pyDockDNA: A new web server for energy-based protein-DNA docking and scoring

Molecular basis of protein-DNA interactions between Halalkalibacterium halodurans MntR and its DNA operator sequence

Transition metals such as iron, zinc and manganese are essential for bacterial survival. A pivotal role in regulation of manganese homeostasis in bacterium Halalkalibacterium halodurans has MntR protein (HhMntR). In this work, molecular dynamics simulations of holoprotein (with Mn2+) and apoprotein (without Mn2+) HhMntR in complex with DNA mntA operator were conducted and enabled understanding of interaction between HhMntR and DNA on molecular level. Molecular mechanism through which affinity of HhMntR towards DNA is increased upon Mn2+ binding was revealed. Holoprotein binds DNA through stable and consistent noncovalent interactions, while apoprotein shows highly dynamic behavior, attaching to and detaching from the DNA backbone and inner grooves on a nanosecond time scale. The same observations are seen even during the simulations that started with protein and DNA separated from the complex. Additionally, key amino acids involved in the formation of the HhMntR-DNA complex were identified, leading to the proposal of a molecular framework that allows HhMntR to perform its biological function as a transcription factor. Overall, observed behaviors promote the lateral movement of HhMntR along the DNA sequence, enabling the protein to remain close to the DNA while it seeks out specific base pairs for strong binding upon activation by Mn2+.

Identification of a novel missense variant in the LMX1B gene associated with nail-patella syndrome in a Chinese family

Background

Nail-patella syndrome (NPS) is an autosomal dominant disorder caused by the variants of the LMX1B gene, affecting several systems, including musculoskeletal, renal, and ocular systems. Despite the well-established genetic basis, the complicated relationship between genotype and phenotype still remains unclear. This study aimed to identify the genetic cause of NPS in a Chinese family and elucidate its potential contribution to the disease's phenotypic spectrum.

Methods

Clinical data and peripheral blood samples were collected from the affected family. Whole-exome sequencing (WES) was conducted to identify potential pathogenic variants, followed by Sanger sequencing to validate the candidate variant. Bioinformatic tools were employed to predict the 3D structure alterations and pathogenicity of the variant. Wild-type and mutant LMX1B overexpression plasmids were constructed to investigate the functional consequences of the variant. Western blotting and immunofluorescence were conducted to measure the expression and localization of the protein.

Results

The proband presented with clinical manifestations, including nail malformation, patella dysplasia, restricted elbow movement, and pes planus. Both his mother and sister exhibited symptoms related to the skeletal system. WES identified a novel c.812G>C (p.R271T) variant in the affected family members. Bioinformatic analyses revealed structural modification in the protein and predicted functional impairment. Western blotting showed no significant difference in the expression level between wild-type and mutant protein. However, immunofluorescence demonstrated distinct changes in the subcellular localization of c.812G>C mutant.

Conclusion

NPS is a rare multisystem disorder with variable clinical presentations. In this family, the skeletal system was mainly involved with variations among different members. Our study identified a novel c.812G > c variant in the LMX1B gene, changing the nuclear localization of the protein.

Mechanisms of DNA Damage Recognition by UDG and PARP1 in the Nucleosome

The DNA base-excision repair (BER) pathway shares the second part of its enzymatic chain with the single-strand break (SSB) repair pathway. BER is initiated by a glycosylase, such as UDG, while SSBR is initiated by the multifunctional enzyme PARP1. The very early steps in the identification of the DNA damage are crucial to the correct initiation of the repair chains, and become even more complex when considering the realistic environment of damage to the DNA in the nucleosome. We performed molecular dynamics computer simulations of the interaction between the glycosylase UDG and a mutated uracil (as could result from oxidative deamination of cytosine), and between the Zn1-Zn2 fragment of PARP1 and a simulated SSB. The model system is a whole nucleosome in which DNA damage is inserted at various typical positions along the 145-bp sequence. It is shown that damage recognition by the enzymes requires very strict conditions, unlikely to be matched by pure random search along the DNA. We propose that mechanical deformation of the DNA around the defective sites may help signaling the presence of the defect, accelerating the search process.

The 'very moment' when UDG recognizes a flipped-out uracil base in dsDNA

Uracil-DNA glycosylase (UDG) is the first enzyme in the base-excision repair (BER) pathway, acting on uracil bases in DNA. How UDG finds its targets has not been conclusively resolved yet. Based on available structural and other experimental evidence, two possible pathways are under discussion. In one, the action of UDG on the DNA bases is believed to follow a 'pinch-push-pull' model, in which UDG generates the base-flip in an active manner. A second scenario is based on the exploitation of bases flipping out thermally from the DNA. Recent molecular dynamics (MD) studies of DNA in trinucleosome arrays have shown that base-flipping can be readily induced by the action of mechanical forces on DNA alone. This alternative mechanism could possibly enhance the probability for the second scenario of UDG-uracil interaction via the formation of a recognition complex of UDG with flipped-out base. In this work, we describe DNA structures with flipped-out uracil bases generated by MD simulations which we then subject to docking simulations with the UDG enzyme. Our results for the UDG-uracil recognition complex support the view that base-flipping induced by DNA mechanics can be a relevant mechanism of uracil base recognition by the UDG glycosylase in chromatin.

Protein-nucleic acid complexes: Docking and binding affinity

Protein-nucleic interactions play essential roles in several biological processes, such as gene regulation, replication, transcription, repair and packaging. The knowledge of three-dimensional structures of protein-nucleic acid complexes and their binding affinities helps to understand these functions. In this review, we focus on two major aspects namely, (i) deciphering the three-dimensional structures of protein-nucleic acid complexes and (ii) predicting their binding affinities. The first part is devoted to the state-of-the-art methods for predicting the native structures and their performances including recent CASP targets. The second part is focused on different aspects of investigating the binding affinity of protein-nucleic acid complexes: (i) databases for thermodynamic parameters to understand the binding affinity, (ii) important features determining protein-nucleic acid binding affinity, (iii) predicting the binding affinity of protein-nucleic acid complexes using sequence and structure-based parameters and (iv) change in binding affinity upon mutation. It includes the latest developments in protein-nucleic acid docking algorithms and binding affinity predictions along with a list of computational resources for understanding protein-DNA and protein-RNA interactions.

Computational epitope-based vaccine design with bioinformatics approach; a review

The significance of vaccine development has gained heightened importance in light of the COVID-19 pandemic. In such critical circumstances, global citizens anticipate researchers in this field to swiftly identify a vaccine candidate to combat the pandemic's root cause. It is widely recognized that the vaccine design process is traditionally both time-consuming and costly. However, a specialized subfield within bioinformatics, known as "multi-epitope vaccine design" or "reverse vaccinology," has significantly decreased the time and costs of the vaccine design process. The methodology reverses itself in this subfield and finds a potential vaccine candidate by analyzing the pathogen's genome. Leveraging the tools available in this domain, we strive to pinpoint the most suitable antigen for crafting a vaccine against our target. Once the optimal antigen is identified, the next step involves uncovering epitopes within this antigen. The immune system recognizes particular areas of an antigen as epitopes. By characterizing these crucial segments, we gain the opportunity to design a vaccine centered around these epitopes. Subsequently, after identifying and assembling the vital epitopes with the assistance of linkers and adjuvants, our vaccine candidate can be formulated. Finally, employing computational techniques, we can thoroughly evaluate the designed vaccine. This review article comprehensively covers the entire multi-epitope vaccine development process, starting from obtaining the pathogen's genome to identifying the relevant vaccine candidate and concluding with an evaluation. Furthermore, we will delve into the essential tools needed at each stage, comparing and introducing them.

FTDMP: A Framework for Protein-Protein, Protein-DNA, and Protein-RNA Docking and Scoring

FTDMP is a software framework for biomolecular docking and scoring. It can perform docking of subunits containing one or more protein, DNA, or RNA chains, followed by subsequent scoring of the resulting models. FTDMP can also be used for the ranking of user-provided models of biomolecular complexes, generated by any structure prediction method. FTDMP evaluates models according to the consensus-based method VoroIF-jury, which combines individual scores derived from the Voronoi tessellation of biomolecular structures. In addition to the default scoring mode, FTDMP can easily adopt additional scores; thus, it may be used as a tool to assess newly developed scoring functions. FTDMP was evaluated during blind testing in recent CAPRI experiments and using protein-protein, protein-DNA, and protein-RNA docking benchmarks. It proved to be a useful tool for different research tasks, related to modeling biomolecular interactions. The software, cleaned docking benchmarks, and benchmarking results are available at https://bioinformatics.lt/software/ftdmp/.

Bioinformatics Approaches for Understanding the Binding Affinity of Protein-Nucleic Acid Complexes

Protein-nucleic acid interactions are involved in various biological processes such as gene expression, replication, transcription, translation, and packaging. Understanding the recognition mechanism of the protein-nucleic acid complexes has been investigated from different perspectives, including the binding affinities of protein-DNA and protein-RNA complexes. Experimentally, protein-nucleic acid interactions are analyzed using X-ray crystallography, Isothermal Titration Calorimetry (ITC), DNA/RNA pull-down assays, DNA/RNA footprinting, and systematic evolution of ligands by exponential enrichment (SELEX). On the other hand, numerous databases and computational tools have been developed to study protein-nucleic acid complexes based on their binding sites, specific interactions between them, and binding affinity. In this chapter, we discuss various databases for protein-nucleic acid complex structures and the tools available to extract features from them. Further, we provide details on databases and prediction methods reported for exploring the binding affinity of protein-nucleic acid complexes along with important structure-based parameters, which govern the binding affinity.

Prevalence of the genetic variant rs61330082 and serum levels of the visfatin gene in Mexican individuals with metabolic syndrome: a clinical and bioinformatics approach

Introduction

Background: metabolic syndrome (MetS) is a group of clinical anomalies that share an inflammatory component of multifactorial etiology. Objectives: the present study aims to relate the genetic variant (rs61330082 C/T) with dietary patterns in the presence of MetS and the application of molecular docking according to the genotype and associated transcription factors. Methods: 197 individuals aged 18 to 65 were included, from whom anthropometric measurements were taken, and a blood sample from the forearm. DNA extraction and enzymatic digestion were performed to determine the genotype of each participant by PCR-RFLP. Dietary patterns were analyzed using a nutritional questionnaire validated for the Mexican population. Serum levels of the protein visfatin were assessed by ELISA. Finally, bioinformatics tools were used for molecular docking to infer the binding of transcriptional factors in the polymorphic region. Results: the TT genotype was present in only 10 % of the population. Women carrying the CT+TT genotype, according to the dominant genetic model, had higher serum levels of triglycerides and VDLD-C. Statistical analysis did not show a significant association between the presence of MetS and the dominant CT+TT model (OR = 1.41, 95 % CI = 0.61-3.44, p = 0.53). We identified PAX5 as a transcription factor binding to the polymorphic site of this genetic variant. Conclusions: this study demonstrated a significant association between the genetic variant (rs61330082 C/T) and lipid parameters. Women carrying the T allele have a higher risk of high triglyceride levels, a criterion for metabolic syndrome.

Active-reset protein sensors enable continuous in vivo monitoring of inflammation

Continuous measurement of proteins in vivo is important for real-time disease management and prevention. Implantable sensors for monitoring small molecules such as glucose have been available for more than a decade. However, analysis of proteins remains an unmet need because the lower physiological levels require that sensors have high affinities, which are linked to long complexation half-lives (t1/2 ~20 hours) and slow equilibration when concentrations decrease. We report active-reset sensors by use of high-frequency oscillations to accelerate dissociation, which enables regeneration of the unbound form of the sensor within 1 minute. When implemented within implanted devices, these sensors allow for real-time, in vivo monitoring of proteins within interstitial fluid. Active-reset protein sensors track biomarker levels on a physiological timescale for inflammation monitoring in living animals.

Transcriptomic and in silico analysis of BLACE (B-cell acute lymphoblastic leukemia expressed), a new non-coding RNA, as a diagnostic biomarker in B-cell ALL

ALL (acute lymphoblastic leukemia) is a type of hematological malignancy that involves developmental and differentiation arrest at the lymphoblast stage. BLACE, a gene specifically expressed in B-cell acute lymphoblastic leukemia shows little or no expression in mature B-lymphocytes. The current pilot study involves transcriptional analysis of BLACE in B-cell ALL patients. Expression of BLACE was high in both pediatric and adult ALL patients. Promoter analysis of the BLACE gene showed the presence of CAAT and TATA box promoters and G-rich sequences with a potential to form G-quadruplexes. Due to identification of TAL1 transcription factor binding sites within the BLACE promoter region, expression of TAL1 gene was measured and found to correlate with the BLACE expression. The presence of an overlapping G-rich sequence and TAL1 binding site at -1291 bps within BLACE promoter indicated a new target site for controlling BLACE expression. The docking studies performed between BLACE-TAL1 protein showed a binding score of -208.68 kcal/mol and identified 21 BLACE nucleotide - TAL1 residues interacting at the docking interface. Together, our findings suggested that BLACE gene specifically expressed in B-cell ALL could serve as a new therapeutic target. Further investigations are required to get a comprehensive understanding of the BLACE gene mechanism.

Gene discovery from microbial gene libraries I: protection against reactive oxygen species-driven DNA damage

Reactive oxygen species (ROS) pose a lethal risk for all life forms by causing damage to cell processes, genome-wide DNA damage-driving mutation, replicative instability, and death. Thus, the development of mechanisms to resist or repair ROS-induced DNA damage is critical for the reliable replication of nucleic acids. DNA repair and protection mechanisms have been discovered in all forms of life. However, the vast array of microbes that may harbor novel repair or protection mechanisms, especially bacterial viruses, have not been adequately assessed. Here, we screened a microbial gene library composed primarily of phage open reading frames (ORFs) to uncover elements that overcome a DNA damage blockade. We report the discovery of one such protein, termed F21, which promotes bacterial survival by possibly repairing or protecting DNA in the face of ROS-induced DNA damage.IMPORTANCEDiscovery of proteins that promote DNA damage repair and protection in the face of reactive oxygen species (ROS) is of vital importance. Our group is in possession of a unique microbial DNA library with which we can screen for undiscovered genes that encode novel proteins with DNA damage repair and protective functions. This library is composed of diverse DNA from a variety of sources, namely bacteriophages, which must be assessed for their novel functions. This work focuses on the discovery of DNA damage repair and protection, but the possibilities for discovery are endless, thus highlighting the significance of this work.

Cooperative dynamics of PARP-1 zinc-finger domains in the detection of DNA single-strand breaks

The DNA single-strand break (SSB) repair pathway is initiated by the multifunctional enzyme PARP-1, which recognizes the broken DNA ends by its two zinc-finger domains, Zn1 and Zn2. Despite a number of experiments performed with different DNA configurations and reduced fragments of PARP-1, many details of this interaction that is crucial to the correct initiation of the repair chain are still unclear. We performed Molecular Dynamics (MD) computer simulations of the interaction between the Zn1/Zn2 domains of PARP-1 and a DNA hairpin including a missing nucleotide to simulate the presence of an SSB, a construct used in recent experiments. The role of Zn1 and Zn2 interacting with the SSB ends is studied in detail, both independently and cooperatively. We also explored, PARP-1 operating as a dimer, with the two Zn-fingers coming from two separate copies of the enzyme. By an extensive set of all-atom molecular simulations employing state-of-the art force fields, assisted by empirical docking and free-energy calculations, we conclude that the particular conformation of the DNA hairpin can indeed spontaneously open up by thermal fluctuations, up to extremely kinked deformations. However, such extreme localized deformations are rarely observed in free, long DNA fragments. Protein side-loops make contact with the DNA hairpin grooves, and help Zn2 to penetrate deep in the SSB gap. In this way, Zn2 can interact with the nucleotides opposite to the missing base. Overall, Zn1 plays a secondary role: the crucial factor for the interaction is rather the relative arrangement of the Zn1/Zn2 couple, and their mutual orientation with respect to the 3 ' and 5 ' SSB end terminals. This helps to obtain an early interacting configuration, which ultimately leads to molecular PARP-1-DNA structures similar to those observed experimentally. Such findings represent an important step toward defining the detailed function of PARP-1 in the early stages of SSB recognition.

Structural insight into the Csx1-Crn2 fusion self-limiting ribonuclease of type III CRISPR system

In the type III CRISPR system, cyclic oligoadenylate (cOA) molecules act as second messengers, activating various promiscuous ancillary nucleases that indiscriminately degrade host and viral DNA/RNA. Conversely, ring nucleases, by specifically cleaving cOA molecules, function as off-switches to protect host cells from dormancy or death, and allow viruses to counteract immune responses. The fusion protein Csx1-Crn2, combining host ribonuclease with viral ring nuclease, represents a unique self-limiting ribonuclease family. Here, we describe the structures of Csx1-Crn2 from the organism of Marinitoga sp., in both its full-length and truncated forms, as well as in complex with cA4. We show that Csx1-Crn2 operates as a homo-tetramer, a configuration crucial for preserving the structural integrity of the HEPN domain and ensuring effective ssRNA cleavage. The binding of cA4 to the CARF domain triggers significant conformational changes across the CARF, HTH, and into the HEPN domains, leading the two R-X4-6-H motifs to form a composite catalytic site. Intriguingly, an acetate ion was found to bind at this composite site by mimicking the scissile phosphate. Further molecular docking analysis reveals that the HEPN domain can accommodate a single ssRNA molecule involving both R-X4-6-H motifs, underscoring the importance of HEPN domain dimerization for its activation.

Gene networks governing the response of a calcareous sponge to future ocean conditions reveal lineage-specific XBP1 regulation of the unfolded protein response

Marine sponges are predicted to be winners in the future ocean due to their exemplary adaptive capacity. However, while many sponge groups exhibit tolerance to a wide range of environmental insults, calcifying sponges may be more susceptible to thermo-acidic stress. To describe the gene regulatory networks that govern the stress response of the calcareous sponge, Leucetta chagosensis (class Calcarea, order Clathrinida), individuals were subjected to warming and acidification conditions based on the climate models for 2100. Transcriptome analysis and gene co-expression network reconstruction revealed that the unfolded protein response (UPR) was activated under thermo-acidic stress. Among the upregulated genes were two lineage-specific homologs of X-box binding protein 1 (XBP1), a transcription factor that activates the UPR. Alternative dimerization between these XBP1 gene products suggests a clathrinid-specific mechanism to reversibly sequester the transcription factor into an inactive form, enabling the rapid regulation of pathways linked to the UPR in clathrinid calcareous sponges. Our findings support the idea that transcription factor duplication events may refine evolutionarily conserved molecular pathways and contribute to ecological success.

CONSTANS, a HUB for all seasons: How photoperiod pervades plant physiology regulatory circuits

How does a plant detect the changing seasons and make important developmental decisions accordingly? How do they incorporate daylength information into their routine physiological processes? Photoperiodism, or the capacity to measure the daylength, is a crucial aspect of plant development that helps plants determine the best time of the year to make vital decisions, such as flowering. The protein CONSTANS (CO) constitutes the central regulator of this sensing mechanism, not only activating florigen production in the leaves but also participating in many physiological aspects in which seasonality is important. Recent discoveries place CO in the center of a gene network that can determine the length of the day and confer seasonal input to aspects of plant development and physiology as important as senescence, seed size, or circadian rhythms. In this review, we discuss the importance of CO protein structure, function, and evolutionary mechanisms that embryophytes have developed to incorporate annual information into their physiology.

Flexible structural arrangement and DNA-binding properties of protein p6 from Bacillus subtillis phage φ29

The genome-organizing protein p6 of Bacillus subtilis bacteriophage φ29 plays an essential role in viral development by activating the initiation of DNA replication and participating in the early-to-late transcriptional switch. These activities require the formation of a nucleoprotein complex in which the DNA adopts a right-handed superhelix wrapping around a multimeric p6 scaffold, restraining positive supercoiling and compacting the viral genome. Due to the absence of homologous structures, prior attempts to unveil p6's structural architecture failed. Here, we employed AlphaFold2 to engineer rational p6 constructs yielding crystals for three-dimensional structure determination. Our findings reveal a novel fold adopted by p6 that sheds light on its self-association mechanism and its interaction with DNA. By means of protein-DNA docking and molecular dynamic simulations, we have generated a comprehensive structural model for the nucleoprotein complex that consistently aligns with its established biochemical and thermodynamic parameters. Besides, through analytical ultracentrifugation, we have confirmed the hydrodynamic properties of the nucleocomplex, further validating in solution our proposed model. Importantly, the disclosed structure not only provides a highly accurate explanation for previously experimental data accumulated over decades, but also enhances our holistic understanding of the structural and functional attributes of protein p6 during φ29 infection.

Evaluation of DNA-protein complex structures using the deep learning method

Biological processes such as transcription, repair, and regulation require interactions between DNA and proteins. To unravel their functions, it is imperative to determine the high-resolution structures of DNA-protein complexes. However, experimental methods for this purpose are costly and technically demanding. Consequently, there is an urgent need for computational techniques to identify the structures of DNA-protein complexes. Despite technological advancements, accurately identifying DNA-protein complexes through computational methods still poses a challenge. Our team has developed a cutting-edge deep-learning approach called DDPScore that assesses DNA-protein complex structures. DDPScore utilizes a 4D convolutional neural network to overcome limited training data. This approach effectively captures local and global features while comprehensively considering the conformational changes arising from the flexibility during the DNA-protein docking process. DDPScore consistently outperformed the available methods in comprehensive DNA-protein complex docking evaluations, even for the flexible docking challenges. DDPScore has a wide range of applications in predicting and designing structures of DNA-protein complexes.

MucR from Sinorhizobium meliloti: New Insights into Its DNA Targets and Its Ability to Oligomerize

Proteins of the MucR/Ros family play a crucial role in bacterial infection or symbiosis with eukaryotic hosts. MucR from Sinorhizobium meliloti plays a regulatory role in establishing symbiosis with the host plant, both dependent and independent of Quorum Sensing. Here, we report the first characterization of MucR isolated from Sinorhizobium meliloti by mass spectrometry and demonstrate that this protein forms higher-order oligomers in its native condition of expression by SEC-MALS. We show that MucR purified from Sinorhizobium meliloti can bind DNA and recognize the region upstream of the ndvA gene in EMSA, revealing that this gene is a direct target of MucR. Although MucR DNA binding activity was already described, a detailed characterization of Sinorhizobium meliloti DNA targets has never been reported. We, thus, analyze sequences recognized by MucR in the rem gene promoter, showing that this protein recognizes AT-rich sequences and does not require a consensus sequence to bind DNA. Furthermore, we investigate the dependence of MucR DNA binding on the length of DNA targets. Taken together, our studies establish MucR from Sinorhizobium meliloti as a member of a new family of Histone-like Nucleoid Structuring (H-NS) proteins, thus explaining the multifaceted role of this protein in many species of alpha-proteobacteria.