scholarly journals Ligand Binding Site Structure Influences the Evolution of Protein Complex Function and Topology

Cell Reports ◽  
2018 ◽  
Vol 22 (12) ◽  
pp. 3265-3276 ◽  
Author(s):  
György Abrusán ◽  
Joseph A. Marsh
Keyword(s):  
Ligand Binding ◽  
Binding Site ◽  
Protein Complex ◽  
Complex Function ◽  
Ligand Binding Site ◽  
Site Structure ◽  
And Topology

scholarly journals Ligand-Binding-Site Structure Shapes Allosteric Signal Transduction and the Evolution of Allostery in Protein Complexes

2019 ◽  
Vol 36 (8) ◽  
pp. 1711-1727 ◽  
Author(s):  
György Abrusán ◽  
Joseph A Marsh
Keyword(s):  
Signal Transduction ◽  
Ligand Binding ◽  
Binding Site ◽  
Binding Sites ◽  
Quaternary Structure ◽  
Protein Complexes ◽  
Signal Transduction Pathways ◽  
Ligand Binding Site ◽  
Single Chain ◽  
Site Structure

Abstract The structure of ligand-binding sites has been shown to profoundly influence the evolution of function in homomeric protein complexes. Complexes with multichain binding sites (MBSs) have more conserved quaternary structure, more similar binding sites and ligands between homologs, and evolve new functions slower than homomers with single-chain binding sites (SBSs). Here, using in silico analyses of protein dynamics, we investigate whether ligand-binding-site structure shapes allosteric signal transduction pathways, and whether the structural similarity of binding sites influences the evolution of allostery. Our analyses show that: 1) allostery is more frequent among MBS complexes than in SBS complexes, particularly in homomers; 2) in MBS homomers, semirigid communities and critical residues frequently connect interfaces and thus they are characterized by signal transduction pathways that cross protein–protein interfaces, whereas SBS homomers usually not; 3) ligand binding alters community structure differently in MBS and SBS homomers; and 4) except MBS homomers, allosteric proteins are more likely to have homologs with similar binding site than nonallosteric proteins, suggesting that binding site similarity is an important factor driving the evolution of allostery.

Constraints of Opsin Structure on the Ligand-binding Site: Studies with Ring-fused Retinals¶

2002 ◽  
Vol 76 (6) ◽  
pp. 606 ◽  
Author(s):  
Takahiro Hirano ◽  
In Taek Lim ◽  
Don Moon Kim ◽  
Xiang-Guo Zheng ◽  
Kazuo Yoshihara ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Binding Site ◽  
Ligand Binding Site

Capturing of the free cysteine residue in the ligand-binding site by affinity labeling of the ORL1 nociceptin receptor

2011 ◽  
Vol 19 (24) ◽  
pp. 7597-7602 ◽  
Author(s):  
Ayami Matsushima ◽  
Hirokazu Nishimura ◽  
Shogo Inamine ◽  
Shiho Uemura ◽  
Yasuyuki Shimohigashi
Keyword(s):  
Ligand Binding ◽  
Binding Site ◽  
Cysteine Residue ◽  
Affinity Labeling ◽  
Ligand Binding Site ◽  
Nociceptin Receptor

A Monoclonal Antibody against the Ligand Binding Site of the Receptor for Mouse Interferon-γ

1989 ◽  
Vol 9 (5) ◽  
pp. 551-562 ◽  
Author(s):  
MITALI BASU ◽  
JUDITH L. PACE ◽  
DAVID M. PINSON ◽  
STEPHEN W. RUSSELL
Keyword(s):  
Monoclonal Antibody ◽  
Ligand Binding ◽  
Binding Site ◽  
Interferon Γ ◽  
Ligand Binding Site
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