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Title: DRoP: Automated detection of conserved solvent‐binding sites on proteins

Abstract

Abstract Water and ligand binding play critical roles in the structure and function of proteins, yet their binding sites and significance are difficult to predict a priori. Multiple solvent crystal structures (MSCS) is a method where several X‐ray crystal structures are solved, each in a unique solvent environment, with organic molecules that serve as probes of the protein surface for sites evolved to bind ligands, while the first hydration shell is essentially maintained. When superimposed, these structures contain a vast amount of information regarding hot spots of protein‐protein or protein‐ligand interactions, as well as conserved water‐binding sites retained with the change in solvent properties. Optimized mining of this information requires reliable structural data and a consistent, objective analysis tool. Detection of related solvent positions (DRoP) was developed to automatically organize and rank the water or small organic molecule binding sites within a given set of structures. It is a flexible tool that can also be used in conserved water analysis given multiple structures of any protein independent of the MSCS method. The DRoP output is an HTML format list of the solvent sites ordered by conservation rank in its population within the set of structures, along with renumbered and recoloredmore » PDB files for visualization and facile analysis. Here, we present a previously unpublished set of MSCS structures of bovine pancreatic ribonuclease A (RNase A) and use it together with published structures to illustrate the capabilities of DRoP.« less

Authors:
 [1];  [2]; ORCiD logo [2];  [3];  [3];  [3]; ORCiD logo [1]
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  1. Department of Chemistry and Chemical Biology Northeastern University Boston Massachusetts, Department of Molecular and Structural Biochemistry North Carolina State University Raleigh North Carolina
  2. Department of Chemistry and Chemical Biology Northeastern University Boston Massachusetts
  3. Department of Molecular and Structural Biochemistry North Carolina State University Raleigh North Carolina
Publication Date:
Sponsoring Org.:
USDOE
OSTI Identifier:
1544453
Resource Type:
Publisher's Accepted Manuscript
Journal Name:
Proteins
Additional Journal Information:
Journal Name: Proteins Journal Volume: 88 Journal Issue: 1; Journal ID: ISSN 0887-3585
Publisher:
Wiley Blackwell (John Wiley & Sons)
Country of Publication:
United States
Language:
English

Citation Formats

Kearney, Bradley M., Schwabe, Michael, Marcus, Kendra C., Roberts, Daniel M., Dechene, Michelle, Swartz, Paul, and Mattos, Carla. DRoP: Automated detection of conserved solvent‐binding sites on proteins. United States: N. p., 2019. Web. doi:10.1002/prot.25781.
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Kearney, Bradley M., Schwabe, Michael, Marcus, Kendra C., Roberts, Daniel M., Dechene, Michelle, Swartz, Paul, & Mattos, Carla. DRoP: Automated detection of conserved solvent‐binding sites on proteins. United States. https://doi.org/10.1002/prot.25781
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Kearney, Bradley M., Schwabe, Michael, Marcus, Kendra C., Roberts, Daniel M., Dechene, Michelle, Swartz, Paul, and Mattos, Carla. Tue . "DRoP: Automated detection of conserved solvent‐binding sites on proteins". United States. https://doi.org/10.1002/prot.25781.
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@article{osti_1544453,
title = {DRoP: Automated detection of conserved solvent‐binding sites on proteins},
author = {Kearney, Bradley M. and Schwabe, Michael and Marcus, Kendra C. and Roberts, Daniel M. and Dechene, Michelle and Swartz, Paul and Mattos, Carla},
abstractNote = {Abstract Water and ligand binding play critical roles in the structure and function of proteins, yet their binding sites and significance are difficult to predict a priori. Multiple solvent crystal structures (MSCS) is a method where several X‐ray crystal structures are solved, each in a unique solvent environment, with organic molecules that serve as probes of the protein surface for sites evolved to bind ligands, while the first hydration shell is essentially maintained. When superimposed, these structures contain a vast amount of information regarding hot spots of protein‐protein or protein‐ligand interactions, as well as conserved water‐binding sites retained with the change in solvent properties. Optimized mining of this information requires reliable structural data and a consistent, objective analysis tool. Detection of related solvent positions (DRoP) was developed to automatically organize and rank the water or small organic molecule binding sites within a given set of structures. It is a flexible tool that can also be used in conserved water analysis given multiple structures of any protein independent of the MSCS method. The DRoP output is an HTML format list of the solvent sites ordered by conservation rank in its population within the set of structures, along with renumbered and recolored PDB files for visualization and facile analysis. Here, we present a previously unpublished set of MSCS structures of bovine pancreatic ribonuclease A (RNase A) and use it together with published structures to illustrate the capabilities of DRoP.},
doi = {10.1002/prot.25781},
journal = {Proteins},
number = 1,
volume = 88,
place = {United States},
year = {2019},
month = {7}
}
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https://doi.org/10.1002/prot.25781
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