because of their highaffinityforpeptidebonds, break the hydrogen bonds and the salt bridges between positive and negative side chains, thereby abolishing the tertiary structure of the peptide chain. When denaturing agents are removed from a protein solution, the native protein re-forms in many cases...
Protein Data Bank refers to a repository of three-dimensional structural data of large biological molecules, such as proteins and nucleic acids, which is maintained by an international organization called the Worldwide Protein Data Bank. It is a valuable resource for structural biologists studying prot...
UniProt Knowledgebase (UniProtKB): a protein database consisting of UniProtKB/Swiss-Prot (curated protein sequence database) and UniProtKB/TrEMBL (automatically annotated entries), which can be accessed through the Expert Protein Analysis System (ExPASy) server (http://expasy.org/sprot/). ...
scoring function, binding free energy, protein-RNA docking, binding affinity benchmarkWe have developed a non-redundant protein–RNA binding benchmark dataset derived from the available protein–RNA structures in the Protein Database Bank. It consists of 73 complexes with measured binding affinity. ...
A method for designing high-affinity, specific binders to peptide–MHC complexes may improve the next generation of antigen-specific T cell-based therapeutics. Pallavi A. Balivada Stephanie A. Gaglione Michael E. Birnbaum News & Views13 Dec 2024 Nature Biotechnology P: 1-2 Enhancing protein ...
Mass Spectrometry: Used in concert with affinity-based methods (such as co-IPs) to isolate binding partners and complexes and to identify the component proteins using standard mass spectral methods (e.g., MALDI-...
et al. UniProt: the universal protein knowledgebase in 2023. Nucleic Acids Res. 51, D523–D531 (2023). Altschul, S. F. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402 (1997). Article PubMed PubMed Central ...
The volume of protein solution for each spot is approximately 0.5 to 1.0 nL. Not all proteins have the same affinity for the ultrathin nitrocellulose coating of the slides. Approximately 10% or less of the protein binds to...
LSP1 is a phosphoprotein that binds polymerized actin with high-affinity via four domains in its C-terminal (Jongstra-Bilen et al., 1992; Wong et al., 2003). LSP1 is expressed in neutrophils, macrophages, B cells, T cells, and endothelial cells (Jongstra-Bilen and Jongstra, 2006) and ...
The Protein-DNA Interface database (PDIdb) is a repository containing relevant structural information of Protein-DNA complexes solved by X-ray crystallography and available at the Protein Data Bank. The database includes a simple functional classification of the protein-DNA complexes that consists of...