summary: Streptococcus oralis, a member of the mitis group of oral streptococci, plays a significant role in periodontal disease, dental caries, and other oral infections. It promotes biofilm growth by coaggregating with other early colonizers such as Actinomyces oris. This study investigates the role of the PI-2 pilus in the mutualistic mechanism between S. oralis and A. oris, and suggests the potential use of galactose monosaccharide as a ligand to inhibit coaggregation and control oral biofilm development.
Article
Biotechnology & Applied Microbiology
Zhi Wang, Mengkai Hu, Ming Fang, Qiang Wang, Ruiqi Lu, Hengwei Zhang, Meijuan Xu, Xian Zhang, Zhiming Rao
Summary: The thermal stability of alpha-glucosidase was significantly improved by constructing cyclized proteins, allowing for continuous production of isomaltooligosaccharides at higher temperatures.
FERMENTATION-BASEL
(2022)
Article
Microbiology
Chris Hadjineophytou, Jan Haug Anonsen, Tina Svingerud, Tatum D. Mortimer, Yonatan H. Grad, Nichollas E. Scott, Michael Koomey
Summary: Protein glycosylation systems in the genus Neisseria show species-specific variations, with different glycoprotein repertoires and target protein selection. The glycosylation of PilE, the pilin subunit of the type IV pilus colonization factor, is determined by the presence or absence of the PglO oligosaccharyltransferase in different species. This study highlights the importance of natural diversity in neisserial protein substrates and oligosaccharyltransferases in understanding the structure-function relationships of bacterial protein glycosylation systems.
Article
Biochemistry & Molecular Biology
Mohammed Kaplan, Catherine M. Oikonomou, Cecily R. Wood, Georges Chreifi, Poorna Subramanian, Davi R. Ortega, Yi-Wei Chang, Morgan Beeby, Carrie L. Shaffer, Grant J. Jensen
Summary: The assembly of flagellar motors is not a simple accumulation of components, but a dynamic process in which accessory components interact transiently to help build the complex nanomachine. Novel cytoplasmic rings were discovered in high-torque motors of Beta-, Gamma-, and Epsilon-proteobacteria, which interact with the cytoplasmic torque ring formed by FliG and are essential for the assembly of stator ring.
Article
Multidisciplinary Sciences
Huan Zhang, Srutha Venkatesan, Emily Ng, Beiyan Nan
Summary: This study found that the inhibited PG synthases can affect bacterial morphology by accelerating the degradation of cell poles through hydrolytic PG peptidase. Disrupting the coordination between PG synthases and hydrolases could be more lethal than eliminating individual enzymes.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Amos J. Nissley, Petar Penev, Zoe L. Watson, Jillian F. Banfield, Jamie H. D. Cate
Summary: Research discovers that Thermoproteota, a phylum of thermophilic Archaea, uses cytidine to replace uridine in the A loop, stabilizing the ribosome at high temperatures and protecting its catalytic function of peptide bond formation.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Microbiology
Courtney K. Ellison, Gregory B. Whitfield, Yves Brun
Summary: This review discusses recent progress in understanding the function, regulation, and mechanisms of T4P dynamics.
FEMS MICROBIOLOGY REVIEWS
(2022)
Article
Multidisciplinary Sciences
Bingliang Xie, Jian Wang, Yong Nie, Jing Tian, Zerui Wang, Dongwei Chen, Beiyu Hu, Xiao-Lei Wu, Wenbin Du
Summary: Recent studies have identified a novel microbial community called TM7, which is an obligate symbiont that binds to its host through twitching-like motility mediated by type IV pili (T4P). This research provides insights into the lifestyle of TM7 and the diversity of CPR bacteria.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Engineering, Environmental
Guosheng Zhang, Jiping Chen, Weiying Li
Summary: This study found that plasmid RP4 can promote bacterial colonization on microplastics, potentially due to the synthesis of conjugative pili proteins and intracellular ATP. Nanoalumina was found to promote bacterial colonization, while free nitrous acid inhibited bacterial colonization.
JOURNAL OF HAZARDOUS MATERIALS
(2022)
Review
Microbiology
Michael J. Sheedlo, Melanie D. Ohi, D. Borden Lacy, Timothy L. Coverid
Summary: Bacterial type IV secretion systems (T4SSs) are versatile nanomachines that can transfer DNA and deliver proteins into various target cells. Cryo-electron tomography has revealed the structures of T4SSs, allowing for comparison of their molecular architectures and core complex structures. Structural variation among T4SSs may confer specialized functional properties.
Article
Physics, Multidisciplinary
Wolfram Poenisch, Vasily Zaburdaev
Summary: This study presents a computational model of a micron-sized turbine powered by bacteria, showing that the turbine can rotate persistently by the collective dynamics of multiple pili, and can rotate permanently in the same direction by altering the pili binding to the turbine surface.
FRONTIERS IN PHYSICS
(2022)
Article
Chemistry, Physical
Benedikt Rennekamp, Fabian Kutzki, Agnieszka Obarska-Kosinska, Christopher Zapp, Frauke Graeter
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2020)
Review
Biochemistry & Molecular Biology
Florian Franz, Csaba Daday, Frauke Graeter
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2020)
Article
Chemistry, Physical
Eduardo R. Cruz-Chu, Gonzalo J. Villegas-Rodriguez, Tobias Jager, Luca Valentini, Nicola M. Pugno, Konstantinos Gkagkas, Frauke Grater
NPJ COMPUTATIONAL MATERIALS
(2020)
Article
Biochemical Research Methods
Fan Jin, Frauke Grater
Summary: The study found that multi-site phosphorylation causes V-shaped changes in collapse propensity of all proteins based on their initial net charge, expanding neutral or overall negatively charged IDPs and shrinking positively charged IDPs. In two of the IDPs, only two biologically relevant phosphorylation sites are enough to significantly expose the adjacent negatively charged active site, increasing the likelihood of interaction with other binding partners.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Chemistry, Physical
Claudia L. Gomez-Flores, Denis Maag, Mayukh Kansari, Van-Quan Vuong, Stephan Irle, Frauke Graeter, Tomas Kubar, Marcus Elstner
Summary: This paper investigates the generation of free energy surfaces in complex reactions using the semiempirical method DFTB and improves its accuracy by developing a specific reaction parametrization (SRP). Through the implementation of an artificial neural network (ANN), the authors successfully generate highly accurate free energy surfaces for thiol-disulfide exchange in two molecular complexes.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Multidisciplinary Sciences
Niccolo Banterle, Adrian P. Nievergelt, Svenja de Buhr, Georgios N. Hatzopoulos, Charlene Brillard, Santiago Andany, Tania Huebscher, Frieda A. Sorgenfrei, Ulrich S. Schwarz, Frauke Graeter, Georg E. Fantner, Pierre Goenczy
Summary: Discovering mechanisms controlling organelle assembly is a fundamental pursuit in biology. The centriole is a conserved organelle with a 9-fold symmetrical arrangement of microtubules. Research shows that the surface can convert the inherent helical propensity of SAS-6 polymers into 9-fold rings, guiding ring stacking and imparting chiral features to centrioles and cilia.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Isabel M. Martin, Michele M. Nava, Sara A. Wickstroem, Frauke Graeter
Summary: This study investigates the mechanotransducing functions of the essential adhesion component integrin-linked kinase (ILK) using force-probe molecular-dynamics simulations. The results suggest that ATP plays a role in facilitating cellular force generation and migration.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Uladzimir Barayeu, Danny Schilling, Mohammad Eid, Thamara Nishida Xavier da Silva, Lisa Schlicker, Nikolina Mitreska, Christopher Zapp, Frauke Graeter, Aubry K. Miller, Reinhard Kappl, Almut Schulze, Jose Pedro Friedmann Angeli, Tobias P. Dick
Summary: Ferroptosis is a type of cell death caused by radical-driven lipid peroxidation. Our study shows that sulfane sulfur species, particularly hydropersulfides, scavenge free radicals and suppress ferroptosis. Cysteine can support ferroptosis resistance independently of the GPX4 pathway by providing sulfur for S-0 biosynthesis.
NATURE CHEMICAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Po-Chia Chen, Fabian Kutzki, Angelika Mojzisch, Bernd Simon, Emma-Ruoqi Xu, Camilo Aponte-Santamaria, Kai Horny, Cy Jeffries, Reinhard Schneppenheim, Matthias Wilmanns, Maria A. Brehm, Frauke Graeter, Janosch Hennig
Summary: Von Willebrand disease is a bleeding disorder associated with mutations in the VWF gene. This study investigates the structure and dynamics of the C6 domain and the G2705R variant in C6, using nuclear magnetic resonance spectroscopy, molecular dynamics simulations and aggregometry. The findings show that the G2705R mutation destabilizes VWF by promoting hinging between the subdomains of C6.
JOURNAL OF STRUCTURAL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Benedikt Rennekamp, Christoph Karfusehr, Markus Kurth, Aysecan uenal, Debora Monego, Kai Riedmiller, Ganna Gryn'ova, David M. Hudson, Frauke Graeter
Summary: The authors used scale-bridging simulations to identify breakage points in collagen and studied the mechanical and chemical impact of these ruptures on the tissue. They found that collagen has a unique failure mode that helps prevent material ageing and macroscopic failure.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Wojtek Treyde, Kai Riedmiller, Frauke Graeter
Summary: Knowledge of reliable X-H bond dissociation energies is crucial for studying the radical chemistry of proteins. By computing the X-H bond dissociation energies of model dipeptides, our work provides a highly valuable and unprecedented data set with accuracy and comprehensiveness. This dataset is likely to be useful for predicting protein biochemistry involving radicals.
Article
Chemistry, Physical
Matthias Brosz, Nicholas Michelarakis, Uwe H. F. Bunz, Camilo Aponte-Santamaria, Frauke Graeter
Summary: Poly(para-phenylene ethynylene)s (PPEs) are a class of conjugated and semi-flexible polymers with a wide range of technological applications. In this study, a coarse-grained model for PPEs was developed using the Martini 3 force field to study large-scale assemblies computationally. The model successfully reproduced key structural and thermodynamic properties of single PPE chains and mixtures. It was found that chain entanglement increased with PPE chain length, while nematic ordering decreased. The Martini 3 PPE model allows for investigation of the structural organization of PPE bulk systems at large spatio-temporal scales and is predicted to be applicable for studying out-of-equilibrium behavior under mechanical force.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Denis Maag, Marina Putzu, Claudia L. Gomez-Flores, Frauke Graeter, Marcus Elstner, Tomas Kubar
Summary: In the study, it was found that the thiol-disulfide exchange reactions were directed by electrostatic interactions, with the sulfur atoms preferring to attack Cys55 over Cys24. These interactions play a significant role in the regioselectivity of the reactions.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
Nicholas Michelarakis, Florian Franz, Konstantinos Gkagkas, Frauke Graeter
Summary: This study used non-equilibrium Molecular Dynamics simulations to investigate the shear viscosity mechanism of Nafion solutions, revealing the presence of rod-shaped Nafion microstructures in the absence or low shear flow, with higher shear rates breaking these structures and aligning Nafion strands in the flow direction to reduce shear viscosities.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
Article
Evolutionary Biology
Gustavo Caetano-Anolles, M. Fayez Aziz, Fizza Mughal, Frauke Graeter, Ibrahim Koc, Kelsey Caetano-Anolles, Derek Caetano-Anolles
EVOLUTIONARY BIOINFORMATICS
(2019)