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The ratio of fibroin to sericin in the middle silk gland of Bombyx mori and its correlation with the extensional behavior of the silk dope Protein Sci. (IF 8.0) Pub Date : 2024-02-21 Teemu Välisalmi, Markus B. Linder
Understanding how native silk spinning occurs is crucial for designing artificial spinning systems. One often overlooked factor in Bombyx mori is the secretion of sericin proteins. Herein, we investigate the variation in amino acid content at different locations in the middle silk gland (MSG) of B. mori. This variation corresponds to an increase in sericin content when moving towards the anterior region
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An intein‐based biosensor to measure protein stability in vivo Protein Sci. (IF 8.0) Pub Date : 2024-02-21 Ahyun Son, John S. Smetana, Scott Horowitz, Christopher W. Lennon
Biosensors to measure protein stability in vivo are valuable tools for a variety of applications. Previous work has demonstrated that a tripartite design, whereby a protein of interest (POI) is inserted within a reporter, can link POI stability to reporter activity. Inteins are translated within other proteins and excised in a self‐mediated protein splicing reaction. Here, we developed a novel folding
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VWD domain stabilization by autocatalytic Asp‐Pro cleavage Protein Sci. (IF 8.0) Pub Date : 2024-02-21 Noa Yeshaya, Prashant Kumar Gupta, Orly Dym, David Morgenstern, Dan Thomas Major, Deborah Fass
Domains known as von Willebrand factor type D (VWD) are found in extracellular and cell‐surface proteins including von Willebrand factor, mucins, and various signaling molecules and receptors. Many VWD domains have a glycine‐aspartate‐proline‐histidine (GDPH) amino‐acid sequence motif, which is hydrolytically cleaved post‐translationally between the aspartate (Asp) and proline (Pro). The Fc IgG binding
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Stepwise introduction of stabilizing mutations reveals nonlinear additive effects in de novoTIM barrels Protein Sci. (IF 8.0) Pub Date : 2024-02-21 Johanna‐Sophie Koch, Sergio Romero‐Romero, Birte Höcker
Over the past decades, the TIM‐barrel fold has served as a model system for the exploration of how changes in protein sequences affect their structural, stability, and functional characteristics, and moreover, how this information can be leveraged to design proteins from the ground up. After numerous attempts to design de novo proteins with this specific fold, sTIM11 was the first validated de novo
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A sequence‐based model for identifying proteins undergoing liquid–liquid phase separation/forming fibril aggregates via machine learning Protein Sci. (IF 8.0) Pub Date : 2024-02-21 Shaofeng Liao, Yujun Zhang, Xinchen Han, Tinglan Wang, Xi Wang, Qinglin Yan, Qian Li, Yifei Qi, Zhuqing Zhang
Liquid–liquid phase separation (LLPS) and the solid aggregate (also referred to as amyloid aggregates) formation of proteins, have gained significant attention in recent years due to their associations with various physiological and pathological processes in living organisms. The systematic investigation of the differences and connections between proteins undergoing LLPS and those forming amyloid fibrils
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Structural insights into peptidoglycan glycosidase EtgA binding to the inner rod protein EscI of the type III secretion system via a designed EscI‐EtgA fusion protein Protein Sci. (IF 8.0) Pub Date : 2024-02-21 J. Boorman, X. Zeng, J. Lin, F. van den Akker
Bacteria express lytic enzymes such as glycosidases, which have potentially self‐destructive peptidoglycan (PG)‐degrading activity and, therefore, require careful regulation in bacteria. The PG glycosidase EtgA is regulated by localization to the assembling type III secretion system (T3SS), generating a hole in the PG layer for the T3SS to reach the outer membrane. The EtgA localization was found to
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Degradation versus fibrillogenesis, two alternative pathways modulated by seeds and glycosaminoglycans Protein Sci. (IF 8.0) Pub Date : 2024-02-21 Guglielmo Verona, Sara Raimondi, Diana Canetti, P. Patrizia Mangione, Loredana Marchese, Alessandra Corazza, Francesca Lavatelli, Julian D. Gillmore, Graham W. Taylor, Vittorio Bellotti, Sofia Giorgetti
The mechanism that converts native human transthyretin into amyloid fibrils in vivo is still a debated and controversial issue. Commonly, non‐physiological conditions of pH, temperature, or organic solvents are used in in vitro models of fibrillogenesis of globular proteins. Transthyretin amyloid formation can be achieved under physiological conditions through a mechano‐enzymatic mechanism involving
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Protein structure accuracy estimation using geometry‐complete perceptron networks Protein Sci. (IF 8.0) Pub Date : 2024-02-21 Alex Morehead, Jian Liu, Jianlin Cheng
Estimating the accuracy of protein structural models is a critical task in protein bioinformatics. The need for robust methods in the estimation of protein model accuracy (EMA) is prevalent in the field of protein structure prediction, where computationally‐predicted structures need to be screened rapidly for the reliability of the positions predicted for each of their amino acid residues and their
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Discovery of broadly-neutralizing antibodies against brown recluse spider and Gadim scorpion sphingomyelinases using consensus toxins as antigens Protein Sci. (IF 8.0) Pub Date : 2024-02-15 Esperanza Rivera-de-Torre, Stefanos Lampadariou, Mark Møiniche, Markus F. Bohn, Seyed Mahdi Kazemi, Andreas H. Laustsen
Broadly-neutralizing monoclonal antibodies are becoming increasingly important tools for treating infectious diseases and animal envenomings. However, designing and developing broadly-neutralizing antibodies can be cumbersome using traditional low-throughput iterative protein engineering methods. Here, we present a new high-throughput approach for the standardized discovery of broadly-neutralizing
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Systematic enhancement of protein crystallization efficiency by bulk lysine-to-arginine (KR) substitution Protein Sci. (IF 8.0) Pub Date : 2024-02-15 Nooriel E. Banayan, Blaine J. Loughlin, Shikha Singh, Farhad Forouhar, Guanqi Lu, Kam-Ho Wong, Matthew Neky, Henry S. Hunt, Larry B. Bateman, Angel Tamez, Samuel K. Handelman, W. Nicholson Price, John F. Hunt
Structural genomics consortia established that protein crystallization is the primary obstacle to structure determination using x-ray crystallography. We previously demonstrated that crystallization propensity is systematically related to primary sequence, and we subsequently performed computational analyses showing that arginine is the most overrepresented amino acid in crystal-packing interfaces
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Exploring the dynamics and structure of PpiB in living Escherichia coli cells using electron paramagnetic resonance spectroscopy Protein Sci. (IF 8.0) Pub Date : 2024-02-15 Yasmin Ben-Ishay, Yoav Barak, Akiva Feintuch, Olivier Ouari, Annalisa Pierro, Elisabetta Mileo, Xun-Cheng Su, Daniella Goldfarb
The combined effects of the cellular environment on proteins led to the definition of a fifth level of protein structural organization termed quinary structure. To explore the implication of potential quinary structure for globular proteins, we studied the dynamics and conformations of Escherichia coli (E. coli) peptidyl-prolyl cis/trans isomerase B (PpiB) in E. coli cells. PpiB plays a major role
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Identification of small-molecule binding sites of a ubiquitin-conjugating enzyme-UBE2T through fragment-based screening Protein Sci. (IF 8.0) Pub Date : 2024-02-15 Yong Yao Loh, Jothi Anantharajan, Qiwei Huang, Weijun Xu, Justina Fulwood, Hui Qi Ng, Elizabeth Yihui Ng, Chong Yu Gea, Meng Ling Choong, Qian Wen Tan, Xiaoying Koh, Wan Hsin Lim, Kassoum Nacro, Joseph Cherian, Nithya Baburajendran, Zhiyuan Ke, CongBao Kang
UBE2T is an attractive target for drug development due to its linkage with several types of cancers. However, the druggability of ubiquitin-conjugating E2 (UBE2T) is low because of the lack of a deep and hydrophobic pocket capable of forming strong binding interactions with drug-like small molecules. Here, we performed fragment screening using 19F-nuclear magnetic resonance (NMR) and validated the
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Modeling membrane geometries implicitly in Rosetta Protein Sci. (IF 8.0) Pub Date : 2024-02-15 Hope Woods, Julia Koehler Leman, Jens Meiler
Interactions between membrane proteins (MPs) and lipid bilayers are critical for many cellular functions. In the Rosetta molecular modeling suite, the implicit membrane energy function is based on a “slab” model, which represent the membrane as a flat bilayer. However, in nature membranes often have a curvature that is important for function and/or stability. Even more prevalent, in structural biology
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Accounting for nonuniformity of bulk-solvent: A mosaic model Protein Sci. (IF 8.0) Pub Date : 2024-02-15 Pavel V. Afonine, Paul D. Adams, Oleg V. Sobolev, Alexandre G. Urzhumtsev
A flat mask-based model is almost universally used in macromolecular crystallography to account for disordered (bulk) solvent. This model assumes any voxel of the crystal unit cell that is not occupied by the atomic model is occupied by the solvent. The properties of this solvent are assumed to be exactly the same across the whole volume of the unit cell. While this is a reasonable approximation in
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Controlling the incorporation of fluorinated amino acids in human cells and its structural impact Protein Sci. (IF 8.0) Pub Date : 2024-02-15 Azzurra Costantino, Lan B. T. Pham, Letizia Barbieri, Vito Calderone, Gili Ben-Nissan, Michal Sharon, Lucia Banci, Enrico Luchinat
Fluorinated aromatic amino acids (FAAs) are promising tools when studying protein structure and dynamics by NMR spectroscopy. The incorporation FAAs in mammalian expression systems has been introduced only recently. Here, we investigate the effects of FAAs incorporation in proteins expressed in human cells, focusing on the probability of incorporation and its consequences on the 19F NMR spectra. By
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Key interaction networks: Identifying evolutionarily conserved non-covalent interaction networks across protein families Protein Sci. (IF 8.0) Pub Date : 2024-02-15 Dariia Yehorova, Rory M. Crean, Peter M. Kasson, Shina C. L. Kamerlin
Protein structure (and thus function) is dictated by non-covalent interaction networks. These can be highly evolutionarily conserved across protein families, the members of which can diverge in sequence and evolutionary history. Here we present KIN, a tool to identify and analyze conserved non-covalent interaction networks across evolutionarily related groups of proteins. KIN is available for download
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The C-terminus is essential for the stability of the mycobacterial channel protein MspA Protein Sci. (IF 8.0) Pub Date : 2024-02-15 Mikhail Pavlenok, Rashmi Ravindran Nair, R. Curtis Hendrickson, Michael Niederweis
Outer membrane proteins perform essential functions in uptake and secretion processes in bacteria. MspA is an octameric channel protein in the outer membrane of Mycobacterium smegmatis and is structurally distinct from any other known outer membrane protein. MspA is the founding member of a family with more than 3000 homologs and is one of the most widely used proteins in nanotechnological applications
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Protective roles of highly conserved motif 1 in tardigrade cytosolic-abundant heat soluble protein in extreme environments Protein Sci. (IF 8.0) Pub Date : 2024-02-15 Donguk Kang, Min June Yang, Hwan Kim, Chin-Ju Park
Tardigrades are remarkable microscopic animals that survive harsh conditions such as desiccation and extreme temperatures. Tardigrade-specific intrinsically disordered proteins (TDPs) play an essential role in the survival of tardigrades in extreme environments. Cytosolic-abundant heat soluble (CAHS) protein, a key TDP, is known to increase desiccation tolerance and to protect the activity of several
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A PDZ scaffolding/CaM-mediated pathway in Cryptochrome signaling Protein Sci. (IF 8.0) Pub Date : 2024-02-15 Massimo Bellanda, Milena Damulewicz, Barbara Zambelli, Elisa Costanzi, Francesco Gregoris, Stefano Mammi, Silvio C. E. Tosatto, Rodolfo Costa, Giovanni Minervini, Gabriella M. Mazzotta
Cryptochromes are cardinal constituents of the circadian clock, which orchestrates daily physiological rhythms in living organisms. A growing body of evidence points to their participation in pathways that have not traditionally been associated with circadian clock regulation, implying that cryptochromes may be subject to modulation by multiple signaling mechanisms. In this study, we demonstrate that
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Crystal structure of the tegument protein UL82 (pp71) from human cytomegalovirus Protein Sci. (IF 8.0) Pub Date : 2024-02-15 Jan Eberhage, Ian P. Bresch, Ramya Ramani, Niklas Viohl, Thalea Buchta, Christopher L. Rehfeld, Petra Hinse, Thomas F. Reubold, Melanie M. Brinkmann, Susanne Eschenburg
Human cytomegalovirus (HCMV) is an opportunistic pathogen that infects a majority of the world population. It may cause severe disease in immunocompromised people and lead to pregnancy loss or grave disabilities of the fetus upon congenital infection. For effective replication and lifelong persistence in its host, HCMV relies on diverse functions of its tegument protein UL82, also known as pp71. Up
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The catalytic domain of free or ligand bound histone deacetylase 4 occurs in solution predominantly in closed conformation Protein Sci. (IF 8.0) Pub Date : 2024-02-15 Markus Schweipert, Thomas Nehls, Anton Frühauf, Cecilé Debarnot, Adarsh Kumar, Stefan Knapp, Frederik Lermyte, Franz-Josef Meyer-Almes
Human histone deacetylase 4 (HDAC4) is a key epigenetic regulator involved in a number of important cellular processes. This makes HDAC4 a promising target for the treatment of several cancers and neurodegenerative diseases, in particular Huntington's disease. HDAC4 is highly regulated by phosphorylation and oxidation, which determine its nuclear or cytosolic localization, and exerts its function through
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Energy, water, and protein folding: A molecular dynamics-based quantitative inventory of molecular interactions and forces that make proteins stable Protein Sci. (IF 8.0) Pub Date : 2024-01-23 Juan José Galano-Frutos, Javier Sancho
Protein folding energetics can be determined experimentally on a case-by-case basis but it is not understood in sufficient detail to provide deep control in protein design. The fundamentals of protein stability have been outlined by calorimetry, protein engineering, and biophysical modeling, but these approaches still face great difficulty in elucidating the specific contributions of the intervening
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Distinct specificities of the HEMK2 protein methyltransferase in methylation of glutamine and lysine residues Protein Sci. (IF 8.0) Pub Date : 2024-01-23 Sara Weirich, Gizem T. Ulu, Thyagarajan T. Chandrasekaran, Jana Kehl, Jasmin Schmid, Franziska Dorscht, Margarita Kublanovsky, Dan Levy, Albert Jeltsch
The HEMK2 protein methyltransferase has been described as glutamine methyltransferase catalyzing ERF1-Q185me1 and lysine methyltransferase catalyzing H4K12me1. Methylation of two distinct target residues is unique for this class of enzymes. To understand the specific catalytic adaptations of HEMK2 allowing it to master this chemically challenging task, we conducted a detailed investigation of the substrate
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Identification of the pyridoxal 5′-phosphate allosteric site in human pyridox(am)ine 5′-phosphate oxidase Protein Sci. (IF 8.0) Pub Date : 2024-01-23 Anna Barile, Claudio Graziani, Lorenzo Antonelli, Alessia Parroni, Annarita Fiorillo, Martino Luigi di Salvo, Andrea Ilari, Alessandra Giorgi, Serena Rosignoli, Alessandro Paiardini, Roberto Contestabile, Angela Tramonti
Adequate levels of pyridoxal 5′-phosphate (PLP), the catalytically active form of vitamin B6, and its proper distribution in the body are essential for human health. The PLP recycling pathway plays a crucial role in these processes and its defects cause severe neurological diseases. The enzyme pyridox(am)ine 5′-phosphate oxidase (PNPO), whose catalytic action yields PLP, is one of the key players in
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ATP-independent assembly machinery of bacterial outer membranes: BAM complex structure and function set the stage for next-generation therapeutics Protein Sci. (IF 8.0) Pub Date : 2024-01-23 Anjana George, Akanksha Gajanan Patil, Radhakrishnan Mahalakshmi
Diderm bacteria employ β-barrel outer membrane proteins (OMPs) as their first line of communication with their environment. These OMPs are assembled efficiently in the asymmetric outer membrane by the β-Barrel Assembly Machinery (BAM). The multi-subunit BAM complex comprises the transmembrane OMP BamA as its functional subunit, with associated lipoproteins (e.g., BamB/C/D/E/F, RmpM) varying across
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Improving enzyme functional annotation by integrating in vitro and in silico approaches: The example of histidinol phosphate phosphatases Protein Sci. (IF 8.0) Pub Date : 2024-01-23 Thomas Kinateder, Carina Mayer, Julian Nazet, Reinhard Sterner
Advances in sequencing technologies have led to a rapid growth of public protein sequence databases, whereby the fraction of proteins with experimentally verified function continuously decreases. This problem is currently addressed by automated functional annotations with computational tools, which however lack the accuracy of experimental approaches and are susceptible to error propagation. Here,
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Tandem repeats of highly bioluminescent NanoLuc are refolded noncanonically by the Hsp70 machinery Protein Sci. (IF 8.0) Pub Date : 2024-01-23 Dimitra Apostolidou, Pan Zhang, Devanshi Pandya, Kaden Bock, Qinglian Liu, Weitao Yang, Piotr E. Marszalek
Chaperones are a large family of proteins crucial for maintaining cellular protein homeostasis. One such chaperone is the 70 kDa heat shock protein (Hsp70), which plays a crucial role in protein (re)folding, stability, functionality, and translocation. While the key events in the Hsp70 chaperone cycle are well established, a relatively small number of distinct substrates were repetitively investigated
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PBITV3: A robust and comprehensive tool for screening pathogenic proteomes for drug targets and prioritizing vaccine candidates Protein Sci. (IF 8.0) Pub Date : 2024-01-03 Shuvechha Chakraborty, Mehdi Askari, Ram Shankar Barai, Susan Idicula-Thomas
Rise of life-threatening superbugs, pandemics and epidemics warrants the need for cost-effective and novel pharmacological interventions. Availability of publicly available proteomes of pathogens supports development of high-throughput discovery platforms to prioritize potential drug-targets and develop testable hypothesis for pharmacological screening. The pipeline builder for identification of target
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A complex network of interdomain interactions underlies the conformational ensemble of monomeric TDP-43 and modulates its phase behavior Protein Sci. (IF 8.0) Pub Date : 2023-12-31 Priyesh Mohanty, Azamat Rizuan, Young C. Kim, Nicolas L. Fawzi, Jeetain Mittal
TAR DNA-binding protein 43 (TDP-43) is a multidomain protein involved in the regulation of RNA metabolism, and its aggregates have been observed in neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Numerous studies indicate TDP-43 can undergo liquid–liquid phase separation (LLPS) in vitro and is a component of biological condensates. Homo-oligomerization
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Structural characterization of the Sel1-like repeat protein LceB from Legionella pneumophila Protein Sci. (IF 8.0) Pub Date : 2023-12-31 Tiffany V. Penner, Neil Lorente Cobo, Deepak T. Patel, Dhruvin H. Patel, Alexei Savchenko, Ann Karen C. Brassinga, Gerd Prehna
Legionella are freshwater Gram-negative bacteria that in their normal environment infect protozoa. However, this adaptation also allows Legionella to infect human alveolar macrophages and cause pneumonia. Central to Legionella pathogenesis are more than 330 secreted effectors, of which there are nine core effectors that are conserved in all pathogenic species. Despite their importance, the biochemical
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Functional production and biochemical investigation of an integral membrane enzyme for olefin biosynthesis Protein Sci. (IF 8.0) Pub Date : 2023-12-31 Subhashini Murugan, Tabish Iqbal, Debasis Das
Integral membrane enzymes play essential roles in a plethora of biochemical processes. The fatty acid desaturases (FADS)-like superfamily is an important group of integral membrane enzymes that catalyze a wide array of reactions, including hydroxylation, desaturation, and cyclization; however, due to the membrane-bound nature, the majority of these enzymes have remained poorly understood. UndB is a
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The mineralocorticoid receptor forms higher order oligomers upon DNA binding Protein Sci. (IF 8.0) Pub Date : 2023-12-31 Gregory Fettweis, Thomas A. Johnson, Brian Almeida-Prieto, Julián Weller-Pérez, Diego M. Presman, Gordon L. Hager, Diego Alvarez de la Rosa
The prevailing model of steroid hormone nuclear receptor function assumes ligand-induced homodimer formation followed by binding to DNA hormone response elements (HREs). This model has been challenged by evidence showing that the glucocorticoid receptor (GR) forms tetramers upon ligand and DNA binding, which then drive receptor-mediated gene transactivation and transrepression. GR and the closely-related
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Structural and functional validation of a highly specific Smurf2 inhibitor Protein Sci. (IF 8.0) Pub Date : 2023-12-26 Tanner M. Tessier, Arvid Chowdhury, Zane Stekel, Julia Fux, Maria Augusta Sartori, Joan Teyra, Nick Jarvik, Jacky Chung, Igor Kurinov, Frank Sicheri, Sachdev S. Sidhu, Alex U. Singer, Wei Zhang
Smurf1 and Smurf2 are two closely related members of the HECT (homologous to E6AP carboxy terminus) E3 ubiquitin ligase family and play important roles in the regulation of various cellular processes. Both were initially identified to regulate transforming growth factor-β and bone morphogenetic protein signaling pathways through regulating Smad protein stability and are now implicated in various pathological
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Crystal structure of human serum albumin in complex with megabody reveals unique human and murine cross-reactive binding site Protein Sci. (IF 8.0) Pub Date : 2023-12-28 Sofia De Felice, Zhanna Romanyuk, Monica Chinellato, Giulia Zoia, Sara Linciano, Yoichi Kumada, Els Pardon, Jan Steyaert, Alessandro Angelini, Laura Cendron
The pharmacokinetic properties of small biotherapeutics can be enhanced via conjugation to cross-reactive albumin-binding ligands in a process that improves their safety and accelerates testing through multiple pre-clinical animal models. In this context, the small and stable heavy-chain-only nanobody NbAlb1, capable of binding both human and murine albumin, has recently been successfully applied to
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Engineering highly stable variants of Corynactis californica green fluorescent proteins Protein Sci. (IF 8.0) Pub Date : 2023-12-27 Li-Wei Hung, Thomas C. Terwilliger, Geoffrey S. Waldo, Hau B. Nguyen
Fluorescent proteins (FPs) are versatile biomarkers that facilitate effective detection and tracking of macromolecules of interest in real time. Engineered FPs such as superfolder green fluorescent protein (sfGFP) and superfolder Cherry (sfCherry) have exceptional refolding capability capable of delivering fluorescent readout in harsh environments where most proteins lose their native functions. Our
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Dimerization of the CNNM extracellular domain Protein Sci. (IF 8.0) Pub Date : 2023-12-27 Ashkan Shahsavan, Emma L. Lee, Katalin Illes, Guennadi Kozlov, Kalle Gehring
Cystathionine- β $$ \beta $$ -synthase (CBS)-pair domain divalent metal cation transport mediators (CNNMs) are an evolutionarily conserved family of magnesium transporters. They mediate magnesium homeostasis directly by transport of Mg2+ ions and indirectly by regulation of the transient receptor potential ion channel subfamily M member 7 (TRPM7). Here, we report the crystal structure of the extracellular
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Helicobacter pylori FlgN binds its substrate FlgK and the flagellum ATPase FliI in a similar manner observed for the FliT chaperone Protein Sci. (IF 8.0) Pub Date : 2023-12-27 Poonam Dhindwal, Michal T. Boniecki, Stanley A. Moore
In bacterial flagellum biogenesis, secretion of the hook–filament junction proteins FlgK and FlgL and completion of the flagellum requires the FlgN chaperone. Similarly, the related FliT chaperone is necessary for the secretion of the filament cap protein FliD and binds the flagellar export gate protein FlhA and the flagellum ATPase FliI. FlgN and FliT require FliJ for effective substrate secretion
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Investigating lysozyme amyloid fibril formation and structural variability dependence on its initial folding state under different pH conditions Protein Sci. (IF 8.0) Pub Date : 2023-12-27 Mantas Ziaunys, Kamile Mikalauskaite, Andrius Sakalauskas, Vytautas Smirnovas
Protein fibril formation and accumulation are associated with dozens of amyloidoses, including the widespread and yet-incurable Alzheimer's and Parkinson's diseases. Currently, there are still several aspects of amyloid aggregation that are not fully understood, which negatively contributes to the development of disease-altering drugs and treatments. One factor which requires a more in-depth analysis
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Self-assembly of temperature-responsive di-block polypeptides functionalized with unnatural amino acids Protein Sci. (IF 8.0) Pub Date : 2023-12-26 Rotem Azulay, Daniela S. Strugach, Miriam Amiram
The incorporation of unnatural amino acids (uAAs) into protein-based polymers has emerged as a powerful methodology to expand their chemical repertoire. Recently, we demonstrated that incorporating uAAs into two temperature-responsive protein-based polymers—namely resilin- and elastin-like polypeptides (RLPs and ELPs, respectively)—can alter their properties. In this study, we incorporated aromatic
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Flexible protein–protein docking with a multitrack iterative transformer Protein Sci. (IF 8.0) Pub Date : 2023-12-26 Lee-Shin Chu, Jeffrey A. Ruffolo, Ameya Harmalkar, Jeffrey J. Gray
Conventional protein–protein docking algorithms usually rely on heavy candidate sampling and reranking, but these steps are time-consuming and hinder applications that require high-throughput complex structure prediction, for example, structure-based virtual screening. Existing deep learning methods for protein–protein docking, despite being much faster, suffer from low docking success rates. In addition
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Probing effects of site-specific aspartic acid isomerization on structure and stability of GB1 through chemical protein synthesis Protein Sci. (IF 8.0) Pub Date : 2023-12-25 Shelby L. Heath, Alex J. Guseman, Angela M. Gronenborn, W. Seth Horne
Chemical modifications of long-lived proteins, such as isomerization and epimerization, have been evoked as prime triggers for protein-damage related diseases. Deamidation of Asn residues, which results in formation of a mixture of l- and d-Asp and isoAsp via an intermediate aspartyl succinimide, can result in the disruption of cellular proteostasis and toxic protein depositions. In contrast to extensive
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Molecular mechanisms of chaperone-directed protein folding: Insights from atomistic simulations Protein Sci. (IF 8.0) Pub Date : 2023-12-25 Matteo Castelli, Andrea Magni, Giorgio Bonollo, Silvia Pavoni, Francesco Frigerio, A. Sofia F. Oliveira, Fabrizio Cinquini, Stefano A. Serapian, Giorgio Colombo
Molecular chaperones, a family of proteins of which Hsp90 and Hsp70 are integral members, form an essential machinery to maintain healthy proteomes by controlling the folding and activation of a plethora of substrate client proteins. This is achieved through cycles in which Hsp90 and Hsp70, regulated by task-specific co-chaperones, process ATP and become part of a complex network that undergoes extensive
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Molecular mechanism of Fe3+ binding inhibition to Vibrio metschnikovii ferric ion-binding protein, FbpA, by rosmarinic acid and its hydrolysate, danshensu Protein Sci. (IF 8.0) Pub Date : 2023-12-25 Peng Lu, Jinyan Jiang, Chang Liu, Suguru Okuda, Hideaki Itoh, Ken Okamoto, Michio Suzuki, Koji Nagata
Global warming has increased the growth of pathogenic Vibrio bacteria, which can cause foodborne illnesses and death. Vibrio bacteria require iron for growth and survival. They utilize a ferric ion-binding protein (FbpA) to bind and transport Fe3+ into the cell. FbpA from Vibrio metschnikovii (Vm) is a potential target for inhibiting its growth. Rosmarinic acid (RA) can block the binding of VmFbpA
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Dynamic proximity interaction profiling suggests that YPEL2 is involved in cellular stress surveillance Protein Sci. (IF 8.0) Pub Date : 2023-12-25 Gizem Turan, Çağla Ece Olgun, Hazal Ayten, Pelin Toker, Annageldi Ashyralyyev, Büşra Savaş, Ezgi Karaca, Mesut Muyan
YPEL2 is a member of the evolutionarily conserved YPEL family involved in cellular proliferation, mobility, differentiation, senescence, and death. However, the mechanism by which YPEL2, or YPEL proteins, mediates its effects is largely unknown. Proteins perform their functions in a network of proteins whose identities, amounts, and compositions change spatiotemporally in a lineage-specific manner
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Structural determination and kinetic analysis of the transketolase from Vibrio vulnificus reveal unexpected cooperative behavior Protein Sci. (IF 8.0) Pub Date : 2023-12-25 Rainier-Numa Georges, Lionel Ballut, Guillaume Octobre, Arnaud Comte, Laurence Hecquet, Franck Charmantray, Bastien Doumèche
Vibrio vulnificus (vv) is a multidrug-resistant human bacterial pathogen whose prevalence is expected to increase over the years. Transketolases (TK), transferases catalyzing two reactions of the nonoxidative branch of the pentose-phosphate pathway and therefore linked to several crucial metabolic pathways, are potential targets for new drugs against this pathogen. Here, the vvTK is crystallized and
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Residues within the LptC transmembrane helix are critical for Escherichia coli LptB2FG ATPase regulation Protein Sci. (IF 8.0) Pub Date : 2023-12-22 Nicholas P. Cina, Dara W. Frank, Candice S. Klug
Lipopolysaccharide (LPS) synthesis in Gram-negative bacteria is completed at the outer leaflet of the inner membrane (IM). Following synthesis, seven LPS transport (Lpt) proteins facilitate the movement of LPS to the outer membrane (OM), an essential process that if disrupted at any stage has lethal effects on bacterial viability. LptB2FG, the IM component of the Lpt bridge system, is a type VI ABC
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Helicity of a tardigrade disordered protein contributes to its protective function during desiccation Protein Sci. (IF 8.0) Pub Date : 2023-12-19 Sourav Biswas, Edith Gollub, Feng Yu, Garrett Ginell, Alex Holehouse, Shahar Sukenik, Thomas C. Boothby
To survive extreme drying (anhydrobiosis), many organisms, spanning every kingdom of life, accumulate intrinsically disordered proteins (IDPs). For decades, the ability of anhydrobiosis-related IDPs to form transient amphipathic helices has been suggested to be important for promoting desiccation tolerance. However, evidence empirically supporting the necessity and/or sufficiency of helicity in mediating
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4-Thiaproline accelerates the slow folding phase of proteins containing cis prolines in the native state by two orders of magnitude Protein Sci. (IF 8.0) Pub Date : 2023-12-19 Jennie O' Loughlin, Kirill Zinovjev, Silvia Napolitano, Marc van der Kamp, Marina Rubini
The cis/trans isomerization of peptidyl-prolyl peptide bonds is often the bottleneck of the refolding reaction for proteins containing cis proline residues in the native state. Proline (Pro) analogues, especially C4-substituted fluoroprolines, have been widely used in protein engineering to enhance the thermodynamic stability of peptides and proteins and to investigate folding kinetics. 4-thiaproline
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Structure-based development of a canine TNF-α-specific antibody using adalimumab as a template Protein Sci. (IF 8.0) Pub Date : 2023-12-19 Cheng-Chung Lee, Wen-Chih Kuo, Ya-Wen Chang, Shu-Fang Hsu, Chia-Hung Wu, Ya-Wen Chen, Jui-Jen Chang, Andrew H.-J. Wang
The canine anti-tumor necrosis factor-alpha (TNF-α) monoclonal antibody is a potential therapeutic option for treating canine arthritis. The current treatments for arthritis in dogs have limitations due to side effects, emphasizing the need for safer and more effective therapies. The crystal structure of canine TNF-α (cTNF-α) was successfully determined at a resolution of 1.85 Å, and the protein was
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Exploring the conformational changes of the Munc18-1/syntaxin 1a complex Protein Sci. (IF 8.0) Pub Date : 2023-12-18 Ioanna Stefani, Justyna Iwaszkiewicz, Dirk Fasshauer
Neurotransmitters are released from synaptic vesicles, the membrane of which fuses with the plasma membrane upon calcium influx. This membrane fusion reaction is driven by the formation of a tight complex comprising the plasma membrane N-ethylmaleimide-sensitive factor attachment receptor (SNARE) proteins syntaxin-1a and SNAP-25 with the vesicle SNARE protein synaptobrevin. The neuronal protein Munc18-1
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A functional and structural comparative analysis of large tumor antigens reveals evolution of different importin α-dependent nuclear localization signals Protein Sci. (IF 8.0) Pub Date : 2023-12-18 Emily M. Cross, Nasim Akbari, Hanieh Ghassabian, Mikayla Hoad, Silvia Pavan, Daryl Ariawan, Camilla M. Donnelly, Enrico Lavezzo, Gayle F. Petersen, Jade K. Forwood, Gualtiero Alvisi
Nucleocytoplasmic transport regulates the passage of proteins between the nucleus and cytoplasm. In the best characterized pathway, importin (IMP) α bridges cargoes bearing basic, classical nuclear localization signals (cNLSs) to IMPβ1, which mediates transport through the nuclear pore complex. IMPα recognizes three types of cNLSs via two binding sites: the major binding site accommodates monopartite
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Structural insights into the unique recognition module between α-synuclein peptide and nanobody Protein Sci. (IF 8.0) Pub Date : 2023-12-17 Zeyaul Islam, Nishant N. Vaikath, Issam Hmila, Omar M. A. El-Agnaf, Prasanna R. Kolatkar
Nanobodies are single-domain fragments of antibodies with comparable specificity and affinity to antibodies. They are emerging as versatile tools in biology due to their relatively small size. Here, we report the crystal structure of a specific nanobody Nbα-syn01, bound to a 14 amino acid long peptide of α-synuclein (αSyn), a 140-residue protein whose aggregation is associated with Parkinson's disease
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Kinetic evidence for multiple aggregation pathways in antibody light chain variable domains Protein Sci. (IF 8.0) Pub Date : 2023-12-15 Sherry Wong, Madeline E. West, Gareth J. Morgan
Aggregation of antibody light chain proteins is associated with the progressive disease light chain amyloidosis. Patient-derived amyloid fibrils are formed from light chain variable domain residues in non-native conformations, highlighting a requirement that light chains unfold from their native structures in order to aggregate. However, mechanistic studies of amyloid formation have primarily focused
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FRAGSITE2: A structure and fragment-based approach for virtual ligand screening Protein Sci. (IF 8.0) Pub Date : 2023-12-15 Hongyi Zhou, Jeffrey Skolnick
Protein function annotation and drug discovery often involve finding small molecule binders. In the early stages of drug discovery, virtual ligand screening (VLS) is frequently applied to identify possible hits before experimental testing. While our recent ligand homology modeling (LHM)-machine learning VLS method FRAGSITE outperformed approaches that combined traditional docking to generate protein–ligand
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Structure-based insights into the mechanism of [4Fe-4S]-dependent sulfur insertase LarE Protein Sci. (IF 8.0) Pub Date : 2023-12-15 Paolo Zecchin, Ludovic Pecqueur, Jonathan Oltmanns, Christophe Velours, Volker Schünemann, Marc Fontecave, Béatrice Golinelli-Pimpaneau
Several essential cellular metabolites, such as enzyme cofactors, contain sulfur atoms and their biosynthesis requires specific thiolation enzymes. LarE is an ATP-dependent sulfur insertase, which catalyzes the sequential conversion of the two carboxylate groups of the precursor of the lactate racemase cofactor into thiocarboxylates. Two types of LarE enzymes are known, one that uses a catalytic cysteine
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Emerging role of carbonyl–carbonyl interactions in the classification of beta turns Protein Sci. (IF 8.0) Pub Date : 2023-12-15 Nancy D'Arminio, Valentina Ruggiero, Giovanni Pierri, Anna Marabotti, Consiglia Tedesco
Carbonyl–carbonyl interactions in peptides and proteins attracted considerable interest in recent years. Here, we report a survey of carbonyl–carbonyl interactions in cyclic peptides, depsipeptides, peptoids and discuss the relationship between backbone torsion angles and CO∙∙∙CO distances. In general, φ values in the range between −40° and −90° and between 40° and 90° correspond to CO∙∙∙CO distances
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Evidence of direct interaction between cisplatin and the caspase-cleaved prostate apoptosis response-4 tumor suppressor Protein Sci. (IF 8.0) Pub Date : 2023-12-13 Krishna K. Raut, Samjhana Pandey, Gyanendra Kharel, Steven M. Pascal
Prostate apoptosis response-4 (Par-4) tumor suppressor protein has gained attention as a potential therapeutic target owing to its unique ability to selectively induce apoptosis in cancer cells, sensitize them to chemotherapy and radiotherapy, and mitigate drug resistance. It has recently been reported that Par-4 interacts synergistically with cisplatin, a widely used anticancer drug. However, the