scholarly journals Conformational selection in protein binding and function

2014 ◽  
Vol 23 (11) ◽  
pp. 1508-1518 ◽  
Author(s):  
Thomas R. Weikl ◽  
Fabian Paul
Keyword(s):  
Protein Binding ◽  
Conformational Selection ◽  
And Function

scholarly journals Inverse Conformational Selection in Lipid–Protein Binding

2021 ◽  
Author(s):  
Amélie Bacle ◽  
Pavel Buslaev ◽  
Rebeca Garcia-Fandino ◽  
Fernando Favela-Rosales ◽  
Tiago Mendes Ferreira ◽  
...  
Keyword(s):  
Protein Binding ◽  
Conformational Selection

Electrostatics in Protein Binding and Function

2002 ◽  
Vol 3 (6) ◽  
pp. 601-614 ◽  
Author(s):  
Neeti Sinha ◽  
Sandra Smith-Gill
Keyword(s):  
Protein Binding ◽  
And Function

scholarly journals Nature and function of insulator protein binding sites in the Drosophila genome

2012 ◽  
Vol 22 (11) ◽  
pp. 2188-2198 ◽  
Author(s):  
Y. B. Schwartz ◽  
D. Linder-Basso ◽  
P. V. Kharchenko ◽  
M. Y. Tolstorukov ◽  
M. Kim ◽  
...  
Keyword(s):  
Protein Binding ◽  
Binding Sites ◽  
Drosophila Genome ◽  
Protein Binding Sites ◽  
Insulator Protein ◽  
And Function

scholarly journals Stochastic and reversible assembly of a multiprotein DNA repair complex ensures accurate target site recognition and efficient repair

2010 ◽  
Vol 189 (3) ◽  
pp. 445-463 ◽  
Author(s):  
Martijn S. Luijsterburg ◽  
Gesa von Bornstaedt ◽  
Audrey M. Gourdin ◽  
Antonio Z. Politi ◽  
Martijn J. Moné ◽  
...  
Keyword(s):  
Dna Repair ◽  
Protein Binding ◽  
Bound State ◽  
Living Cells ◽  
Dna Lesions ◽  
Trade Off ◽  
Nucleotide Excision ◽  
And Function ◽  
Site Recognition

To understand how multiprotein complexes assemble and function on chromatin, we combined quantitative analysis of the mammalian nucleotide excision DNA repair (NER) machinery in living cells with computational modeling. We found that individual NER components exchange within tens of seconds between the bound state in repair complexes and the diffusive state in the nucleoplasm, whereas their net accumulation at repair sites evolves over several hours. Based on these in vivo data, we developed a predictive kinetic model for the assembly and function of repair complexes. DNA repair is orchestrated by the interplay of reversible protein-binding events and progressive enzymatic modifications of the chromatin substrate. We demonstrate that faithful recognition of DNA lesions is time consuming, whereas subsequently, repair complexes form rapidly through random and reversible assembly of NER proteins. Our kinetic analysis of the NER system reveals a fundamental conflict between specificity and efficiency of chromatin-associated protein machineries and shows how a trade off is negotiated through reversibility of protein binding.

scholarly journals Phosphorylation in Protein-Protein Binding: Effect on Stability and Function

Structure ◽  
2011 ◽  
Vol 19 (12) ◽  
pp. 1807-1815 ◽  
Author(s):  
Hafumi Nishi ◽  
Kosuke Hashimoto ◽  
Anna R. Panchenko
Keyword(s):  
Protein Binding ◽  
Binding Effect ◽  
And Function

scholarly journals Molecular mechanism of multispecific recognition of Calmodulin through conformational changes

2017 ◽  
Vol 114 (20) ◽  
pp. E3927-E3934 ◽  
Author(s):  
Fei Liu ◽  
Xiakun Chu ◽  
H. Peter Lu ◽  
Jin Wang
Keyword(s):  
Protein Binding ◽  
Conformational Change ◽  
Molecular Mechanism ◽  
Conformational Changes ◽  
Electrostatic Interaction ◽  
Hydrophobic Interaction ◽  
High Specificity ◽  
Binding Peptide ◽  
Conformational Selection ◽  
High Affinity

Calmodulin (CaM) is found to have the capability to bind multiple targets. Investigations on the association mechanism of CaM to its targets are crucial for understanding protein–protein binding and recognition. Here, we developed a structure-based model to explore the binding process between CaM and skMLCK binding peptide. We found the cooperation between nonnative electrostatic interaction and nonnative hydrophobic interaction plays an important role in nonspecific recognition between CaM and its target. We also found that the conserved hydrophobic anchors of skMLCK and binding patches of CaM are crucial for the transition from high affinity to high specificity. Furthermore, this association process involves simultaneously both local conformational change of CaM and global conformational changes of the skMLCK binding peptide. We found a landscape with a mixture of the atypical “induced fit,” the atypical “conformational selection,” and “simultaneously binding–folding,” depending on the synchronization of folding and binding. Finally, we extend our discussions on multispecific binding between CaM and its targets. These association characteristics proposed for CaM and skMLCK can provide insights into multispecific binding of CaM.

scholarly journals TSPO protein binding partners in bacteria, animals, and plants

2021 ◽  
Author(s):  
Carrie Hiser ◽  
Beronda L. Montgomery ◽  
Shelagh Ferguson-Miller
Keyword(s):  
Protein Binding ◽  
Helical Structure ◽  
Additional Stress ◽  
Binding Partners ◽  
Diverse Species ◽  
Ancestral Function ◽  
Primary Amino ◽  
Exogenous Ligands ◽  
And Function ◽  
Induced Changes

AbstractThe ancient membrane protein TSPO is phylogenetically widespread from archaea and bacteria to insects, vertebrates, plants, and fungi. TSPO’s primary amino acid sequence is only modestly conserved between diverse species, although its five transmembrane helical structure appears mainly conserved. Its cellular location and orientation in membranes have been reported to vary between species and tissues, with implications for potential diverse binding partners and function. Most TSPO functions relate to stress-induced changes in metabolism, but in many cases it is unclear how TSPO itself functions—whether as a receptor, a sensor, a transporter, or a translocator. Much evidence suggests that TSPO acts indirectly by association with various protein binding partners or with endogenous or exogenous ligands. In this review, we focus on proteins that have most commonly been invoked as TSPO binding partners. We suggest that TSPO was originally a bacterial receptor/stress sensor associated with porphyrin binding as its most ancestral function and that it later developed additional stress-related roles in eukaryotes as its ability to bind new partners evolved.

scholarly journals Centrality Measures in Residue Interaction Networks to Highlight Amino Acids in Protein–Protein Binding

2021 ◽  
Vol 1 ◽  
Author(s):  
Guillaume Brysbaert ◽  
Marc F. Lensink
Keyword(s):  
Protein Binding ◽  
Interaction Networks ◽  
Centrality Measures ◽  
Good Precision ◽  
Eigenvector Centrality ◽  
Protein Protein Interaction ◽  
Residue Interaction ◽  
Binding Residues ◽  
Optimal Approach ◽  
And Function

Residue interaction networks (RINs) describe a protein structure as a network of interacting residues. Central nodes in these networks, identified by centrality analyses, highlight those residues that play a role in the structure and function of the protein. However, little is known about the capability of such analyses to identify residues involved in the formation of macromolecular complexes. Here, we performed six different centrality measures on the RINs generated from the complexes of the SKEMPI 2 database of changes in protein–protein binding upon mutation in order to evaluate the capability of each of these measures to identify major binding residues. The analyses were performed with and without the crystallographic water molecules, in addition to the protein residues. We also investigated the use of a weight factor based on the inter-residue distances to improve the detection of these residues. We show that for the identification of major binding residues, closeness, degree, and PageRank result in good precision, whereas betweenness, eigenvector, and residue centrality analyses give a higher sensitivity. Including water in the analysis improves the sensitivity of all measures without losing precision. Applying weights only slightly raises the sensitivity of eigenvector centrality analysis. We finally show that a combination of multiple centrality analyses is the optimal approach to identify residues that play a role in protein–protein interaction.

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