New insights into protein-DNA binding specificity from hydrogen bond based comparative study

Factors Affecting Liquid-Liquid Phase Separation of RGG Peptides with DNA G-Quadruplex

Liquid-liquid phase separation (LLPS), mediated by G-quadruplexes (G4 s) and intrinsically disordered proteins, particularly those containing RGG domains, plays a critical role in cellular processes and diseases. However, the molecular mechanism and the role of individual amino acid residues of the protein in LLPS with G4 (G4-LLPS) are still unknown. Here, we systematically designed peptides and investigated the roles of arginine residues in G4-LLPS. It was found that the FMRP-derived RGG peptide induced LLPS with G4-forming Myc-DNA, whereas a point-mutated peptide, in which all arginine residues were replaced with lysine, was unable to undergo LLPS, indicating the importance of arginine residues. Moreover, systematically truncated peptides showed that at least five positive net charges of peptide are required to induce G4-LLPS. Furthermore, quantitative investigation demonstrated that the higher binding affinity of peptides with G4 led to a higher LLPS ability, whereas threshold of the binding affinity for undergoing LLPS was identified. These insights elucidate the pivotal role of arginine in G4-LLPS and the specific requirement for multiple arginine residues, contributing to a deeper understanding of the complex interplay between intrinsically disordered proteins and nucleic acids.

DNAproDB: an updated database for the automated and interactive analysis of protein-DNA complexes

DNAproDB (https://dnaprodb.usc.edu/) is a database, visualization tool, and processing pipeline for analyzing structural features of protein-DNA interactions. Here, we present a substantially updated version of the database through additional structural annotations, search, and user interface functionalities. The update expands the number of pre-analyzed protein-DNA structures, which are automatically updated weekly. The analysis pipeline identifies water-mediated hydrogen bonds that are incorporated into the visualizations of protein-DNA complexes. Tertiary structure-aware nucleotide layouts are now available. New file formats and external database annotations are supported. The website has been redesigned, and interacting with graphs and data is more intuitive. We also present a statistical analysis on the updated collection of structures revealing salient patterns in protein-DNA interactions.

Molecular Analysis of Changes in DNA Binding Affinity and Bending Extent Induced by the Mutations on the Aromatic Amino Residues in Cren7

Proteins from Crenarchaeal organisms exhibit remarkable thermal stability. The aromatic amino acids in Cren7, a Crenarchaeal protein, regulate protein stability and further modulate DNA binding and its compaction. Specific aromatic amino acids were mutated, and using spectroscopic and theoretical approaches, we have examined the effect of the mutation on the structure, DNA binding affinity, and DNA bending ability of Cren7. The mutants were compared to the structure and function of wild-type (WT) Cren7. The reverse titration profiles were analysed by a noncooperative McGhee-von Hippel model to estimate affinity constant (Ka) and binding site size (n) associated with binding to the DNA. The biolayer interferometry (BLI) measurements showed that the binding affinity decreased at higher salt concentrations. For theoretical analysis of the extent of DNA bending, radius of gyration and bending angle were compared for WT and mutants. The time evolution of order parameters based on the translational and rotational motion of tryptophan residue (W26) was used for the qualitative detection of stacking interactions between W26 of Cren7 and DNA nucleobases. It was observed that the orientation of W26 in F41A favored the formation of a new lone pair-lone pair interaction between DNA and Cren7. Consequently, in thermostable proteins, the aromatic residues at the terminus maintain structural stability, whereas the residues at the core optimize the degree of DNA bending and compaction.

ETS1 and RBPJ transcriptionally regulate METTL14 to suppress TGF-β1-induced epithelial-mesenchymal transition in human bronchial epithelial cells

Asthma is a chronic respiratory disease characterized by airway inflammation and remodeling. Epithelial-mesenchymal transition (EMT) of bronchial epithelial cells is considered to be a crucial player in asthma. Methyltransferase-like 14 (METTL14), an RNA methyltransferase, is implicated in multiple pathological processes, including EMT, cell proliferation and migration. However, the role of METTL14 in asthma remains uncertain. This research aimed to explore the biological functions of METTL14 in asthma and its underlying upstream mechanisms. METTL14 expression was down-regulated in asthmatic from three GEO datasets (GSE104468, GSE165934, and GSE74986). Consistent with this trend, METTL14 was decreased in the lung tissues of OVA-induced asthmatic mice and transforming growth factor-β1 (TGF-β1)-stimulated human bronchial epithelial cells (Beas-2B) in this study. Overexpression of METTL14 caused reduction in mesenchymal markers (FN1, N-cad, Col-1 and α-SMA) in TGF-β1-treated cells, but caused increase in epithelial markers (E-cad), thus inhibiting EMT. Also, METTL14 suppressed the proliferation and migration ability of TGF-β1-treated Beas-2B cells. Two transcription factors, ETS1 and RBPJ, could both bind to the promoter region of METTL14 and drive its expression. Elevating METTL14 expression could reversed EMT, cell proliferation and migration promoted by ETS1 or RBPJ deficiency. These results indicate that the ETS1/METTL14 and RBPJ/METTL14 transcription axes exhibit anti-EMT, anti-proliferation and anti-migration functions in TGF-β1-induced bronchial epithelial cells, implying that METTL14 may be considered an alternative candidate target for the treatment of asthma.

Supercharged coiled-coil protein with N-terminal decahistidine tag boosts siRNA complexation and delivery efficiency of a lipoproteoplex

Short interfering RNA (siRNA) therapeutics have soared in popularity due to their highly selective and potent targeting of faulty genes, providing a non-palliative approach to address diseases. Despite their potential, effective transfection of siRNA into cells requires the assistance of an accompanying vector. Vectors constructed from non-viral materials, while offering safer and non-cytotoxic profiles, often grapple with lackluster loading and delivery efficiencies, necessitating substantial milligram quantities of expensive siRNA to confer the desired downstream effects. We detail the recombinant synthesis of a diverse series of coiled-coil supercharged protein (CSP) biomaterials systematically designed to investigate the impact of two arginine point mutations (Q39R and N61R) and decahistidine tags on liposomal siRNA delivery. The most efficacious variant, N8, exhibits a twofold increase in its affinity to siRNA and achieves a twofold enhancement in transfection activity with minimal cytotoxicity in vitro. Subsequent analysis unveils the destabilizing effect of the Q39R and N61R supercharging mutations and the incorporation of C-terminal decahistidine tags on α-helical secondary structure. Cross-correlational regression analyses reveal that the amount of helical character in these mutants is key in N8's enhanced siRNA complexation and downstream delivery efficiency.

Unraveling the complexity: Advanced methods in analyzing DNA, RNA, and protein interactions

Exploring the intricate interplay within and between nucleic acids, as well as their interactions with proteins, holds pivotal significance in unraveling the molecular complexities steering cancer initiation and progression. To investigate these interactions, a diverse array of highly specific and sensitive molecular techniques has been developed. The selection of a particular technique depends on the specific nature of the interactions. Typically, researchers employ an amalgamation of these different techniques to obtain a comprehensive and holistic understanding of inter- and intramolecular interactions involving DNA-DNA, RNA-RNA, DNA-RNA, or protein-DNA/RNA. Examining nucleic acid conformation reveals alternative secondary structures beyond conventional ones that have implications for cancer pathways. Mutational hotspots in cancer often lie within sequences prone to adopting these alternative structures, highlighting the importance of investigating intra-genomic and intra-transcriptomic interactions, especially in the context of mutations, to deepen our understanding of oncology. Beyond these intramolecular interactions, the interplay between DNA and RNA leads to formations like DNA:RNA hybrids (known as R-loops) or even DNA:DNA:RNA triplex structures, both influencing biological processes that ultimately impact cancer. Protein-nucleic acid interactions are intrinsic cellular phenomena crucial in both normal and pathological conditions. In particular, genetic mutations or single amino acid variations can alter a protein's structure, function, and binding affinity, thus influencing cancer progression. It is thus, imperative to understand the differences between wild-type (WT) and mutated (MT) genes, transcripts, and proteins. The review aims to summarize the frequently employed methods and techniques for investigating interactions involving nucleic acids and proteins, highlighting recent advancements and diverse adaptations of each technique.

Molecular insights into the fine-tuning of pH-dependent ArsR-mediated regulation of the SabA adhesin in Helicobacter pylori

Adaptation to variations in pH is crucial for the ability of Helicobacter pylori to persist in the human stomach. The acid responsive two-component system ArsRS, constitutes the global regulon that responds to acidic conditions, but molecular details of how transcription is affected by the ArsR response regulator remains poorly understood. Using a combination of DNA-binding studies, in vitro transcription assays, and H. pylori mutants, we demonstrate that phosphorylated ArsR (ArsR-P) forms an active protein complex that binds DNA with high specificity in order to affect transcription. Our data showed that DNA topology is key for DNA binding. We found that AT-rich DNA sequences direct ArsR-P to specific sites and that DNA-bending proteins are important for the effect of ArsR-P on transcription regulation. The repression of sabA transcription is mediated by ArsR-P with the support of Hup and is affected by simple sequence repeats located upstream of the sabA promoter. Here stochastic events clearly contribute to the fine-tuning of pH-dependent gene regulation. Our results reveal important molecular aspects for how ArsR-P acts to repress transcription in response to acidic conditions. Such transcriptional control likely mediates shifts in bacterial positioning in the gastric mucus layer.

Quantitative and systematic NMR measurements of sequence-dependent A-T Hoogsteen dynamics uncovers unique conformational specificity in the DNA double helix

The propensities to form lowly-populated short-lived conformations of DNA could vary with sequence, providing an important source of sequence-specificity in biochemical reactions. However, comprehensively measuring how these dynamics vary with sequence is challenging. Using 1H CEST and 13C R 1 ρ NMR, we measured Watson-Crick to Hoogsteen dynamics for an A-T base pair in thirteen trinucleotide sequence contexts. The Hoogsteen population and exchange rate varied 4-fold and 16-fold, respectively, and were dependent on both the 3'- and 5'-neighbors but only weakly dependent on monovalent ion concentration (25 versus 100 mM NaCl) and pH (6.8 versus 8.0). Flexible TA and CA dinucleotide steps exhibited the highest Hoogsteen populations, and their kinetics rates strongly depended on the 3'-neighbor. In contrast, the stiffer AA and GA steps had the lowest Hoogsteen population, and their kinetics were weakly dependent on the 3'-neighbor. The Hoogsteen lifetime was especially short when G-C neighbors flanked the A-T base pair. The Hoogsteen dynamics had a distinct sequence-dependence compared to duplex stability and minor groove width. Thus, our results uncover a unique source of sequence-specificity hidden within the DNA double helix in the form of A-T Hoogsteen dynamics and establish the utility of 1H CEST to quantitively measure sequence-dependent DNA dynamics.

Discovering DNA shape motifs with multiple DNA shape features: generalization, methods, and validation

DNA motifs are crucial patterns in gene regulation. DNA-binding proteins (DBPs), including transcription factors, can bind to specific DNA motifs to regulate gene expression and other cellular activities. Past studies suggest that DNA shape features could be subtly involved in DNA-DBP interactions. Therefore, the shape motif annotations based on intrinsic DNA topology can deepen the understanding of DNA-DBP binding. Nevertheless, high-throughput tools for DNA shape motif discovery that incorporate multiple features altogether remain insufficient. To address it, we propose a series of methods to discover non-redundant DNA shape motifs with the generalization to multiple motifs in multiple shape features. Specifically, an existing Gibbs sampling method is generalized to multiple DNA motif discovery with multiple shape features. Meanwhile, an expectation-maximization (EM) method and a hybrid method coupling EM with Gibbs sampling are proposed and developed with promising performance, convergence capability, and efficiency. The discovered DNA shape motif instances reveal insights into low-signal ChIP-seq peak summits, complementing the existing sequence motif discovery works. Additionally, our modelling captures the potential interplays across multiple DNA shape features. We provide a valuable platform of tools for DNA shape motif discovery. An R package is built for open accessibility and long-lasting impact: https://zenodo.org/doi/10.5281/zenodo.10558980.

Secondary metabolites in topical infectious diseases and nanomedicine applications

Topical infection affects nearly one-third of the world's population; it may result from poor sanitation, hygienic conditions and crowded living and working conditions that accelerate the spread of topical infectious diseases. The problems associated with the anti-infective agents are drug resistance and long-term therapy. Secondary metabolites are obtained from plants, microorganisms and animals, but they are metabolized inside the human body. The integration of nanotechnology into secondary metabolites is gaining attention due to their interaction at the subatomic and skin-tissue levels. Hydrogel, liposomes, lipidic nanoparticles, polymeric nanoparticles and metallic nanoparticles are the most suitable carriers for secondary metabolite delivery. Therefore, the present review article extensively discusses the topical applications of nanomedicines for the effective delivery of secondary metabolites.

Deficiency of Transcription Factor Sp1 Contributes to Hypertrophic Cardiomyopathy

BACKGROUND

Hypertrophic cardiomyopathy (HCM) is the most prevalent monogenic heart disorder. However, the pathogenesis of HCM, especially its nongenetic mechanisms, remains largely unclear. Transcription factors are known to be involved in various biological processes including cell growth. We hypothesized that SP1 (specificity protein 1), the first purified TF in mammals, plays a role in the cardiomyocyte growth and cardiac hypertrophy of HCM.

METHODS

Cardiac-specific conditional knockout of Sp1 mice were constructed to investigate the role of SP1 in the heart. The echocardiography, histochemical experiment, and transmission electron microscope were performed to analyze the cardiac phenotypes of cardiac-specific conditional knockout of Sp1 mice. RNA sequencing, chromatin immunoprecipitation sequencing, and adeno-associated virus experiments in vivo were performed to explore the downstream molecules of SP1. To examine the therapeutic effect of SP1 on HCM, an SP1 overexpression vector was constructed and injected into the mutant allele of Myh6 R404Q/+ (Myh6 c. 1211C>T) HCM mice. The human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) from a patient with HCM were used to detect the potential therapeutic effects of SP1 in human HCM.

RESULTS

The cardiac-specific conditional knockout of Sp1 mice developed a typical HCM phenotype, displaying overt myocardial hypertrophy, interstitial fibrosis, and disordered myofilament. In addition, Sp1 knockdown dramatically increased the cell area of hiPSC-CMs and caused intracellular myofibrillar disorganization, which was similar to the hypertrophic cardiomyocytes of HCM. Mechanistically, Tuft1 was identified as the key target gene of SP1. The hypertrophic phenotypes induced by Sp1 knockdown in both hiPSC-CMs and mice could be rescued by TUFT1 (tuftelin 1) overexpression. Furthermore, SP1 overexpression suppressed the development of HCM in the mutant allele of Myh6 R404Q/+ mice and also reversed the hypertrophic phenotype of HCM hiPSC-CMs.

CONCLUSIONS

Our study demonstrates that SP1 deficiency leads to HCM. SP1 overexpression exhibits significant therapeutic effects on both HCM mice and HCM hiPSC-CMs, suggesting that SP1 could be a potential intervention target for HCM.

Understanding the structural basis of the binding specificity of c-di-AMP to M. smegmatis RecA using computational biology approach

Mycobacterium tuberculosis RecA (MtRecA), a protein involved in DNA repair, homologous recombination and SOS pathway, contributes to the development of multidrug resistance. ATP binding-site in RecA has been a drug target to disable RecA dependent DNA repair. For the first time, experiments have shown the existence and binding of c-di-AMP to a novel allosteric site in the C-terminal-Domain (CTD) of Mycobacterium smegmatis RecA (MsRecA), a close homolog of MtRecA. In addition, it was observed that the c-di-AMP was not binding to Escherichia coli RecA (EcRecA). This article analyses the possible interactions of the three RecA homologs with the various c-di-AMP conformations to gain insights into the structural basis of the natural preference of c-di-AMP to MsRecA and not to EcRecA, using the structural biology tools. The comparative analysis, based on amino acid composition, homology, motifs, residue types, docking, molecular dynamics simulations and binding free energy calculations, indeed, conclusively indicates strong binding of c-di-AMP to MsRecA. Having very similar results as MsRecA, it is highly plausible for c-di-AMP to strongly bind MtRecA as well. These insights from the in-silico studies adds a new therapeutic approach against TB through design and development of novel allosteric inhibitors for the first time against MtRecA.Communicated by Ramaswamy H. Sarma.

GMean-a semi-supervised GRU and K-mean model for predicting the TF binding site

The transcription factor binding site is a deoxyribonucleic acid sequence that binds to transcription factors. Transcription factors are proteins that regulate the transcription gene. Abnormal turnover of transcription factors can lead to uncontrolled cell growth. Therefore, discovering the relationships between transcription factors and deoxyribonucleic acid sequences is an important component of bioinformatics research. Numerous deep learning and machine learning language models have been developed to accomplish these tasks. Our goal in this work is to propose a GMean model for predicting unlabelled deoxyribonucleic acid sequences. The GMean model is a hybrid model with a combination of gated recurrent unit and K-mean clustering. The GMean model is developed in three phases. The labelled and unlabelled data are processed based on k-mers and tokenization. The labelled data is used for training. The unlabelled data are used for testing and prediction. The experimental data consists of deoxyribonucleic acid experimental of GM12878, K562 and HepG2. The experimental results show that GMean is feasible and effective in predicting deoxyribonucleic acid sequences, as the highest accuracy is 91.85% in predicting K562 and HepG2. This is followed by the prediction of the sequence between GM12878 and K562 with an accuracy of 89.13%. The lowest accuracy is the prediction of the sequence between HepG2 and GM12828, which is 88.80%.

Probing the role of the protonation state of a minor groove-linker histidine in Exd-Hox-DNA binding

DNA recognition and targeting by transcription factors (TFs) through specific binding are fundamental in biological processes. Furthermore, the histidine protonation state at the TF-DNA binding interface can significantly influence the binding mechanism of TF-DNA complexes. Nevertheless, the role of histidine in TF-DNA complexes remains underexplored. Here, we employed all-atom molecular dynamics simulations using AlphaFold2-modeled complexes based on previously solved co-crystal structures to probe the role of the His-12 residue in the Extradenticle (Exd)-Sex combs reduced (Scr)-DNA complex when binding to Scr and Ultrabithorax (Ubx) target sites. Our results demonstrate that the protonation state of histidine notably affected the DNA minor-groove width profile and binding free energy. Examining flanking sequences of various binding affinities derived from SELEX-seq experiments, we analyzed the relationship between binding affinity and specificity. We uncovered how histidine protonation leads to increased binding affinity but can lower specificity. Our findings provide new mechanistic insights into the role of histidine in modulating TF-DNA binding.

Designing Epigenome Editors: Considerations of Biochemical and Locus Specificities

The advent of locus-specific protein recruitment technologies has enabled a new class of studies in chromatin biology. Epigenome editors (EEs) enable biochemical modifications of chromatin at almost any specific endogenous locus. Their locus-specificity unlocks unique information including the functional roles of distinct modifications at specific genomic loci. Given the growing interest in using these tools for biological and translational studies, there are many specific design considerations depending on the scientific question or clinical need. Here, we present and discuss important design considerations and challenges regarding the biochemical and locus specificities of epigenome editors. These include how to: account for the complex biochemical diversity of chromatin; control for potential interdependency of epigenome editors and their resultant modifications; avoid sequestration effects; quantify the locus specificity of epigenome editors; and improve locus-specificity by considering concentration, affinity, avidity, and sequestration effects.

Lambda CI Binding to Related Phage Operator Sequences Validates Alignment Algorithm and Highlights the Importance of Overlooked Bonds

Bacteriophage λ's CI repressor protein controls a genetic switch between the virus's lysogenic and lytic lifecycles, in part, by selectively binding to six different DNA sequences within the phage genome-collectively referred to as operator sites. However, the minimal level of information needed for CI to recognize and specifically bind these six unique-but-related sequences is unclear. In a previous study, we introduced an algorithm that extracts the minimal direct readout information needed for λ-CI to recognize and bind its six binding sites. We further revealed direct readout information shared among three evolutionarily related lambdoid phages: λ-phage, Enterobacteria phage VT2-Sakai, and Stx2 converting phage I, suggesting that the λ-CI protein could bind to the operator sites of these other phages. In this study, we show that λ-CI can indeed bind the other two phages' cognate binding sites as predicted using our algorithm, validating the hypotheses from that paper. We go on to demonstrate the importance of specific hydrogen bond donors and acceptors that are maintained despite changes to the nucleobase itself, and another that has an important role in recognition and binding. This in vitro validation of our algorithm supports its use as a tool to predict alternative binding sites for DNA-binding proteins.

Studying Nucleoid-Associated Protein-DNA Interactions Using Polymer Microgels as Synthetic Mimics

Microfluidically fabricated polymer microgels are used as an experimental platform to analyze protein-DNA interactions regulating bacterial cell division. In particular, we focused on the nucleoid-associated protein SlmA, which forms a nucleoprotein complex with short DNA binding sequences (SBS) that acts as a negative regulator of the division ring stability in Escherichia coli. To mimic the bacterial nucleoid as a dense DNA region of a bacterial cell and investigate the influence of charge and permeability on protein binding and diffusion in there, we have chosen nonionic polyethylene glycol and anionic hyaluronic acid as precursor materials for hydrogel formation, previously functionalized with SBS. SlmA binds specifically to the coupled SBS for both types of microgels while preferentially accumulating at the microgels' surface. We could control the binding specificity by adjusting the buffer composition of the DNA-functionalized microgels. The microgel charge did not impact protein binding; however, hyaluronic acid-based microgels exhibit a higher permeability, promoting protein diffusion; thus, they were the preferred choice for preparing nucleoid mimics. The approaches described here provide attractive tools for bottom-up reconstitution of essential cellular processes in media that more faithfully reproduce intracellular environments.

DNA groove preference shift upon phosphorylation of a protamine-like cationic peptide

Protamines, arginine-rich DNA-binding proteins, are responsible for chromatin compaction in sperm cells, but their DNA groove preference, major or minor, is not clearly identified. We herein study the DNA groove preference of a short protamine-like cationic peptide before and after phosphorylation, using all-atom molecular dynamics and umbrella sampling simulations. According to various thermodynamic and structural analyses, a peptide in its non-phosphorylated native state prefers the minor groove over the major groove, but phosphorylation of the peptide bound to the minor groove not only reduces its binding affinity but also brings a serious deformation of the minor groove, eliminating the minor-groove preference. As protamines are heavily phosphorylated before binding to DNA, we expect that the structurally disordered phosphorylated protamines would prefer major grooves to enter into DNA during spermatogenesis.

Structural basis for transcription factor ZBTB7A recognition of DNA and effects of ZBTB7A somatic mutations that occur in human acute myeloid leukemia

ZBTB7A belongs to a small family of transcription factors having three members in humans (7A, 7B, and 7C). They share a BTB/POZ protein interaction domain at the amino end and a zinc-finger DNA-binding domain at the carboxyl end. They control the transcription of a wide range of genes, having varied functions in hematopoiesis, oncogenesis, and metabolism (in particular glycolysis). ZBTB7A-binding profiles at gene promoters contain a consensus G(a/c)CCC motif, followed by a CCCC sequence in some instances. Structural and mutational investigations suggest that DNA-specific contacts with the four-finger tandem array of ZBTB7A are formed sequentially, initiated from ZF1-ZF2 binding to G(a/c)CCC before spreading to ZF3-ZF4, which bind the DNA backbone and the 3' CCCC sequence, respectively. Here, we studied some mutations found in t(8;21)-positive acute myeloid leukemia patients that occur within the ZBTB7A DNA-binding domain. We determined that these mutations generally impair ZBTB7A DNA binding, with the most severe disruptions resulting from mutations in ZF1 and ZF2, and the least from a frameshift mutation in ZF3 that results in partial mislocalization. Information provided here on ZBTB7A-DNA interactions is likely applicable to ZBTB7B/C, which have overlapping functions with ZBTB7A in controlling primary metabolism.

Missense MED12 variants in 22 males with intellectual disability: From nonspecific symptoms to complete syndromes

We describe the phenotype of 22 male patients (20 probands) carrying a hemizygous missense variant in MED12. The phenotypic spectrum is very broad ranging from nonspecific intellectual disability (ID) to the three well-known syndromes: Opitz-Kaveggia syndrome, Lujan-Fryns syndrome, or Ohdo syndrome. The identified variants were randomly distributed throughout the gene (p = 0.993, χ² test), but mostly outside the functional domains (p = 0.004; χ² test). Statistical analyses did not show a correlation between the MED12-related phenotypes and the locations of the variants (p = 0.295; Pearson correlation), nor the protein domain involved (p = 0.422; Pearson correlation). In conclusion, establishing a genotype-phenotype correlation in MED12-related diseases remains challenging. Therefore, we think that patients with a causative MED12 variant are currently underdiagnosed due to the broad patients' clinical presentations.

Effect of phosphorylation of protamine-like cationic peptide on the binding affinity to DNA

Protamines are more arginine-rich and more basic than histones and are responsible for providing a highly compacted shape to the sperm heads in the testis. Phosphorylation and dephosphorylation are two events that occur in the late phase of spermatogenesis before the maturation of sperms. In this work, we have studied the effect of phosphorylation of protamine-like cationic peptides using all-atom molecular dynamics simulations. Through thermodynamic analyses, we found that phosphorylation reduces the binding efficiency of such cationic peptides on DNA duplexes. Peptide phosphorylation leads to a less efficient DNA condensation, due to a competition between DNA-peptide and peptide-peptide interactions. We hypothesize that the decrease of peptide bonds between DNA together with peptide self-assembly might allow an optimal re-organization of chromatin and an efficient condensation through subsequent peptide dephosphorylation. Based on the globular and compact conformations of phosphorylated peptides mediated by arginine-phosphoserine H-bonding, we furthermore postulate that phosphorylated protamines could more easily intrude into chromatin and participate to histone release through disruption of histone-histone and histone-DNA binding during spermatogenesis.

Conformational Change of Transcription Factors from Search to Specific Binding: A lac Repressor Case Study

In a process known as facilitated diffusion, DNA-binding proteins find their target sites by combining three-dimensional diffusion and one-dimensional scanning of the DNA. Following the trade-off between speed and stability, agile exploration of DNA requires loose binding, whereas, at the DNA target site, the searching protein needs to establish tight interactions with the DNA. To enable both efficient search and stable binding, DNA-binding proteins and DNA often switch conformations upon recognition. Here, we study the one-dimensional diffusion and DNA binding of the dimeric lac repressor (LacI), which was reported to adopt two different conformations when binding different conformations of DNA. Using coarse-grained molecular dynamic simulations, we studied the diffusion and the sequence-specific binding of these conformations of LacI, as well as their truncated or monomeric variants, with two DNA conformations: straight and bent. The simulations were compared to experimental observables. This study supports that linear diffusion along DNA combines tight rotation-coupled groove tracking and rotation-decoupled hopping, where the protein briefly dissociates and reassociates just a few base pairs away. Tight groove tracking is crucial for target-site recognition, while hopping speeds up the overall search process. We investigated the diffusion of different LacI conformations on DNA and show how the flexibility of LacI's hinge regions ensures agility on DNA as well as faithful groove tracking. If the hinge regions instead form α-helices at the protein-DNA interface, tight groove tracking is not possible. On the contrary, the helical hinge region is essential for tight binding to bent, specific DNA, for the formation of the specific complex. Based on our study of different encounter complexes, we argue that the conformational change in LacI and DNA bending are somewhat coupled. Our findings underline the importance of two distinct protein conformations for facilitated diffusion and specific binding, respectively.

Alignment of major-groove hydrogen bond arrays uncovers shared information between different DNA sequences that bind the same protein

Protein-DNA binding is of a great interest due to its importance in many biological processes. Previous studies have presented many factors responsible for the recognition and specificity, but understanding the minimal informational requirements for proteins that bind to multiple DNA-sites is still an understudied area of bioinformatics. Here we focus on the hydrogen bonds displayed by the target DNA in the major groove that take part in protein-binding. We show that analyses focused on the base pair identity may overlook key hydrogen bonds. We have developed an algorithm that converts a nucleotide sequence into an array of hydrogen bond donors and acceptors and methyl groups. It then aligns these non-covalent interaction arrays to identify what information is being maintained among multiple DNA sequences. For three different DNA-binding proteins, Lactose repressor, controller protein and λ-CI repressor, we uncovered the minimal pattern of hydrogen bonds that are common amongst all the binding sequences. Notably in the three proteins, key interacting hydrogen bonds are maintained despite nucleobase mutations in the corresponding binding sites. We believe this work will be useful for developing new DNA binding proteins and shed new light on evolutionary relationships.

Genome-scale prediction of bacterial promoters

A key step in the transcription of RNA is the binding of the RNA polymerase protein complex to a short promoter sequence that is typically upstream of the gene to be expressed. Automated identification of promoters would serve as a valuable complement to experimental validation in determining which genes are likely to be expressed and when; however, promoter sequences are short and highly variable, which makes them very difficult to accurately classify. The many tools developed to identify promoters in DNA have generally been tested on small and balanced subsets of genomic sequence, and the results may not reflect their expected performance on genomes with millions of DNA base pairs where promoters are likely to comprise less than ∼1% of the sequence. Here we introduce Expositor, a neural-network-based method that uses different types of DNA encodings and tunable sensitivity and specificity parameters. Expositor showed higher sensitivity and precision on the E. coli K-12 MG1655 chromosome than other tested approaches. Expositor predictions were more consistent in the homologous subset of sequence from a strain of Salmonella than they were with another strain of E. coli. We also examined the accuracy of Expositor in distinguishing different classes of promoters and found that misclassification between classes was consistent with the biological similarity between promoters.

Insights into the binding mode of AS1411 aptamer to nucleolin

AS1411 aptamer can function as a recognition probe to detect the cell surface nucleolin overexpressed in cancer cells, however, little is known about their binding process. This study proposed a feasible binding mode for the first time and provided atomic-level descriptions for the high affinity and specific binding of AS1411. The binding pose predicted by docking was screened using knowledge-based criteria, and a microsecond molecular dynamics (MD) simulation showed the stable existence of the predicted structure in the solution. Structural analysis shows that the unique capping of the 5′ end of AS1411 provides the specific binding with RBD1, and the interactions of hydrogen bond, salt bridge, and water-mediated network between AS1411 and RBD1,2 stabilize the binding. The calculation of per-residue decomposition emphasizes the dominant contribution of van der Waals energy and critical residues are screened. Our study provides the molecular basis of this specific binding and can guide rational AS1411-based aptamers design. Further insights require tight collaborations between the experiments and in silico studies.

Single-Stranded DNA Binding Proteins and Their Identification Using Machine Learning-Based Approaches

Single-stranded DNA (ssDNA) binding proteins (SSBs) are critical in maintaining genome stability by protecting the transient existence of ssDNA from damage during essential biological processes, such as DNA replication and gene transcription. The single-stranded region of telomeres also requires protection by ssDNA binding proteins from being attacked in case it is wrongly recognized as an anomaly. In addition to their critical roles in genome stability and integrity, it has been demonstrated that ssDNA and SSB-ssDNA interactions play critical roles in transcriptional regulation in all three domains of life and viruses. In this review, we present our current knowledge of the structure and function of SSBs and the structural features for SSB binding specificity. We then discuss the machine learning-based approaches that have been developed for the prediction of SSBs from double-stranded DNA (dsDNA) binding proteins (DSBs).

Interrogating the substrate specificity landscape of UvrC reveals novel insights into its non-canonical function

Although it is relatively unexplored, accumulating data highlight the importance of tripartite crosstalk between nucleotide excision repair (NER), DNA replication, and recombination in the maintenance of genome stability; however, elucidating the underlying mechanisms remains challenging. While Escherichia coli uvrA and uvrB can fully complement polAΔ cells in DNA replication, uvrC attenuates this alternative DNA replication pathway, but the exact mechanism by which uvrC suppresses DNA replication is unknown. Furthermore, the identity of bona fide canonical and non-canonical substrates for UvrCs are undefined. Here, we reveal that Mycobacterium tuberculosis UvrC (MtUvrC) strongly binds to, and robustly cleaves, key intermediates of DNA replication/recombination as compared with the model NER substrates. Notably, inactivation of MtUvrC ATPase activity significantly attenuated its endonuclease activity, thus suggesting a causal link between these two functions. We built an in silico model of the interaction of MtUvrC with the Holliday junction (HJ), using a combination of homology modeling, molecular docking, and molecular dynamic simulations. The model predicted residues that were potentially involved in HJ binding. Six of these residues were mutated either singly or in pairs, and the resulting MtUvrC variants were purified and characterized. Among them, residues Glu595 and Arg597 in the helix-hairpin-helix motif were found to be crucial for the interaction between MtUvrC and HJ; consequently, mutations in these residues, or inhibition of ATP hydrolysis, strongly abrogated its DNA-binding and endonuclease activities. Viewed together, these findings expand the substrate specificity landscape of UvrCs and provide crucial mechanistic insights into the interplay between NER and DNA replication/recombination.

Insights into protein-DNA interactions from hydrogen bond energy-based comparative protein-ligand analyses

Hydrogen bonds play important roles in protein folding and protein-ligand interactions, particularly in specific protein-DNA recognition. However, the distributions of hydrogen bonds, especially hydrogen bond energy (HBE) in different types of protein-ligand complexes, is unknown. Here we performed a comparative analysis of hydrogen bonds among three non-redundant datasets of protein-protein, protein-peptide, and protein-DNA complexes. Besides comparing the number of hydrogen bonds in terms of types and locations, we investigated the distributions of HBE. Our results indicate that while there is no significant difference of hydrogen bonds within protein chains among the three types of complexes, interfacial hydrogen bonds are significantly more prevalent in protein-DNA complexes. More importantly, the interfacial hydrogen bonds in protein-DNA complexes displayed a unique energy distribution of strong and weak hydrogen bonds whereas majority of the interfacial hydrogen bonds in protein-protein and protein-peptide complexes are of predominantly high strength with low energy. Moreover, there is a significant difference in the energy distributions of minor groove hydrogen bonds between protein-DNA complexes with different binding specificity. Highly specific protein-DNA complexes contain more strong hydrogen bonds in the minor groove than multi-specific complexes, suggesting important role of minor groove in specific protein-DNA recognition. These results can help better understand protein-DNA interactions and have important implications in improving quality assessments of protein-DNA complex models.

Quantum biology. π-π entanglement signatures in Protein-DNA interactions

DNA biological functions are carried out by individual proteins that interact with specific sequences along DNA to prime molecular processes required by cellular metabolism. Protein-DNA interactions include DNA replication, gene expression and its regulation, DNA repair, DNA restriction and modification by endonucleases, generally classified as enzymatic functions, or transcription factors functions. To find specific binding target sequences and finalize their activities, proteins must operate in symbiosis with cellular crowded environment identifying extremely small cognate sequences along the DNA chain, ranging from 15-20 bps for repressors to 4-6 bps for restriction enzymes in less than one second.

Dinuclear platinum(II) complexes as the pattern for phosphate backbone binding: a new perspective for recognition of binding modes to DNA

The mechanism of action of most approved drugs in use today is based on their binding to specific proteins or DNA. One of the achievements of this research is a new perspective for recognition of binding modes to DNA by monitoring of changes in measured and stoichiometric values of absorbance at 260 nm. UV-Vis and IR spectroscopy, gel electrophoresis and docking study were used for investigation of binding properties of three dinuclear platinum(II) complexes containing different pyridine-based bridging ligands, [{Pt(en)Cl}₂(μ-4,4'-bipy)]Cl₂·2H₂O (Pt1), [{Pt(en)Cl}₂(μ-bpa)]Cl₂·4H₂O (Pt2) and [{Pt(en)Cl}₂(μ-bpe)]Cl₂·4H₂O (Pt3) to DNA (4,4'-bipy, bpa and bpe are 4,4'-bipyridine, 1,2-bis(4-pyridyl)ethane and 1,2-bis(4-pyridyl)ethene, respectively). In contrast to the system with well-known intercalated ligand (EtBr), covalently bound ligand (cis-Pt) and with minor groove binder (Hoechst 33258), which do not have significant differences in measured and stoichiometric values, the most pronounced deviations are recorded for two dinuclear platinum(II) complexes (Pt1 and Pt2), as a consequence of complex binding to the phosphate backbone and bending of DNA helix. The hydrolysis of complexes and changes in DNA conformation were also analysed as phenomena that may have an impact on the changes in absorbance.

Optical-Dissymmetry Phase Transitions in an Achiral Helical-Spring Polymer through Controlled Noncovalent Interactions

Noncovalent chemistry may offer diversity in the functions and applications for artificial polymers by allowing various ordered-disordered phase transitions in a precisely controlled manner. To verify this notion from a fundamental perspective, we examined an achiral poly(phenylacetylene) derivative with an α-helical structure as a helical-spring polymer for revealing phase changes through control of intramolecular hydrogen bonding with the chiral solvent and temperature. When an amine capable of hydrogen bonding was used as the chiral solvent, either an irreversible helix-helix or a reversible helix-coil phase change occurred in an optically dissymmetric manner according to the amount of the chiral solvent added and ambient temperature. Considering the hydrogen-bonding strength values of the solvent mixture and the thermodynamic parameters, we could predict if the optical-dissymmetry phase changes would occur and, if so, how they occur. Our results were similar to those see for the denaturation of proteins, induced by solvent and temperature, based on helix-coil phase transition.

Revealing atomic-scale molecular diffusion of a plant-transcription factor WRKY domain protein along DNA

In transcription factors’ search for target genes, one-dimensional diffusion of the protein along DNA is essential. Experimentally, it remains challenging to resolve the individual diffusional steps of protein on DNA. Here, we report mainly all-atom equilibrium simulations of a WRKY domain protein in association with and diffusion along DNA. We demonstrate a complete stepping cycle of the protein for one base pair on DNA within microseconds, along with stochastic motions. Processive protein diffusions on DNA have been further sampled in a coarse-grained model. We have also found preferential DNA-strand association of the domain protein, which becomes most prominent at specific DNA binding, and it can be common for small-domain proteins to balance movements on the DNA with the sequence recognition.

Transcription factor (TF) target search on genome is highly essential for gene expression and regulation. High-resolution determination of TF diffusion along DNA remains technically challenging. Here, we constructed a TF model system using the plant WRKY domain protein in complex with DNA from crystallography and demonstrated microsecond diffusion dynamics of WRKY on DNA by employing all-atom molecular-dynamics (MD) simulations. Notably, we found that WRKY preferentially binds to one strand of DNA with significant energetic bias compared with the other, or nonpreferred strand. The preferential DNA-strand binding becomes most prominent in the static process, from nonspecific to specific DNA binding, but less distinct during diffusive movements of the domain protein on the DNA. Remarkably, without employing acceleration forces or bias, we captured a complete one-base-pair stepping cycle of the protein tracking along major groove of DNA with a homogeneous poly-adenosine sequence, as individual hydrogen bonds break and reform at the protein–DNA binding interface. Further DNA-groove tracking motions of the protein forward or backward, with occasional sliding as well as strand crossing to minor groove of DNA, were also captured. The processive diffusion of WRKY along DNA has been further sampled via coarse-grained MD simulations. The study thus provides structural dynamics details on diffusion of a small TF domain protein, suggests how the protein approaches a specific recognition site on DNA, and supports further high-precision experimental detection. The stochastic movements revealed in the TF diffusion also provide general clues about how other protein walkers step and slide along DNA.

Protein-DNA/RNA Interactions: An Overview of Investigation Methods in the -Omics Era

The fields of application of functional proteomics are not limited to the study of protein–protein interactions; they also extend to those involving protein complexes that bind DNA or RNA. These interactions affect fundamental processes such as replication, transcription, and repair in the case of DNA, as well as transport, translation, splicing, and silencing in the case of RNA. Analytical or preparative experimental approaches, both in vivo and in vitro, have been developed to isolate and identify DNA/RNA binding proteins by exploiting the advantage of the affinity shown by these proteins toward a specific oligonucleotide sequence. The present review proposes an overview of the approaches most commonly employed in proteomics applications for the identification of nucleic acid-binding proteins, such as affinity purification (AP) protocols, EMSA, chromatin purification methods, and CRISPR-based chromatin affinity purification, which are generally associated with mass spectrometry methodologies for the unbiased protein identification.

A comparative study of protein-ssDNA interactions

Single-stranded DNA-binding proteins (SSBs) play crucial roles in DNA replication, recombination and repair, and serve as key players in the maintenance of genomic stability. While a number of SSBs bind single-stranded DNA (ssDNA) non-specifically, the others recognize and bind specific ssDNA sequences. The mechanisms underlying this binding discrepancy, however, are largely unknown. Here, we present a comparative study of protein-ssDNA interactions by annotating specific and non-specific SSBs and comparing structural features such as DNA-binding propensities and secondary structure types of residues in SSB-ssDNA interactions, protein-ssDNA hydrogen bonding and π-π interactions between specific and non-specific SSBs. Our results suggest that protein side chain-DNA base hydrogen bonds are the major contributors to protein-ssDNA binding specificity, while π-π interactions may mainly contribute to binding affinity. We also found the enrichment of aspartate in the specific SSBs, a key feature in specific protein-double-stranded DNA (dsDNA) interactions as reported in our previous study. In addition, no significant differences between specific and non-specific groups with respect of conformational changes upon ssDNA binding were found, suggesting that the flexibility of SSBs plays a lesser role than that of dsDNA-binding proteins in conferring binding specificity.

How human serum albumin-selective DNA aptamer binds to bovine and canine serum albumins

Serum albumin (SA) is the most abundant carrier protein in blood. SA carries a diverse range of nutrients, drugs, and metal ions. It has wide clinical and biochemical applications. Human serum albumin (HSA) can be used as a biomarker for kidney and liver diseases. Aptasensor is one of potential HSA detection methods. HSA-specific aptamer was selected for HSA detection. In animals, bovine serum albumin (BSA) and canine serum albumins (CSA) share high sequence similarities to HSA. Thus, it is interesting to explore the possibility of using HSA-selective aptamer for BSA and CSA aptasensor. In this study, molecular dynamics (MD) simulations were initially employed to investigate the binding of aptamer to BSA and CSA in comparison to HSA. Like HSA, both BSA and CSA can bind aptamer, but different binding affinities are observed. BSA shows the tighter binding to aptamer than CSA. Domain III is found to be the aptamer-binding domain although no specific aptamer conformation is captured. However, in all cases, the aptamer utilizes the 3'-end to attach on an albumin surface. Both nucleobases and phosphate backbones on a DNA aptamer are important for albumin-aptamer complexation. Our results imply the possibility of using HSA-specific aptamer for BSA detection due to tighter binding observed, but may be less effective in CSA. However, the test in actual complicated condition must be further studied.

Structural Patterns and Stabilities of Hydrogen-Bonded Pairs Involving Ribonucleotide Bases and Arginine, Glutamic Acid, or Glutamine Residues of Proteins from Quantum Mechanical Calculations

Ribonucleotide:protein interactions play crucial roles in a number of biological processes. Unlike the RNA:protein interface where van der Waals contacts are prevalent, the recognition of a single ribonucleotide such as ATP by a protein occurs predominantly through hydrogen-bonding interactions. As a first step toward understanding the role of hydrogen bonding in ribonucleotide:protein recognition, the present work employs density functional theory to provide a detailed quantum-mechanical analysis of the structural and energetic characteristics of 18 unique hydrogen-bonded pairs involving the nucleobase/nucleoside moiety of four canonical ribonucleotides and the side chains of three polar amino-acid residues (arginine, glutamine, and glutamic acid) of proteins. In addition, we model five new pairs that are till now not observed in crystallographically identified ribonucleotide:protein complexes but may be identified in complexes crystallized in the future. We critically examine the characteristics of each pair in its ribonucleotide:protein crystal structure occurrence and (gas phase and water phase) optimized intrinsic structure. We further evaluated the interaction energy of each pair and characterized the associated hydrogen bonds using a number of quantum mechanics-based relationships including natural bond orbital analysis, quantum theory atoms in molecules analysis, Iogansen relationships, Nikolaienko-Bulavin-Hovorun relationships, and noncovalent interaction-reduced density gradient analysis. Our analyses reveal rich variability in hydrogen bonds in the crystallographic as well as intrinsic structure of each pair, which includes conventional O/N-H···N/O and C-H···O hydrogen bonds as well as donor/acceptor-bifurcated hydrogen bonds. Further, we identify five combinations of nucleobase and amino acid moieties; each of which exhibits at least two alternate (i.e., multimodal) structures that interact through the same nucleobase edge. In fact, one such pair exhibits four multimodal structures; one of which possesses unconventional "amino-acceptor" hydrogen bonding with comparable (-9.4 kcal mol^-1) strength to the corresponding conventional (i.e., amino:donor) structure (-9.2 kcal mol^-1). This points to the importance of amino-acceptor hydrogen bonds in RNA:protein interactions and suggests that such interactions must be considered in the future while studying the dynamics in the context of molecular recognition. Overall, our study provides preliminary insights into the intrinsic features of ribonucleotide:amino acid interactions, which may help frame a clearer picture of the molecular basis of RNA:protein recognition and further appreciate the role of such contacts in biology.