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Coevolutionary analysis of Forkhead box protein P3 and its physical binary interactors E3 ubiquitin-protein ligase CHIP, Zfp-90, and nuclear receptor ROR-α

期刊: PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2023; 91 (8)

Forkhead box protein P3 (FOXP3) is known to orchestrate the development and maintenance of T regulatory cells, a cell population specialized in immune......

Ligands-induced open-close conformational change during DapE catalysis: Insights from molecular dynamics simulations

期刊: PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2023; 91 (6)

The microbial enzyme DapE plays a critical role in the lysine biosynthetic pathway and is considered as a potentially safe antibiotic target. In this ......

The alteration of structural network upon transient association between proteins studied using graph theory

期刊: PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2023; ()

Proteins such as enzymes perform their function by predominant non-covalent bond interactions between transiently interacting units. There is an impac......

Insight into the structural basis of the dual inhibitory mode of Lima bean (Phaseolus lunatus) serine protease inhibitor

期刊: PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2023; 91 (1)

Bovine pancreatic trypsin was crystallized, in-complex with Lima bean trypsin inhibitor (LBTI) (Phaseolus lunatus L.), in the form of a ternary comple......

Understanding the helical stability of charged peptides

期刊: PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2023; 91 (2)

Cationic helical peptides play a crucial role in applications such as anti-microbial and anticancer activity. The activity of these peptides directly ......

New simulation insights on the structural transition mechanism of bovine rhodopsin activation

期刊: PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2023; 91 (6)

Inactive rhodopsin can absorb photons, which induces different structural transitions that finally activate rhodopsin. We have examined the change in ......

Challenges in bridging the gap between protein structure prediction and functional interpretation

期刊: PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2023; ()

The rapid evolution of protein structure prediction tools has significantly broadened access to protein structural data. Although predicted structure ......

Dynamics and recognition of homeodomain containing protein-DNA complex of IRX4

期刊: PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2023; ()

Iroquois Homeobox 4 (IRX4) belongs to a family of homeobox TFs having roles in embryogenesis, cell specification, and organ development. Recently, lar......

Insights into the solution structure and transcriptional regulation of the MazE9 antitoxin in Mycobacterium tuberculosis

期刊: PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2023; ()

The present study endeavors to decode the details of the transcriptional autoregulation effected by the MazE9 antitoxin of the Mycobacterium tuberculo......

MPA-Pred: A machine learning approach for predicting the binding affinity of membrane protein-protein complexes

期刊: PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2023; ()

Membrane protein-protein interactions are essential for several functions including cell signaling, ion transport, and enzymatic activity. These inter......

Transmembrane proteins-Different anchoring systems

期刊: PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2023; ()

Transmembrane proteins are active in amphipathic environments. To stabilize the protein in such surrounding the exposure of hydrophobic residues on th......

Initiation factor 3 bound to the 30S ribosomal subunit in an initial step of translation

期刊: PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2023; ()

Bacterial ribosomes require three initiation factors IF1, IF2, and IF3 during the initial steps of translation. These IFs ensure correct base pairing ......

Exploring the structural and dynamic differences between human carnosinase I (CN1) and II (CN2)

期刊: PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2023; 91 (6)

Human carnosinases (CNs) are dimeric dipeptidases in the metallopeptidase M20 family. Two isoforms of carnosinases (Zn2+-containing carnosinase 1 (CN1......

VoroIF-GNN: Voronoi tessellation-derived protein-protein interface assessment using a graph neural network

期刊: PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2023; 91 (12)

We present VoroIF-GNN (Voronoi InterFace Graph Neural Network), a novel method for assessing inter-subunit interfaces in a structural model of a prote......

Structural implications of amyloidogenic rare variants Ser282Leu and Gln356Arg identified in h-BRCA1

期刊: PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2023; ()

Preliminary studies have shown BRCA1 (170-1600) residues to be intrinsically disordered with unknown structural details. However, thousands of clinica......

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