Code and Analysis for: LacI strikes a balance between stability and inducibility
type: Dataset
description: Transcription factors (TFs) efficiently locate their target DNA sequences by combining three-dimensional diffusion and one-dimensional sliding on nonspecific DNA. To balance rapid sliding with strong specific binding, TFs were proposed to switch between search and recognition conformations. For E. coli lac repressor (LacI), the folding of the hinge helices has been implicated in the conformational switch. Here, we tested how mutations in the hinge region impact the search speed and binding stability. Based on molecular dynamics simulations, we selected two LacI mutants favoring either search or recognition conformation. We measured the binding kinetics of the mutants both in vitro on DNA microarrays with 2,479 different Lac operators and in vivo via single-molecule experiments. We identified a mutation that enhances the specificity but reduces binding strength globally, and another mutation that makes the operator binding stronger but also reduces the specificity. However, the altered specificity impacts the search time less than expected. Instead, the major effect was impaired dissociation in response to IPTG induction for the strongly binding mutant. Together with earlier reports of affinity–inducibility trade-offs in LacI, our data support the model in which the trade-off is between binding stability and inducibility rather than between speed and binding stability. This repository contains the molecular dynamics (MD) simulation datasets, analysis scripts, and code necessary to reproduce the results of our study. It also provides information on the datasets from single-molecule live-cell experiments and Protein Binding Microarray (PBM) assays, which are available in the BioImage Archive. File list: - Analysis: Analysis.tar - For plotting all figures in the main text and supplementary - Code: Code.tar - Utility scripts - Data: - Folders with prefix: 'Microscopy_Data_' - DataSets for Protein Binding Microarray experiments and Single Molecule experiments (raw fluores…
creative work status: completed
  type: DefinedTerm
  in defined term set: http://publications.europa.eu/resource/authority/dataset-status
  term code: COMPLETED
creator: Jinwen Yuan
creator: Malin Lüking
creator: Spartak Zikrin
  type: Person
  family name: Zikrin
  given name: Spartak
creator: Beer Chakra Sen
  type: Person
  family name: Chakra Sen
  given name: Beer
creator: Emil Marklund
  type: Person
  affiliation: Science for Life Laboratory
  family name: Marklund
  given name: Emil
creator: David van der Spoel
creator: David Fange
  type: Person
  affiliation: Science for Life Laboratory
  family name: Fange
  given name: David
creator: Johan Elf
  type: Person
  family name: Elf
  given name: Johan
date modified: 2026-04-15
date published: 2026-03-31
has part: S-BIAD1940
keywords: Medical and Health Sciences
  type: DefinedTerm
  term code: 3
keywords: Structural Biology
  type: DefinedTerm
  term code: 10601
keywords: Biological Sciences
  type: DefinedTerm
  term code: 106
keywords: Systems biology
keywords: Structural biology (incl. macromolecular modelling)
keywords: Molecular, biological, and multi-scale communications
license: https://creativecommons.org/licenses/by/4.0/
publisher: Uppsala University
version: 0

PropertyValue
property ID: DOI
value: 10.17044/SCILIFELAB.29040599

Jinwen Yuan
type: Person
affiliation: Science for Life Laboratory
family name: Yuan
given name: Jinwen

Science for Life Laboratory
type: Organization

Malin Lüking
type: Person
affiliation: Science for Life Laboratory
family name: Lüking
given name: Malin

David van der Spoel
type: Person
family name: van der Spoel
given name: David

Uppsala University
type: Organization