Data on Publications, Structural Analyses, and Queries Used to Build and Utilize the AlloRep Database

Overview

Journal Data Brief

Date 2016 Aug 11

PMID 27508249

Citations 3

Authors

Filipa L Sousa

Daniel J Parente

Jacob A Hessman

Allen Chazelle

Sarah A Teichmann

Liskin Swint-Kruse

Affiliations

Soon will be listed here.

Abstract

The AlloRep database (www.AlloRep.org) (Sousa et al., 2016) [1] compiles extensive sequence, mutagenesis, and structural information for the LacI/GalR family of transcription regulators. Sequence alignments are presented for >3000 proteins in 45 paralog subfamilies and as a subsampled alignment of the whole family. Phenotypic and biochemical data on almost 6000 mutants have been compiled from an exhaustive search of the literature; citations for these data are included herein. These data include information about oligomerization state, stability, DNA binding and allosteric regulation. Protein structural data for 65 proteins are presented as easily-accessible, residue-contact networks. Finally, this article includes example queries to enable the use of the AlloRep database. See the related article, "AlloRep: a repository of sequence, structural and mutagenesis data for the LacI/GalR transcription regulators" (Sousa et al., 2016) [1].

Citing Articles

Substitutions at rheostat position 52 of LacI have long-range effects on the LacI conformational landscape.

Kariyawasam N, Sivchenko A, Swint-Kruse L, Smith P Biophys Chem. 2025; 320-321:107414.

PMID: 39987706 PMC: 11893255. DOI: 10.1016/j.bpc.2025.107414.

Dynamics-based protein network features accurately discriminate neutral and rheostat positions.

Campitelli P, Ross D, Swint-Kruse L, Ozkan S Biophys J. 2024; 123(20):3612-3626.

PMID: 39277794 PMC: 11494493. DOI: 10.1016/j.bpj.2024.09.013.

Rheostats, toggles, and neutrals, Oh my! A new framework for understanding how amino acid changes modulate protein function.

Swint-Kruse L, Fenton A J Biol Chem. 2024; 300(3):105736.

PMID: 38336297 PMC: 10914490. DOI: 10.1016/j.jbc.2024.105736.

AlloRep: A Repository of Sequence, Structural and Mutagenesis Data for the LacI/GalR Transcription Regulators.

Sousa F, Parente D, Shis D, Hessman J, Chazelle A, Bennett M J Mol Biol. 2015; 428(4):671-678.

PMID: 26410588 PMC: 4783282. DOI: 10.1016/j.jmb.2015.09.015.

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