COZOID: contact zone identifier for visual analysis of protein-protein interactions

Effect of high-molecular-weight glutenin subunit deletion on gluten functionality and Chinese southern-type steamed bread quality

High-molecular-weight glutenin subunit (HMW-GS) is key factor in gluten strength and end-use quality. However, the contribution of individual HMW-GS on dough strength and Chinese southern-type steamed bread (CSTSB) quality remained unknown. In this study, we investigated the effects of individual HMW-GS deletion on CSTSB quality. The HMW-GS deletion led to significant reductions in glutenin/gliadin ratios, disulfide bond content, and SDS-unextractable polymeric protein formation. Additionally, HMW-GS deletion resulted in decreased gluten protein chain length, molecular weight, and particle size, contributing to increased thermal instability and reduced crosslinking. The HMW-GS deletion weakened dough strength but improved CSTSB performance, particularly in Dx2d and Dy12d. In-silico analysis further revealed strong interactions between Bx7 and Dx2, primarily driven by desolvation energy, highlighting their crucial role in stabilizing gluten protein interactions.

Molecular simulation reveals that pathogenic mutations in BTB/ANK domains of Arabidopsis thaliana NPR1 circumscribe the EDS1-mediated immune regulation

The NPR1 (nonexpressor of pathogenesis-related genes 1) is a key regulator of the salicylic-acid-mediated immune response caused by pathogens in Arabidopsis thaliana. Mutations C150Y and H334Y in the BTB/ANK domains of NPR1 inhibit the defense response, and transcriptional co-activity with enhanced disease susceptibility 1 (EDS1) has been revealed experimentally. This study examined the conformational changes and reduced NPR1-EDS1 interaction upon mutation using a molecular dynamics simulation. Initially, BTBC150YNPR1 and ANKH334YNPR1 were categorized as pathological mutations rather than others based on sequence conservation. A distant ortholog was used to map the common residues shared among the wild-type because the mutations were highly conserved. Overall, 179 of 373 residues were determining the secondary structures and fold versatility of conformations. In addition, the mutational hotspots Cys150, Asp152, Glu153, Cys155, His157, Cys160, His334, Arg339 and Lys370 were crucial for oligomer-to-monomer exchange. Subsequently, the atomistic simulations with free energy (MM/PB(GB)SA) calculations predicted structural displacements engaging in the N-termini α5133-178α7 linker connecting the central ANK regions (α13260-290α14 and α18320-390α22), where prominent long helices (α516) and short helices (α310) replaced with β-turns and loops disrupting hydrogen bonds and salt bridges in both mutants implicating functional regulation and activation. Furthermore, the mutation repositions the intact stability of multiple regions (L13C149-N356α20BTB/ANK-α17W301-E357α21N-ter/coiled-coil) compromising a dynamic interaction of NPR1-EDS1. By unveiling the transitions between the distinct functions of mutational perception, this study paves the way for future investigation to orchestrate additive host-adapted transcriptional reprogramming that controls defense-related regulatory mechanisms of NPR1s in plants.

From complex data to clear insights: visualizing molecular dynamics trajectories

Advances in simulations, combined with technological developments in high-performance computing, have made it possible to produce a physically accurate dynamic representation of complex biological systems involving millions to billions of atoms over increasingly long simulation times. The analysis of these computed simulations is crucial, involving the interpretation of structural and dynamic data to gain insights into the underlying biological processes. However, this analysis becomes increasingly challenging due to the complexity of the generated systems with a large number of individual runs, ranging from hundreds to thousands of trajectories. This massive increase in raw simulation data creates additional processing and visualization challenges. Effective visualization techniques play a vital role in facilitating the analysis and interpretation of molecular dynamics simulations. In this paper, we focus mainly on the techniques and tools that can be used for visualization of molecular dynamics simulations, among which we highlight the few approaches used specifically for this purpose, discussing their advantages and limitations, and addressing the future challenges of molecular dynamics visualization.

Short Linear Motifs in Colorectal Cancer Interactome and Tumorigenesis

Colorectal tumorigenesis is driven by alterations in genes and proteins responsible for cancer initiation, progression, and invasion. This multistage process is based on a dense network of protein-protein interactions (PPIs) that become dysregulated as a result of changes in various cell signaling effectors. PPIs in signaling and regulatory networks are known to be mediated by short linear motifs (SLiMs), which are conserved contiguous regions of 3-10 amino acids within interacting protein domains. SLiMs are the minimum sequences required for modulating cellular PPI networks. Thus, several in silico approaches have been developed to predict and analyze SLiM-mediated PPIs. In this review, we focus on emerging evidence supporting a crucial role for SLiMs in driver pathways that are disrupted in colorectal cancer (CRC) tumorigenesis and related PPI network alterations. As a result, SLiMs, along with short peptides, are attracting the interest of researchers to devise small molecules amenable to be used as novel anti-CRC targeted therapies. Overall, the characterization of SLiMs mediating crucial PPIs in CRC may foster the development of more specific combined pharmacological approaches.

Role of Nse1 Subunit of SMC5/6 Complex as a Ubiquitin Ligase

Structural Maintenance of Chromosomes (SMC) complexes are important for many aspects of the chromosomal organization. Unlike cohesin and condensin, the SMC5/6 complex contains a variant RING domain carried by its Nse1 subunit. RING domains are characteristic for ubiquitin ligases, and human NSE1 has been shown to possess ubiquitin-ligase activity in vitro. However, other studies were unable to show such activity. Here, we confirm Nse1 ubiquitin-ligase activity using purified Schizosaccharomyces pombe proteins. We demonstrate that the Nse1 ligase activity is stimulated by Nse3 and Nse4. We show that Nse1 specifically utilizes Ubc13/Mms2 E2 enzyme and interacts directly with ubiquitin. We identify the Nse1 mutation (R188E) that specifically disrupts its E3 activity and demonstrate that the Nse1-dependent ubiquitination is particularly important under replication stress. Moreover, we determine Nse4 (lysine K181) as the first known SMC5/6-associated Nse1 substrate. Interestingly, abolition of Nse4 modification at K181 leads to suppression of DNA-damage sensitivity of other SMC5/6 mutants. Altogether, this study brings new evidence for Nse1 ubiquitin ligase activity, significantly advancing our understanding of this enigmatic SMC5/6 function.

HyperLabels: Browsing of Dense and Hierarchical Molecular 3D Models

We present a method for the browsing of hierarchical 3D models in which we combine the typical navigation of hierarchical structures in a 2D environment-using clicks on nodes, links, or icons-with a 3D spatial data visualization. Our approach is motivated by large molecular models, for which the traditional single-scale navigational metaphors are not suitable. Multi-scale phenomena, e. g., in astronomy or geography, are complex to navigate due to their large data spaces and multi-level organization. Models from structural biology are in addition also densely crowded in space and scale. Cutaways are needed to show individual model subparts. The camera has to support exploration on the level of a whole virus, as well as on the level of a small molecule. We address these challenges by employing HyperLabels: active labels that-in addition to their annotational role-also support user interaction. Clicks on HyperLabels select the next structure to be explored. Then, we adjust the visualization to showcase the inner composition of the selected subpart and enable further exploration. Finally, we use a breadcrumbs panel for orientation and as a mechanism to traverse upwards in the model hierarchy. We demonstrate our concept of hierarchical 3D model browsing using two exemplary models from meso-scale biology.

ALKBH1-8 and FTO: Potential Therapeutic Targets and Prognostic Biomarkers in Lung Adenocarcinoma Pathogenesis

The AlkB family consists of Fe(II)- and α-ketoglutarate-dependent dioxygenases that can catalyze demethylation on a variety of substrates, such as RNA and DNA, subsequently affecting tumor progression and prognosis. However, their detailed functional roles in lung adenocarcinoma (LUAD) have not been clarified in a comprehensive manner. In this study, several bioinformatics databases, such as ONCOMINE, TIMER, and DiseaseMeth, were used to evaluate the expression profiles and prognostic significance of the AlkB family (ALKBH1-8 and FTO) in LUAD. The expression levels of ALKBH1/2/4/5/7/8 were significantly increased in LUAD tissues, while the expression levels of ALKBH3/6 and FTO were decreased. The main functions of differentially expressed AlkB homologs are related to the hematopoietic system and cell adhesion molecules. We also found that the expression profiles of the AlkB family are highly correlated with infiltrating immune cells (i.e., B cells, CD8 + T cells, CD4 + T cells, macrophages, neutrophils and dendritic cells). In addition, DNA methylation analysis indicated that the global methylation levels of ALKBH1/2/4/5/6/8 and FTO were decreased, while the global methylation levels of ALKBH3/7 were increased. In addition, the patients with upregulated ALKBH2 have significantly poor overall survival (OS) and post-progressive survival (PPS). Taken together, our work could provide insightful information about aberrant AlkB family members as potential biomarkers for the diagnostic and prognostic evaluation of LUAD. Especially, ALKBH2 could be served as a therapeutic candidate for treating LUAD.

A role of the Nse4 kleisin and Nse1/Nse3 KITE subunits in the ATPase cycle of SMC5/6

The SMC (Structural Maintenance of Chromosomes) complexes are composed of SMC dimers, kleisin and kleisin-interacting (HAWK or KITE) subunits. Mutual interactions of these subunits constitute the basal architecture of the SMC complexes. In addition, binding of ATP molecules to the SMC subunits and their hydrolysis drive dynamics of these complexes. Here, we developed new systems to follow the interactions between SMC5/6 subunits and the relative stability of the complex. First, we show that the N-terminal domain of the Nse4 kleisin molecule binds to the SMC6 neck and bridges it to the SMC5 head. Second, binding of the Nse1 and Nse3 KITE proteins to the Nse4 linker increased stability of the ATP-free SMC5/6 complex. In contrast, binding of ATP to SMC5/6 containing KITE subunits significantly decreased its stability. Elongation of the Nse4 linker partially suppressed instability of the ATP-bound complex, suggesting that the binding of the KITE proteins to the Nse4 linker constrains its limited size. Our data suggest that the KITE proteins may shape the Nse4 linker to fit the ATP-free complex optimally and to facilitate opening of the complex upon ATP binding. This mechanism suggests an important role of the KITE subunits in the dynamics of the SMC5/6 complexes.

Molecular Insights into the Architecture of the Human SMC5/6 Complex

A family of Structural Maintenance of Chromosome (SMC) complexes is essential for key cellular processes ensuring proper cohesion, condensation and replication. They share a common SMC-kleisin architecture allowing them to embrace DNA. In SMC5/6, the NSE1 and NSE3 KITE and NSE4 kleisin subunits form a stable subcomplex that binds DNA and regulates essential processes. In addition, NSE5 and NSE6 subunits associate with the core SMC5/6 complex and recruit it to DNA repair sites. The architecture of the SMC5/6 complex is crucial for its proper functioning, and mutations within the human SMC5/6 subunits result in severe syndromes. Therefore, we aimed to analyze interactions within the human SMC5/6 complex and determine its detailed architecture. Firstly, we analyzed different parts of SMC5/6 by crosslinking and MS/MS analysis. Our data suggested domain arrangements of hNSE1-hNSE3 and orientation of hNSE4 within the hNSE1-hNSE3-hNSE4 subcomplex. The crosslinking and electron microscopic analysis of the SMC5/6 core complex showed its rod-like architecture with juxtaposed hSMC5-hSMC6 arms. Additionally, we observed fully or partially opened hSMC5-hSMC6 shapes with the hNSE1-hNSE3-hNSE4 trimer localized in the SMC head domains. To complete mapping of the human SMC5/6 complex architecture, we analyzed positions of hNSE5-hNSE6 at the hSMC5-hSMC6 arms. We showed that hNSE6 binding to hNSE5 and the coiled-coil arm of hSMC6 is mediated by a conserved FAM178 domain, which we therefore renamed CANIN (Coiled-coil SMC6 And NSE5 INteracting) domain. Interestingly, hNSE6 bound both hSMC5 and hSMC6 arms, suggesting that hNSE6 may lock the arms and regulate the dynamics of the human SMC5/6 complex.

Multiscale Visual Drilldown for the Analysis of Large Ensembles of Multi-Body Protein Complexes

When studying multi-body protein complexes, biochemists use computational tools that can suggest hundreds or thousands of their possible spatial configurations. However, it is not feasible to experimentally verify more than only a very small subset of them. In this paper, we propose a novel multiscale visual drilldown approach that was designed in tight collaboration with proteomic experts, enabling a systematic exploration of the configuration space. Our approach takes advantage of the hierarchical structure of the data - from the whole ensemble of protein complex configurations to the individual configurations, their contact interfaces, and the interacting amino acids. Our new solution is based on interactively linked 2D and 3D views for individual hierarchy levels. At each level, we offer a set of selection and filtering operations that enable the user to narrow down the number of configurations that need to be manually scrutinized. Furthermore, we offer a dedicated filter interface, which provides the users with an overview of the applied filtering operations and enables them to examine their impact on the explored ensemble. This way, we maintain the history of the exploration process and thus enable the user to return to an earlier point of the exploration. We demonstrate the effectiveness of our approach on two case studies conducted by collaborating proteomic experts.

Visual Analysis of Protein-Protein Interaction Docking Models Using COZOID Tool

Networks of protein-protein interactions (PPI) constitute either stable or transient complexes in every cell. Most of the cellular complexes keep their function, and therefore stay similar, during evolution. The evolutionary constraints preserve most cellular functions via preservation of protein structures and interactions. The evolutionary conservation information is utilized in template-based approaches, like protein structure modeling or docking. Here we use the combination of the template-free docking method with conservation-based selection of the best docking model using our newly developed COZOID tool.We describe a step-by-step protocol for visual selection of docking models, based on their similarity to the original protein complex structure. Using the COZOID tool, we first analyze contact zones of the original complex structure and select contact amino acids for docking restraints. Then we model and dock the homologous proteins. Finally, we utilize different analytical modes of our COZOID tool to select the docking models most similar to the original complex structure.

A Single Conserved Amino Acid Residue as a Critical Context-Specific Determinant of the Differential Ability of Mdm2 and MdmX RING Domains to Dimerize

Mdm2 and MdmX are related proteins serving in the form of the Mdm2 homodimer or Mdm2/MdmX heterodimer as an E3 ubiquitin ligase for the tumor suppressor p53. The dimerization is required for the E3 activity and is mediated by the conserved RING domains present in both proteins, but only the RING domain of Mdm2 can form homodimers efficiently. We performed a systematic mutational analysis of human Mdm2, exchanging parts of the RING with the corresponding MdmX sequence, to identify the molecular determinants of this difference. Mdm2 can also promote MdmX degradation, and we identified several mutations blocking it. They were located mainly at the Mdm2/E2 interface and did not disrupt the MdmX-Mdm2 interaction. Surprisingly, some mutations of the Mdm2/E2 interface inhibited MdmX degradation, which is mediated by the Mdm2/MdmX heterodimer, but did not affect p53 degradation, mediated by the Mdm2 homodimer. Only one mutant, replacing a conserved cysteine 449 with asparagine (C449N), disrupted the ability of Mdm2 to dimerize with MdmX. When we introduced the cysteine residue into the corresponding site in MdmX, the RING domain became capable of forming dimers with other MdmX molecules in vivo, suggesting that one conserved amino acid residue in the RINGs of Mdm2 and MdmX could serve as the determinant of the differential ability of these domains to form dimers and their E3 activity. In immunoprecipitations, however, the homodimerization of MdmX could be observed only when the asparagine residue was replaced with cysteine in both RINGs. This result suggested that heterocomplexes consisting of one mutated MdmX RING with cysteine and one wild-type MdmX RING with asparagine might be less stable, despite being readily detectable in the cell-based assay. Moreover, Mdm2 C449N blocked Mdm2-MdmX heterodimerization but did not disrupt the ability of Mdm2 homodimer to promote p53 degradation, suggesting that the effect of the conserved cysteine and asparagine residues on dimerization was context-specific. Collectively, our results indicate that the effects of individual exchanges of conserved residues between Mdm2 and MdmX RING domains might be context-specific, supporting the hypothesis that Mdm2 RING homodimers and Mdm2-MdmX heterodimers may not be entirely structurally equivalent, despite their apparent similarity.