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BMC bioinformatics
Apr 30, 2024;25 (1): 172.

Cold Spot SCANNER: Colab Notebook for predicting cold spots in protein-protein interfaces.

Sagara N S Gurusinghe, Julia M Shifman
Author Information
  1. Sagara N S Gurusinghe: Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
  2. Julia M Shifman: Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel. jshifman@mail.huji.ac.il.
PMID: 38689238 DOI: 10.1186/s12859-024-05796-5

Abstract

BACKGROUND: Protein-protein interactions (PPIs) are conveyed through binding interfaces or surface patches on proteins that become buried upon binding. Structural and biophysical analysis of many protein-protein interfaces revealed certain unique features of these surfaces that determine the energetics of interactions and play a critical role in protein evolution. One of the significant aspects of binding interfaces is the presence of binding hot spots, where mutations are highly deleterious for binding. Conversely, binding cold spots are positions occupied by suboptimal amino acids and several mutations in such positions could lead to affinity enhancement. While there are many software programs for identification of hot spot positions, there is currently a lack of software for cold spot detection.
RESULTS: In this paper, we present Cold Spot SCANNER, a Colab Notebook, which scans a PPI binding interface and identifies cold spots resulting from cavities, unfavorable charge-charge, and unfavorable charge-hydrophobic interactions. The software offers a Py3DMOL-based interface that allows users to visualize cold spots in the context of the protein structure and generates a zip file containing the results for easy download.
CONCLUSIONS: Cold spot identification is of great importance to protein engineering studies and provides a useful insight into protein evolution. Cold Spot SCANNER is open to all users without login requirements and can be accessible at: https://colab.
RESEARCH: google.com/github/sagagugit/Cold-Spot-Scanner/blob/main/Cold_Spot_Scanner.ipynb .

Keywords

Binding affinity Binding interface Cavities Cold spots Protein–protein interactions

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Grants

  1. 3486/20/Israel Science Foundation
  2. Pilot Project Grant (517)/Instruct

MeSH Term

Proteins
Software
Protein Interaction Mapping
Protein Binding
Protein Conformation
Models, Molecular
Binding Sites
Hydrophobic and Hydrophilic Interactions

Chemicals

Proteins
Journal Article

Word Cloud

Created with Highcharts 10.0.0bindingspotscoldColdinteractionsinterfacesproteinpositionssoftwarespotSpotinterfacemanyprotein-proteinevolutionhotmutationsaffinityidentificationSCANNERColabNotebookunfavorableusersBindingBACKGROUND:Protein-proteinPPIsconveyedsurfacepatchesproteinsbecomeburieduponStructuralbiophysicalanalysisrevealedcertainuniquefeaturessurfacesdetermineenergeticsplaycriticalroleOnesignificantaspectspresencehighlydeleteriousConverselyoccupiedsuboptimalaminoacidsseveralleadenhancementprogramscurrentlylackdetectionRESULTS:paperpresentscansPPIidentifiesresultingcavitiescharge-chargecharge-hydrophobicoffersPy3DMOL-basedallowsvisualizecontextstructuregenerateszipfilecontainingresultseasydownloadCONCLUSIONS:greatimportanceengineeringstudiesprovidesusefulinsightopenwithoutloginrequirementscanaccessibleat:https://colabRESEARCH:googlecom/github/sagagugit/Cold-Spot-Scanner/blob/main/Cold_Spot_ScanneripynbSCANNER:predictingCavitiesProtein–protein

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