The X‐ray crystal structure of human A15C neuroglobin reveals both native/ de novo disulfide bonds and unexpected ligand‐binding sites

2022 ◽  
Author(s):  
Shu‐Qin Gao ◽  
Hong Yuan ◽  
Xi‐Chun Liu ◽  
Lianzhi Li ◽  
Xiangshi Tan ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Ligand Binding ◽  
Binding Sites ◽  
Disulfide Bonds ◽  
De Novo ◽  
X Ray ◽  
Ligand Binding Sites

scholarly journals Identification of Iron-Sulfur (Fe-S) and Zn-binding Sites Within Proteomes Predicted by DeepMind′s AlphaFold2 Program Dramatically Expands the Metalloproteome

2021 ◽  
Author(s):  
Zachary J Wehrspan ◽  
Robert T McDonnell ◽  
Adrian Elcock
Keyword(s):  
Ligand Binding ◽  
Binding Sites ◽  
Structure Prediction ◽  
Disulfide Bonds ◽  
3D Protein Structure ◽  
E Coli ◽  
Iron Sulfur ◽  
Ligand Binding Sites ◽  
Potential Ligand ◽  
Binding Orientations

DeepMind′s AlphaFold2 software has ushered in a revolution in high quality, 3D protein structure prediction. In very recent work by the DeepMind team, structure predictions have been made for entire proteomes of twenty-one organisms, with >360,000 structures made available for download. Here we show that thousands of novel binding sites for iron-sulfur (Fe-S) clusters and zinc ions can be identified within these predicted structures by exhaustive enumeration of all potential ligand-binding orientations. We demonstrate that AlphaFold2 routinely makes highly specific predictions of ligand binding sites: for example, binding sites that are comprised exclusively of four cysteine sidechains fall into three clusters, representing binding sites for 4Fe-4S clusters, 2Fe-2S clusters, or individual Zn ions. We show further: (a) that the majority of known Fe-S cluster and Zn-binding sites documented in UniProt are recovered by the AlphaFold2 structures, (b) that there are occasional disputes between AlphaFold2 and UniProt with AlphaFold2 predicting highly plausible alternative binding sites, (c) that the Fe-S cluster binding sites that we identify in E. coli agree well with previous bioinformatics predictions, (d) that cysteines predicted here to be part of Fe-S cluster or Zn-binding sites show little overlap with those shown via chemoproteomics techniques to be highly reactive, and (e) that AlphaFold2 occasionally appears to build erroneous disulfide bonds between cysteines that should instead coordinate a ligand. These results suggest that AlphaFold2 could be an important tool for the functional annotation of proteomes, and the methodology presented here is likely to be useful for predicting other ligand-binding sites.

scholarly journals De novo protein fold families expand the designable ligand binding site space

2021 ◽  
Vol 17 (11) ◽  
pp. e1009620
Author(s):  
Xingjie Pan ◽  
Tanja Kortemme
Keyword(s):  
Ligand Binding ◽  
Binding Site ◽  
Binding Sites ◽  
De Novo ◽  
Protein Structures ◽  
Protein Fold ◽  
Protein Families ◽  
Existing Structures ◽  
Fold Family ◽  
Ligand Binding Sites

A major challenge in designing proteins de novo to bind user-defined ligands with high affinity is finding backbones structures into which a new binding site geometry can be engineered with high precision. Recent advances in methods to generate protein fold families de novo have expanded the space of accessible protein structures, but it is not clear to what extend de novo proteins with diverse geometries also expand the space of designable ligand binding functions. We constructed a library of 25,806 high-quality ligand binding sites and developed a fast protocol to place (“match”) these binding sites into both naturally occurring and de novo protein families with two fold topologies: Rossman and NTF2. Each matching step involves engineering new binding site residues into each protein “scaffold”, which is distinct from the problem of comparing already existing binding pockets. 5,896 and 7,475 binding sites could be matched to the Rossmann and NTF2 fold families, respectively. De novo designed Rossman and NTF2 protein families can support 1,791 and 678 binding sites that cannot be matched to naturally existing structures with the same topologies, respectively. While the number of protein residues in ligand binding sites is the major determinant of matching success, ligand size and primary sequence separation of binding site residues also play important roles. The number of matched binding sites are power law functions of the number of members in a fold family. Our results suggest that de novo sampling of geometric variations on diverse fold topologies can significantly expand the space of designable ligand binding sites for a wealth of possible new protein functions.

scholarly journals De novo protein fold families expand the designable ligand binding site space

2021 ◽  
Author(s):  
Xingjie Pan ◽  
Tanja Kortemme
Keyword(s):  
Ligand Binding ◽  
Binding Site ◽  
Binding Sites ◽  
Method Development ◽  
De Novo ◽  
Protein Structures ◽  
Protein Fold ◽  
Ligand Binding Site ◽  
Protein Families ◽  
Ligand Binding Sites

AbstractA major challenge in designing proteins de novo to bind user-defined ligands with high specificity and affinity is finding backbones structures that can accommodate a desired binding site geometry with high precision. Recent advances in methods to generate protein fold families de novo have expanded the space of accessible protein structures, but it is not clear to what extend de novo proteins with diverse geometries also expand the space of designable ligand binding functions. We constructed a library of 25,806 high-quality ligand binding sites and developed a fast protocol to place (“match”) these binding sites into both naturally occurring and de novo protein families with two fold topologies: Rossman and NTF2. 5,896 and 7,475 binding sites could be matched to the Rossmann and NTF2 fold families, respectively. De novo designed Rossman and NTF2 protein families can support 1,791 and 678 binding sites that cannot be matched to naturally existing structures with the same topologies, respectively. While the number of protein residues in ligand binding sites is the major determinant of matching success, ligand size and primary sequence separation of binding site residues also play important roles. The number of matched binding sites are power law functions of the number of members in a fold family. Our results suggest that de novo sampling of geometric variations on diverse fold topologies can significantly expand the space of designable ligand binding sites for a wealth of possible new protein functions.Author summaryDe novo design of proteins that can bind to novel and highly diverse user-defined small molecule ligands could have broad biomedical and synthetic biology applications. Because ligand binding site geometries need to be accommodated by protein backbone scaffolds at high accuracy, the diversity of scaffolds is a major limitation for designing new ligand binding functions. Advances in computational protein structure design methods have significantly increased the number of accessible stable scaffold structures. Understanding how many new ligand binding sites can be accommodated by the de novo scaffolds is important for designing novel ligand binding proteins. To answer this question, we constructed a large library of ligand binding sites from the Protein Data Bank (PDB). We tested the number of ligand binding sites that can be accommodated by de novo scaffolds and naturally existing scaffolds with same fold topologies. The results showed that de novo scaffolds significantly expanded the ligand binding space of their respective fold topologies. We also identified factors that affect difficulties of binding site accommodation, as well as the relationship between the number of scaffolds and the accessible ligand binding site space. We believe our findings will benefit future method development and applications of ligand binding protein design.

scholarly journals Diaqua[(1R,2S,4R,8R,9S,11R)-2,9-dimethyl-1,4,8,11-tetraazacyclotetradecane]nickel(II) dichloride dihydrate

2012 ◽  
Vol 68 (8) ◽  
pp. m1111-m1112
Author(s):  
James Alan Townsend ◽  
John Desper
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Ligand Binding ◽  
Binding Sites ◽  
Title Complex ◽  
Ligand Binding Sites

The crystal structure of the title complex, [Ni(C12H28N4)(H2O)2]Cl2·2H2O, displays O—H...Cl and O—H...O hydrogen bonding. The tetraazacyclotetradecane ligand interacts with the NiIIatom in thecisV configuration and the final two ligand binding sites are occupied by water.

scholarly journals Diversity in the structures and ligand-binding sites of nematode fatty acid and retinol-binding proteins revealed by Na-FAR-1 from Necator americanus

2015 ◽  
Vol 471 (3) ◽  
pp. 403-414 ◽  
Author(s):  
M. Florencia Rey-Burusco ◽  
Marina Ibáñez-Shimabukuro ◽  
Mads Gabrielsen ◽  
Gisela R. Franchini ◽  
Andrew J. Roe ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Ligand Binding ◽  
Tissue Distribution ◽  
Binding Sites ◽  
Binding Proteins ◽  
Retinol Binding Protein ◽  
Internal Cavity ◽  
Binding Characteristics ◽  
Necator Americanus ◽  
Ligand Binding Sites

Necator americanus fatty acid and retinol-binding protein-1 (Na-FAR-1) is an abundantly expressed FAR from a parasitic hookworm. The present work describes its tissue distribution, structure and ligand-binding characteristics and shows that Na-FAR-1 expands to transport multiple FA molecules in its internal cavity.

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