Results 1 to 10 of about 2,123,992 (119)

Anchor extension: a structure-guided approach to design cyclic peptides targeting enzyme active sites

Nature Communications, 2021
Despite recent success in computational design of structured cyclic peptides, de novo design of cyclic peptides that bind to any protein functional site remains difficult.
Parisa Hosseinzadeh, Paris R. Watson, Timothy W. Craven, Xinting Li, Stephen Rettie, Fátima Pardo-Avila, Asim K. Bera, Vikram Khipple Mulligan, Peilong Lu, Alexander S. Ford, Brian D. Weitzner, Lance J. Stewart, Adam P. Moyer, Maddalena Di Piazza, Joshua G. Whalen, Per Jr. Greisen, David W. Christianson, David Baker   +17 more
doaj   +1 more source

Improved protein structure refinement guided by deep learning based accuracy estimation

Nature Communications, 2021
Here the authors present DeepAccNet, a deep learning framework that estimates per-residue accuracy and residue-residue distance signed error in protein models, which are used to guide Rosetta protein structure refinement.
Naozumi Hiranuma, Hahnbeom Park, Minkyung Baek, Ivan Anishchenko, Justas Dauparas, David Baker   +5 more
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Introducing or removing heparan sulfate binding sites does not alter brain uptake of the blood–brain barrier shuttle scFv8D3

Scientific Reports, 2022
The blood–brain barrier (BBB) greatly limits the delivery of protein-based drugs into the brain and is a major obstacle for the treatment of brain disorders. Targeting the transferrin receptor (TfR) is a strategy for transporting protein-based drugs into
Andrés de la Rosa, Nicole G. Metzendorf, Jamie I. Morrison, Rebecca Faresjö, Fadi Rofo, Alex Petrovic, Paul O’Callaghan, Stina Syvänen, Greta Hultqvist   +8 more
doaj   +1 more source

A rational blueprint for the design of chemically-controlled protein switches

Nature Communications, 2021
Small-molecule responsive protein switches are crucial components to control synthetic cellular activities. Here, we present a computational protein design strategy to repurpose drug-inhibited protein-protein interactions into OFF- and ON-switches active
Sailan Shui, Pablo Gainza, Leo Scheller, Che Yang, Yoichi Kurumida, Stéphane Rosset, Sandrine Georgeon, Raphaël B. Di Roberto, Rocío Castellanos-Rueda, Sai T. Reddy, Bruno E. Correia   +10 more
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Single-molecule FRET unmasks structural subpopulations and crucial molecular events during FUS low-complexity domain phase separation

Nature Communications, 2023
Biomolecular condensates formed via phase separation of proteins and nucleic acids are thought to be associated with a wide range of cellular functions and dysfunctions.
Ashish Joshi, Anuja Walimbe, Anamika Avni, Sandeep K. Rai, Lisha Arora, Snehasis Sarkar, Samrat Mukhopadhyay   +6 more
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Spatiotemporal modulations in heterotypic condensates of prion and α-synuclein control phase transitions and amyloid conversion

Nature Communications, 2022
The authors show that prion protein and α-synuclein undergo phase separation through domain-specific electrostatic interactions. These complex coacervates possess electrostatic nanoclusters and can convert into multiphasic condensates and amyloids.
Aishwarya Agarwal, Lisha Arora, Sandeep K. Rai, Anamika Avni, Samrat Mukhopadhyay   +4 more
doaj   +1 more source

Single-droplet surface-enhanced Raman scattering decodes the molecular determinants of liquid-liquid phase separation

Nature Communications, 2022
The authors introduce a unique single-droplet surface-enhanced Raman scattering (SERS) methodology that illuminates a wealth of molecular information within the mesoscopic liquid condensed phase of Fused in Sarcoma in the absence and presence of RNA.
Anamika Avni, Ashish Joshi, Anuja Walimbe, Swastik G. Pattanashetty, Samrat Mukhopadhyay   +4 more
doaj   +1 more source

Adjuvanting a subunit SARS-CoV-2 vaccine with clinically relevant adjuvants induces durable protection in mice

npj Vaccines, 2022
Adjuvants enhance the magnitude and the durability of the immune response to vaccines. However, there is a paucity of comparative studies on the nature of the immune responses stimulated by leading adjuvant candidates.
Lilit Grigoryan, Audrey Lee, Alexandra C. Walls, Lilin Lai, Benjamin Franco, Prabhu S. Arunachalam, Yupeng Feng, Wei Luo, Abigail Vanderheiden, Katharine Floyd, Samuel Wrenn, Deleah Pettie, Marcos C. Miranda, Elizabeth Kepl, Rashmi Ravichandran, Claire Sydeman, Natalie Brunette, Michael Murphy, Brooke Fiala, Lauren Carter, Robert L. Coffman, David Novack, Harry Kleanthous, Derek T. O’Hagan, Robbert van der Most, Jason S. McLellan, Mehul Suthar, David Veesler, Neil P. King, Bali Pulendran   +29 more
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Antibody Profiling: Kinetics with Native Biomarkers for Diagnostic Assay and Drug Developments

Biosensors, 2023
Despite remarkable progress in applied Surface Plasmon Resonance (SPR)-based methods, concise monitoring of kinetic properties for native biomarkers from patient samples is still lacking.
Ute Jucknischke, Sebastian Friebe, Markus Rehle, Laura Quast, Sven H. Schmidt   +4 more
doaj   +1 more source

Single-chain dimers from de novo immunoglobulins as robust scaffolds for multiple binding loops

Nature Communications, 2023
Antibody derivatives have sought to recapitulate the antigen binding properties of antibodies, but with improved biophysical attributes convenient for therapeutic, diagnostic and research applications.
Jorge Roel-Touris, Marta Nadal, Enrique Marcos   +2 more
doaj   +1 more source