Long Time-Scale Atomistic Simulations of the Structure and Dynamics of Transcription Factor-DNA Recognition

p.p1 {margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px 'Helvetica Neue'} <p>Recent years have witnessed an explosion of interest in computational studies of DNA binding proteins, including both coarse grained and atomistic simulations of transcription factor-DNA recognition, in order to understand how these transcription factors recognize their binding sites on the DNA with such exquisite specificity. The present study performs μs-timescale all-atom simulations of the dimeric form of the lactose repressor (LacI), both in the absence of any DNA, and in the presence of both specific and non-specific complexes, considering three different DNA sequences. We examine, specifically, the conformational differences between specific and non-specific protein-DNA interactions, as well as the behavior of the helix-turn-helix motif of LacI when interacting with the DNA. Our simulations suggest that stable LacI binding occurs primarily to bent A-form DNA, with a loss of LacI conformational entropy and optimization of correlated conformational equilibria across the protein. In addition, binding to the specific operator sequence involves a slightly larger number of stabilizing DNA-protein hydrogen bonds (in comparison to non-specific complexes), that may account for the experimentally observed specificity for this operator. In doing so, our simulations provide a detailed atomistic description of potential structural drivers for LacI selectivity.</p>

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Long Time-Scale Atomistic Simulations of the Structure and Dynamics of Transcription Factor-DNA Recognition

The Journal of Physical Chemistry B ◽

10.1021/acs.jpcb.8b12363 ◽

2019 ◽

Vol 123 (17) ◽

pp. 3576-3590 ◽

Cited By ~ 3

Author(s):

Qinghua Liao ◽

Malin Lüking ◽

Dennis M. Krüger ◽

Sebastian Deindl ◽

Johan Elf ◽

...

Keyword(s):

Transcription Factor ◽

Time Scale ◽

Dna Recognition ◽

Atomistic Simulations ◽

Structure And Dynamics ◽

Long Time

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Dynamic and Structural Modeling of the Specificity in Protein-DNA Interactions Guided by Binding Assay and Structure Data

10.1101/288795 ◽

2018 ◽

Author(s):

Cheng Tan ◽

Shoji Takada

Keyword(s):

Structure Data ◽

Dna Sequences ◽

Complex Structure ◽

Specific Protein ◽

Coarse Grained ◽

Binding Modes ◽

Binding Assays ◽

Dna Interactions ◽

Protein Dna Interactions ◽

Dynamics Simulations

ABSTRACTHow transcription factors (TFs) recognize their DNA sequences is often investigated complementarily by high-throughput protein binding assays and by structural biology experiments. The former quantifies the specificity of TF binding sites for numerous DNA sequences, often represented as the position-weight-matrix (PWM). The latter provides mechanistic insights into the interactions via the protein-DNA complex structures. However, these two types of data are not readily integrated. Here, we propose and test a new modeling method that incorporates the PWM with complex structure data. Based on pre-tuned coarse-grained models for proteins and DNAs, we model the specific protein-DNA interactions, PWMcos, in terms of an orientation-dependent potential function, which enables us to perform molecular dynamics simulations at unprecedentedly large scales. We show that the PWMcos model reproduces subtle specificity in the protein-DNA recognition. During the target search in genomic sequences, TF moves on highly rugged landscapes and occasionally flips on DNA depending on the sequence. The TATA-binding protein exhibits two remarkably distinct binding modes, of which frequencies differ between TATA-containing and TATA-less promoters. The PWMcos is general and can be applied to any protein-DNA interactions given their PWMs and complex structure data are available.

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Co-operation between the PAI and RED subdomains of Pax-8 in the interaction with the thyroglobulin promoter

Biochemical Journal ◽

10.1042/bj3370253 ◽

1999 ◽

Vol 337 (2) ◽

pp. 253-262 ◽

Cited By ~ 13

Author(s):

Lucia PELLIZZARI ◽

Gianluca TELL ◽

Giuseppe DAMANTE

Keyword(s):

Transcription Factor ◽

Transcription Factors ◽

Dna Sequences ◽

Target Genes ◽

Dna Recognition ◽

Cell Types ◽

Full Length ◽

Paired Domain ◽

Binding Properties ◽

Evolutionarily Conserved

Pax proteins are transcription factors that play an important role in the differentiation of several cell types. These proteins bind to specific DNA sequences through the paired domain. This evolutionarily conserved element is composed of two subdomains (PAI and RED), located at the N- and C-terminals, respectively. Due to the presence of these two subdomains, Pax proteins may recognize DNA in different modes, a possibility that has not been exhaustively explored yet. The C site of the thyroglobulin promoter is bound by the thyroid-specific transcription factor Pax-8. In this study we have characterized the mode by which the Pax-8 paired domain interacts with the C site. Results allow the identification of the respective positions of the PAI and RED subdomains when the full-length protein is bound to the C site. The binding of the isolated PAI and RED subdomains to the C site and to several related mutants was also evaluated. Both subdomains interact with DNA as a monomer and display a lower binding affinity than the full-length protein. Therefore, the Pax-8 paired domain–C site interaction occurs through a co-operation between the two subdomains. The binding properties of the PAI subdomain suggest that the co-operation between PAI and RED subdomains does not merely consist of the sum of contacts established by the single subdomain: the presence of the RED subdomain is necessary for correct DNA recognition by the PAI subdomain, thus accounting for a sort of chronology of events during DNA binding. Since the RED subdomain is much more variable than the PAI subdomain among Pax proteins, these results could explain how distinct Pax proteins may select different target genes.

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Transcription factor/DNA interactions visualized by electron spectroscopic imaging

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100122654 ◽

1992 ◽

Vol 50 (1) ◽

pp. 450-451

Author(s):

David P. Bazett-Jones ◽

Mark L. Brown

Keyword(s):

Transcription Factor ◽

Dna Sequences ◽

Transcription Initiation ◽

Molecular Mechanisms ◽

Phosphorus Content ◽

Spectroscopic Imaging ◽

Electron Spectroscopic Imaging ◽

Dna Backbone ◽

Two Parameters ◽

High Level

A multisubunit RNA polymerase enzyme is ultimately responsible for transcription initiation and elongation of RNA, but recognition of the proper start site by the enzyme is regulated by general, temporal and gene-specific trans-factors interacting at promoter and enhancer DNA sequences. To understand the molecular mechanisms which precisely regulate the transcription initiation event, it is crucial to elucidate the structure of the transcription factor/DNA complexes involved. Electron spectroscopic imaging (ESI) provides the opportunity to visualize individual DNA molecules. Enhancement of DNA contrast with ESI is accomplished by imaging with electrons that have interacted with inner shell electrons of phosphorus in the DNA backbone. Phosphorus detection at this intermediately high level of resolution (≈lnm) permits selective imaging of the DNA, to determine whether the protein factors compact, bend or wrap the DNA. Simultaneously, mass analysis and phosphorus content can be measured quantitatively, using adjacent DNA or tobacco mosaic virus (TMV) as mass and phosphorus standards. These two parameters provide stoichiometric information relating the ratios of protein:DNA content.

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The structure of ORC–Cdc6 on an origin DNA reveals the mechanism of ORC activation by the replication initiator Cdc6

Nature Communications ◽

10.1038/s41467-021-24199-1 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Xiang Feng ◽

Yasunori Noguchi ◽

Marta Barbon ◽

Bruce Stillman ◽

Christian Speck ◽

...

Keyword(s):

Dna Sequences ◽

Origin Recognition Complex ◽

Molecular Level ◽

Dna Recognition ◽

Winged Helix ◽

Replicative Helicase ◽

The Core ◽

Α Helix ◽

Replication Initiator ◽

Winged Helix Domain

AbstractThe Origin Recognition Complex (ORC) binds to sites in chromosomes to specify the location of origins of DNA replication. The S. cerevisiae ORC binds to specific DNA sequences throughout the cell cycle but becomes active only when it binds to the replication initiator Cdc6. It has been unclear at the molecular level how Cdc6 activates ORC, converting it to an active recruiter of the Mcm2-7 hexamer, the core of the replicative helicase. Here we report the cryo-EM structure at 3.3 Å resolution of the yeast ORC–Cdc6 bound to an 85-bp ARS1 origin DNA. The structure reveals that Cdc6 contributes to origin DNA recognition via its winged helix domain (WHD) and its initiator-specific motif. Cdc6 binding rearranges a short α-helix in the Orc1 AAA+ domain and the Orc2 WHD, leading to the activation of the Cdc6 ATPase and the formation of the three sites for the recruitment of Mcm2-7, none of which are present in ORC alone. The results illuminate the molecular mechanism of a critical biochemical step in the licensing of eukaryotic replication origins.

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Unveiling the Dynamics of KRAS4b on Lipid Model Membranes

The Journal of Membrane Biology ◽

10.1007/s00232-021-00176-z ◽

2021 ◽

Author(s):

Cesar A. López ◽

Animesh Agarwal ◽

Que N. Van ◽

Andrew G. Stephen ◽

S. Gnanakaran

Keyword(s):

Molecular Mechanisms ◽

Hypervariable Region ◽

Small Gtpase ◽

Model Systems ◽

Coarse Grained ◽

Regulatory Function ◽

Limited Information ◽

Long Time ◽

Cell Growth And Differentiation ◽

State Models

AbstractSmall GTPase proteins are ubiquitous and responsible for regulating several processes related to cell growth and differentiation. Mutations that stabilize their active state can lead to uncontrolled cell proliferation and cancer. Although these proteins are well characterized at the cellular scale, the molecular mechanisms governing their functions are still poorly understood. In addition, there is limited information about the regulatory function of the cell membrane which supports their activity. Thus, we have studied the dynamics and conformations of the farnesylated KRAS4b in various membrane model systems, ranging from binary fluid mixtures to heterogeneous raft mimics. Our approach combines long time-scale coarse-grained (CG) simulations and Markov state models to dissect the membrane-supported dynamics of KRAS4b. Our simulations reveal that protein dynamics is mainly modulated by the presence of anionic lipids and to some extent by the nucleotide state (activation) of the protein. In addition, our results suggest that both the farnesyl and the polybasic hypervariable region (HVR) are responsible for its preferential partitioning within the liquid-disordered (Ld) domains in membranes, potentially enhancing the formation of membrane-driven signaling platforms. Graphic Abstract

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Promoter activity of human renin 5'-flanking DNA sequences is activated by the pituitary-specific transcription factor Pit-1.

Journal of Biological Chemistry ◽

10.1016/s0021-9258(18)53879-5 ◽

1993 ◽

Vol 268 (3) ◽

pp. 1505-1508

Author(s):

J. Sun ◽

C. Oddoux ◽

A. Lazarus ◽

M.T. Gilbert ◽

D.F. Catanzaro

Keyword(s):

Transcription Factor ◽

Dna Sequences ◽

Promoter Activity ◽

Specific Transcription Factor ◽

Human Renin

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Tc, an unusual promoter element required for constitutive transcription of the yeast HIS3 gene

Molecular and Cellular Biology ◽

10.1128/mcb.10.9.4447-4455.1990 ◽

1990 ◽

Vol 10 (9) ◽

pp. 4447-4455

Author(s):

S Mahadevan ◽

K Struhl

Keyword(s):

Transcription Factor ◽

Dna Sequences ◽

Base Pair ◽

Point Mutations ◽

Proximal Promoter ◽

Promoter Element ◽

Tata Element ◽

Typical Sequence ◽

His3 Gene ◽

Transcriptional Stimulation

Tc is the proximal promoter element required for constitutive his3 transcription that occurs in the absence of the canonical TATA element (TR) and is initiated from the +1 site. The TC element, unlike TR, does not respond to transcriptional stimulation by the GCN4 or GAL4 activator protein. Analysis of deletion, substitution, and point mutations indicates that Tc mapped between nucleotides -54 and -83 and is a sequence-dependent element because it could not be functionally replaced by other DNA sequences. However, in contrast to the behavior of typical promoter elements, it was surprisingly difficult to eliminate Tc function by base pair substitutions. Of 15 derivatives averaging four substitutions in the Tc region and representing 40% of all possible single changes, only 1 inactivated the Tc element. Moreover, the phenotypes of mutant and hybrid elements indicated that inactivation of Tc required multiple changes. The spacing between Tc and the initiation region could be varied over a 30-base-pair range without significantly affecting the level of transcription from the +1 site. From these results, we consider it possible that Tc may not interact with TFIID or some other typical sequence-specific transcription factor, but instead might influence transcription, either directly or indirectly, by its DNA structure.

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