Predicting Target DNA Sequences of DNA-Binding Proteins Based on Unbound Structures

Z-DNA is stabilized by various Z-DNA binding proteins (ZBPs) that play important roles in RNA editing, innate immune response, and viral infection. In this review, the structural and dynamics of various ZBPs complexed with Z-DNA are summarized to better understand the mechanisms by which ZBPs selectively recognize d(CG)-repeat DNA sequences in genomic DNA and efficiently convert them to left-handed Z-DNA to achieve their biological function. The intermolecular interaction of ZBPs with Z-DNA strands is mediated through a single continuous recognition surface which consists of an α3 helix and a β-hairpin. In the ZBP-Z-DNA complexes, three identical, conserved residues (N173, Y177, and W195 in the Zα domain of human ADAR1) play central roles in the interaction with Z-DNA. ZBPs convert a 6-base DNA pair to a Z-form helix via the B-Z transition mechanism in which the ZBP first binds to B-DNA and then shifts the equilibrium from B-DNA to Z-DNA, a conformation that is then selectively stabilized by the additional binding of a second ZBP molecule. During B-Z transition, ZBPs selectively recognize the alternating d(CG)n sequence and convert it to a Z-form helix in long genomic DNA through multiple sequence discrimination steps. In addition, the intermediate complex formed by ZBPs and B-DNA, which is modulated by varying conditions, determines the degree of B-Z transition.

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Grammatical analysis of DNA sequences provides a rationale for the regulatory control of an entire chromosome

Genetics Research ◽

10.1017/s0016672300035187 ◽

1990 ◽

Vol 56 (2-3) ◽

pp. 115-120 ◽

Cited By ~ 7

Author(s):

Susumu Ohno

Keyword(s):

Dna Binding ◽

Dna Sequences ◽

Binding Proteins ◽

Somatic Hybrids ◽

Dna Binding Proteins ◽

Regulatory Control ◽

Banding Patterns ◽

High Frequencies ◽

Grammatical Analysis ◽

Grammatical Rule

SummaryRegardless of their origins, functions, and base compositions, all DNAs are scriptures written following the same grammatical rule. At the level of syllables, two, CG and TA are seldom used, while three, TG, CT and CA are utilized with abundance. Accordingly, at the level of three-letter words, two complementary base trimers, CTG and CAG, invariably enjoy frequent usage. Inasmuch as two of the three frequently used syllables, TG and CA are complementary to each other, while two seldom used syllables, CG and TA, are both palindromes, two complementary strands of DNA are inherently symmetrical with each other. Consequently, palindromic sequences as favourite targets of DNA-binding proteins occur at unsuspectedly high frequencies, if they contain TG and CA or CTG and CAG. Nevertheless, there are grammatical rules operating among these high frequency palindromes as well; e.g. the palindromic tetramer TGCA occurs nearly two times more often than its reciprocal; CATG. Thus, DNA-binding proteins are provided with a wealth of abundant targets whose densities are influenced by a regional difference in GC/AT ratios to variable degrees. One palindromic heptamer CAGNCTG is an ideal target of one DNA-binding protein engaged in chromosome packaging and in generation of banding patterns. This heptamer occurs once every 1000 bases in moderately GC-rich sequences, while its incidence is reduced to once every 3000 bases in extremely AT-rich sequences. The above must be the very reason that a solitary human X-chromosome DNA coated with mouse DNA-binding proteins in mouse-man somatic hybrids still maintains the original banding pattern and that the inactive X remains inactive, while the active X remains active.

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Differential Contributions of DNA-Binding Proteins to Polycomb Response Element Activity at the Drosophila giant Gene

Genetics ◽

10.1534/genetics.119.302981 ◽

2020 ◽

Vol 214 (3) ◽

pp. 623-634

Author(s):

Elnaz Ghotbi ◽

Kristina Lackey ◽

Vicki Wong ◽

Katie T. Thompson ◽

Evan G. Caston ◽

...

Keyword(s):

Dna Binding ◽

Dna Sequences ◽

Transcriptional Repression ◽

Binding Proteins ◽

Target Genes ◽

Dna Binding Proteins ◽

Polycomb Group ◽

Link Type ◽

Element Activity

Polycomb-group (PcG) proteins are evolutionarily conserved epigenetic regulators whose primary function is to maintain the transcriptional repression of target genes. Recruitment of Drosophila melanogaster PcG proteins to target genes requires the presence of one or more Polycomb Response Elements (PREs). The functions or necessity for more than one PRE at a gene are not clear and individual PREs at some loci may have distinct regulatory roles. Various combinations of sequence-specific DNA-binding proteins are present at a given PRE, but only Pleiohomeotic (Pho) is present at all strong PREs. The giant (gt) locus has two PREs, a proximal PRE1 and a distal PRE2. During early embryonic development, Pho binds to PRE1 ∼30-min prior to stable binding to PRE2. This observation indicated a possible dependence of PRE2 on PRE1 for PcG recruitment; however, we find here that PRE2 recruits PcG proteins and maintains transcriptional repression independently of Pho binding to PRE1. Pho-like (Phol) is partially redundant with Pho during larval development and binds to the same DNA sequences in vitro. Although binding of Pho to PRE1 is dependent on the presence of consensus Pho-Phol-binding sites, Phol binding is less so and appears to play a minimal role in recruiting other PcG proteins to gt. Another PRE-binding protein, Sp1/Kruppel-like factor, is dependent on the presence of Pho for PRE1 binding. Further, we show that, in addition to silencing gene expression, PcG proteins dampen transcription of an active gene.

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Facilitated diffusion in the presence of obstacles on the DNA

Physical Chemistry Chemical Physics ◽

10.1039/c6cp00307a ◽

2016 ◽

Vol 18 (16) ◽

pp. 11184-11192 ◽

Cited By ~ 11

Author(s):

David Gomez ◽

Stefan Klumpp

Keyword(s):

Dna Binding ◽

Diffusion Process ◽

Dna Sequences ◽

Binding Proteins ◽

Dna Binding Proteins ◽

Facilitated Diffusion ◽

Dna Concentration

Recognition of specific DNA sequences by DNA-binding proteins (DBPs) takes place by a facilitated diffusion process that depends, among other parameters, on the DBP's sliding length on the DNA and the DNA concentration. In addition, facilitated diffusion is variously impaired by the presence of obstacles with different dynamics on the DNA.

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A colony color assay for Saccharomyces cerevisiae mutants defective in kinetochore structure and function.

Genetics ◽

10.1093/genetics/132.1.39 ◽

1992 ◽

Vol 132 (1) ◽

pp. 39-51

Author(s):

F Périer ◽

J Carbon

Keyword(s):

Saccharomyces Cerevisiae ◽

Dna Binding ◽

Dna Sequences ◽

Binding Proteins ◽

Dna Binding Proteins ◽

Blue Color ◽

Yeast Saccharomyces Cerevisiae ◽

Gal1 Promoter ◽

Colony Color ◽

Yeast Genes

Abstract We have designed a colony color assay for monitoring centromere DNA-protein interactions in yeast (Saccharomyces cerevisiae). The assay is based on the ability of centromere DNA sequences to block (in cis) transcription initiated from a hybrid CEN-GAL1 promoter. Using a IacZ reporter gene under control of the CEN-GAL1 promoter, we screened colonies derived from mutagenized cells for a blue color phenotype indicative of derepression of the hybrid construct. A limited screen in which a 61-bp CEN11 DNA fragment containing an intact CDEIII subregion plus flanking sequences was used as the "pseudo-operator" led to the identification of mutations (blu) in three complementation groups. The blu1 mutants exhibited a decrease in activity of the major CEN DNA-binding proteins in vitro. The BLU1 gene was shown to be identical to the previously isolated SPT3 gene, known to be involved in the transcriptional regulation of a subset of yeast genes. Our results indicate that the BLU1/SPT3 gene product may also be required to maintain optimal levels of functional centromere DNA-binding proteins.

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Disparity in anomalous diffusion of proteins searching for their target DNA sites in a crowded medium is controlled by the size, shape and mobility of macromolecular crowders

Soft Matter ◽

10.1039/c8sm01933a ◽

2019 ◽

Vol 15 (9) ◽

pp. 1960-1969 ◽

Cited By ~ 8

Author(s):

Pinki Dey ◽

Arnab Bhattacherjee

Keyword(s):

Dna Binding ◽

Physical Properties ◽

Computer Simulations ◽

Anomalous Diffusion ◽

Binding Proteins ◽

Dna Binding Proteins ◽

Molecular Crowding ◽

Target Search ◽

Target Dna

Using extensive computer simulations, we analyzed the role of physical properties of molecular crowding agents such as size, shape and mobility in the target search dynamics of DNA binding proteins.

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A family of dispersed repetitive DNA sequences in tobacco contain clusters of W-box elements recognized by pathogen-induced WRKY DNA-binding proteins

Plant Science ◽

10.1016/s0168-9452(01)00454-x ◽

2001 ◽

Vol 161 (4) ◽

pp. 655-664 ◽

Cited By ~ 8

Author(s):

Peizhen Yang ◽

Zhixiang Chen

Keyword(s):

Dna Binding ◽

Repetitive Dna ◽

Dna Sequences ◽

Binding Proteins ◽

Dna Binding Proteins ◽

Repetitive Dna Sequences

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Structural Basis of Enhanced Facilitated Diffusion of DNA Binding Proteins in Crowded Cellular Milieu

10.1101/701557 ◽

2019 ◽

Author(s):

P. Dey ◽

A. Bhattacherjee

Keyword(s):

Dna Binding ◽

Binding Proteins ◽

Dna Binding Proteins ◽

Structural Basis ◽

Facilitated Diffusion ◽

Molecular Crowding ◽

Cellular Environment ◽

Target Dna ◽

Nonspecific Interactions ◽

Search Modes

ABSTRACTDNA binding proteins (DBPs) rapidly recognize and specifically associate with their target DNA sites inside cell nucleus that contains up to 400 g/L macromolecules, most of which are proteins. While the fast association between DBPs and DNA is explained by a facilitated diffusion mechanism, where DBPs adopt a weighted combination of 3D diffusion and 1D sliding and hopping modes of transportation, the role of cellular environment that contains many nonspecifically interacting proteins and other biomolecules is mostly overlooked. By performing large scale computational simulations with an appropriately tuned model of protein and DNA in the presence of nonspecifically interacting bulk and DNA bound crowders (genomic crowders), we demonstrate the structural basis of the enhanced facilitated diffusion of DBPs inside a crowded cellular milieu through novel 1D scanning mechanisms. In the presence of bulk crowders, we identify the protein to float along the DNA under the influence of protein-crowder nonspecific interactions. The search mode is distinctly different compared to usual 1D sliding and hopping dynamics where protein diffusion is regulated by the DNA electrostatics. In contrast, the presence of genomic crowders expedite the target search process by transporting the protein over DNA segments through the formation of a transient protein-crowder bridged complex. By analyzing the ruggedness of the associated potential energy landscape, we underpin the molecular origin of the kinetic advantages of these search modes and show that they successfully explain the experimentally observed acceleration of facilitated diffusion of DBPs by molecular crowding agents and crowder concentration dependent enzymatic activity of transcription factors. Our findings provide crucial insights into gene regulation kinetics inside the crowded cellular milieu.SIGNIFICANCE10-40% of the intracellular volume is occupied by proteins, and other biomolecules, collectively known as macromolecular crowders. Their presence has been found to promote faster translocation of DNA binding proteins (DBPs) during the search of their target DNA sites for crucial cellular processes. Using molecular simulations, we probe the underlying structural basis and underscore the existence of novel DNA scanning mechanisms actuated by protein-crowder nonspecific interactions. We show that the observed search modes are kinetically beneficial and can successfully explain the acceleration of facilitated diffusion of DBPs by molecular crowding agents and crowderconcentration dependent enzymatic activity of transcription factors.Our study sheds new light on the long-standing facilitated diffusion problem of DBPs in the crowded cellular environment for regulating gene expression.

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Destruction of DNA-binding proteins by programmable O’PROTAC: Oligonucleotide-based PROTAC

10.1101/2021.03.08.434493 ◽

2021 ◽

Author(s):

Jingwei Shao ◽

Yuqian Yan ◽

Donglin Ding ◽

Dejie Wang ◽

Yundong He ◽

...

Keyword(s):

Transcription Factors ◽

Dna Binding ◽

Binding Proteins ◽

Binding Pocket ◽

Dna Binding Proteins ◽

Target Dna ◽

Dna Replication And Repair ◽

Proteasome Pathway ◽

Double Stranded Oligonucleotide ◽

Large Repertoire

AbstractDNA-binding proteins including transcription factors (TFs) play essential roles in gene transcription and DNA replication and repair during normal organ development and pathogenesis of diseases such as cancer, cardiovascular disease and obesity, deeming to be a large repertoire of attractive therapeutic targets. However, this group of proteins are generally considered undruggable as they lack an enzymatic catalytic site or a ligand binding pocket. PROteolysis-TArgeting Chimera (PROTAC) technology has been developed by engineering a bifunctional small molecule chimera to bring a protein of interest (POI) to the proximity of an E3 ubiquitin ligase, thus inducing the ubiquitination of POI and further degradation through proteasome pathway. Here we report the development of Oligonucleotide-based PROTAC (O’PROTACs), a class of noncanonical PROTACs in which a TF-recognizing double-stranded oligonucleotide is incorporated as a binding moiety of POI. We demonstrate that O’PROTACs of ERG and LEF1, two highly cancer-related transcription factors selectively promote degradation of these proteins and inhibit their transcriptional activity in cancer cells. The programmable nature of O’PROTACs indicates that this approach is applicable to destruct other TFs. O’PROTACs not only can serve as a research tool, but also can be harnessed as a therapeutic arsenal to target DNA binding proteins for effective treatment of diseases such as cancer.

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DNA binding proteins: outline of functional classification

BioMolecular Concepts ◽

10.1515/bmc.2011.023 ◽

2011 ◽

Vol 2 (4) ◽

pp. 293-303 ◽

Cited By ~ 2

Author(s):

Zhiming Zheng ◽

Ya Wang

Keyword(s):

Dna Repair ◽

Dna Replication ◽

Dna Binding ◽

Dna Sequences ◽

Binding Proteins ◽

Excision Repair ◽

Dna Structure ◽

Dna Binding Proteins ◽

Dna Binding Domains ◽

Binding Domains

AbstractDNA-binding proteins composed of DNA-binding domains directly affect genomic functions, mainly by performing transcription, DNA replication or DNA repair. Here, we briefly describe the DNA-binding proteins according to these three major functions. Transcription factors that usually bind to specific sequences of DNA could be classified based on their sequence similarity and the structure of the DNA-binding domains, such as basic, zinc-coordinating, helix-turn-helix domains, etc. Most DNA replication factors do not need a specific sequence of DNA, but instead mainly depend on a DNA structure, with the exception of the origin recognition complex in yeast or Escherichia coli that recognizes the DNA sequences at particular origins. DNA replication includes initiation and elongation. The major DNA-binding proteins involved in these two steps are briefly described. DNA repair proteins bound to DNA depend on the damaged DNA structure. They are classified to base excision repair, DNA mismatch repair, nucleotide excision repair, homologous recombination repair and non-homologous end joining. The major DNA-binding proteins involved in these pathways are briefly described. Histone and high mobility group are two examples of DNA-binding proteins that do not belong to the three categories above and are briefly described. Finally, we warn that the non-specific binding proteins might have an affinity to some non-specific medium materials such as protein A or G beads that are commonly used for immune precipitation, which can easily generate false positive signals while detecting protein-protein interaction; therefore, the results need to be carefully analyzed using positive/negative controls.

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