Biology subjects

Ben-Tal, N.

Publications and source records attributed to Ben-Tal, N..

13 recordsLinked to original sources

bioRxiv2026

N-Zinclopedia: A database of predicted transition metal-binding sites and metalloenzymes

Metal ions are among the most common enzymatic cofactors, yet metal utilization remains poorly mapped. Here, we present N-Zinclopedia, an atlas of predicted transition metal-binding sites and candidate metalloenzymes across protein fold space. N-Zinclopedia catalogs protein sites compatible with transition metal coordination, identified using ZincSight screening of protein structure model databases. We focused on previously uncharacterized domains and proteins, screening for transition metal-binding sites within over a million of these, spanning both poorly annotated and canonical folds. We also classified the predicted sites, using MAHOMES-II, as candidate catalytic or non-catalytic metal-binding sites. Experimental characterization of a previously unknown zinc binding site confirms that ZincSight can determine previously un-annotated zinc binding. N-Zinclopedia significantly expands the known landscape of metal utilization, providing numerous predictions that await experimental examination. N-Zinclopedia is available at: https://bentallab.github.io/nzinclopedia.

bioinformatics↗

bioRxiv2025

Contrastive learning unites sequence and structure in a global representation of protein space

Amino acid sequence dictates the three-dimensional structure and biological function of proteins. Yet, despite decades of research, our understanding of the interplay between sequence and structure is incomplete. To meet this challenge, we introduce Contrastive Learning Sequence-Structure (CLSS), an AI-based contrastive learning model trained to co-embed sequence and structure information in a self-supervised manner. We trained CLSS on large and diverse sets of protein building blocks called domains. CLSS represents both sequences and structures as vectors in the same high-dimensional space, where distance relates to sequence-structure similarity. Thus, CLSS provides a natural way to represent the protein universe, reflecting evolutionary relationships, as well as structural changes. We find that CLSS refines expert knowledge about the global organization of protein space, and highlights transitional forms that resist hierarchical classification. CLSS reveals linkage between domains of seemingly separate lineages, thereby significantly improving our understanding of evolutionary design.

bioinformatics↗

bioRxiv2023

Computational analysis of long-range allosteric communications in CFTR

Malfunction of the CFTR protein results in cystic fibrosis, one of the most common hereditary diseases. CFTR functions as an anion channel, the gating of which is controlled by long- range allosteric communications. Allostery also has direct bearings on CF treatment: the most effective CFTR drugs modulate its activity allosterically. Herein, we integrated Gaussian Network Model, Transfer Entropy, and Anisotropic Normal Mode-Langevin dynamics and investigated the allosteric communications network of CFTR. The results are in remarkable agreement with experimental observations and mutational analysis and provide extensive novel insight. We identified residues that serve as pivotal allosteric sources and transducers, many of which correspond to disease causing mutations. We find that in the ATP-free form, dynamic fluctuations of the residues that comprise the ATP binding sites facilitate the initial binding of the nucleotide. Subsequent binding of ATP then brings to the fore and focuses dynamic fluctuations that were present in a latent and diffuse form in the absence of ATP. We demonstrate that drugs that potentiate CFTRs conductance do so not by directly acting on the gating residues, but rather by mimicking the allosteric signal sent by the ATP binding sites. We have also uncovered a previously undiscovered allosteric "hotspot" located proximal to the docking site of the phosphorylated Regulatory (R) domain, thereby establishing a molecular foundation for its phosphorylation- dependent excitatory role. This study unveils the molecular underpinnings of allosteric connectivity within CFTR and highlights a novel allosteric "hotspot" that could serve as a promising target for the development of novel therapeutic interventions.

biophysics↗

bioRxiv2023

Alleviating the barrier of adventitious roots formation in recalcitrant mature tissue by slow release of a synthetic auxin

Clonal propagation of plants by induction of adventitious roots (ARs) from stem cuttings is a requisite step in breeding programs. A major barrier exists for propagating valuable plants that naturally have low capacity to form ARs. Due to the central role of auxin in organogenesis, indole-3-butyric acid (IBA) is often used as part of commercial rooting mixtures, yet many recalcitrant plants do not form ARs in response to this treatment. Here, we describe the synthesis and screening of a focused library of synthetic auxin conjugates in Eucalyptus grandis cuttings and identify 4-chlorophenoxyacetic acid-L-tryptophan-OMe as a competent enhancer of adventitious rooting in a number of recalcitrant woody plants, including apple and argan. Comprehensive metabolic and functional analyses reveal that this activity is engendered by prolonged auxin signaling due to initial fast uptake and slow release and clearance of the free auxin 4-chlorophenoxyacetic acid. This work highlights the utility of a slow-release strategy for bioactive compounds for more effective plant growth regulation.

plant biology↗

bioRxiv2022

Proteins with multiple G protein-coupled receptor domains

Currently known G protein-coupled receptors (GPCRs) have a single transmembrane domain. Many GPCRs form dimers that have two transmembrane domains (one per protein), and there are indications that this dimeric interaction is functionally meaningful. Here, based on sequence analysis and structure predictions, we report the existence of 57 proteins with two, three, or four GPCR domains within the same protein chain. We analyze the structures of these multi-GPCRs and show that almost all have DRY/NPxxY motifs, a strong indication of signaling activity. By homology, most of the multi-GPCRs that we identified are olfactory-related; a few are chemokine-related. Multi-GPCR candidates are found in various Chordata species including fish, camel, marmite, Chinese hamster, and new world monkeys. The discovery of receptors with multiple transmembrane domains suggests the possibility for signal regulation and amplification within an individual receptor, revealing another step in GPCR evolution and a new layer of complexity in signal transduction.

bioinformatics↗

bioRxiv2022

Allosteric links between the hydrophilic N-terminus and transmembrane core of human Na+/H+ antiporter NHA2

The human Na+/H+ antiporter NHA2 (SLC9B2) transports Na+ or Li+ across the plasma membrane in exchange for protons, and is implicated in various pathologies. It is a 537 amino acids protein with an 82 residues long hydrophilic cytoplasmic N-terminus followed by a transmembrane part comprising 14 transmembrane helices. We optimized the functional expression of HsNHA2 in the plasma membrane of a salt-sensitive Saccharomyces cerevisiae strain and characterized a set of mutated or truncated versions of HsNHA2 in terms of their substrate specificity, transport activity, localization and protein stability. We identified a highly conserved proline 246, located in the core of the protein, as being crucial for ion selectivity. The replacement of P246 with serine or threonine resulted in antiporters with altered substrate specificity and increased resistance to the HsNHA2-specific inhibitor phloretin that were not only highly active at an acidic pH of 4.0 (like the native antiporter), but also at neutral pH. We also experimentally confirmed the importance of a putative salt bridge between E215 and R432 for antiporter function and structural integrity. Truncations of the first 50 - 70 residues of the N-terminus doubled the transport activity of HsNHA2, whilst changes in the charge at positions E47, E56, K57, or K58 decreased the antiporters transport activity. Thus, the hydrophilic N-terminal part of the protein appears to allosterically autoinhibit its cation transport. Our data also show this in vivo approach to be useful for a rapid screening of SNPs effect on HsNHA2 activity.

molecular biology↗

bioRxiv2021

PredictProtein - Predicting Protein Structure and Function for 29 Years

Since 1992 PredictProtein (https://predictprotein.org) is a one-stop online resource for protein sequence analysis with its main site hosted at the Luxembourg Centre for Systems Biomedicine (LCSB) and queried monthly by over 3,000 users in 2020. PredictProtein was the first Internet server for protein predictions. It pioneered combining evolutionary information and machine learning. Given a protein sequence as input, the server outputs multiple sequence alignments, predictions of protein structure in 1D and 2D (secondary structure, solvent accessibility, transmembrane segments, disordered regions, protein flexibility, and disulfide bridges) and predictions of protein function (functional effects of sequence variation or point mutations, Gene Ontology (GO) terms, subcellular localization, and protein-, RNA-, and DNA binding). PredictProteins infrastructure has moved to the LCSB increasing throughput; the use of MMseqs2 sequence search reduced runtime five-fold; user interface elements improved usability, and new prediction methods were added. PredictProtein recently included predictions from deep learning embeddings (GO and secondary structure) and a method for the prediction of proteins and residues binding DNA, RNA, or other proteins. PredictProtein.org aspires to provide reliable predictions to computational and experimental biologists alike. All scripts and methods are freely available for offline execution in high-throughput settings. AvailabilityFreely accessible webserver PredictProtein.org; Source and docker images: github.com/rostlab

bioinformatics↗

bioRxiv2021

Gram-negative outer membrane proteins with multiple β-barrel domains

Outer membrane beta barrels (OMBBs) are found in the outer membrane of Gram-negative bacteria and eukaryotic organelles. OMBBs fold as antiparallel {beta}-sheets that close onto themselves, forming pores that traverse the membrane. Currently known structures include only one barrel, of 8-36 strands, per chain. The lack of multi-OMBB chains is surprising, as most OMBBs form oligomers and some function only in this state. Using a combination of sensitive sequence-comparison methods and co-evolutionary analysis tools, we identify many proteins combining multiple beta barrels within a single chain; combinations that include 8-stranded barrels prevail. These multi-barrels seem to be the result of independent, lineage-specific fusion and amplification events. The absence of multi-barrels that are universally conserved in bacteria with an outer membrane, coupled with their frequent de novo genesis suggests that their functions are not essential, but rather beneficial in specific environments. Adjacent barrels of complementary function within the same chain may allow for new functions beyond those of the individual barrels.

biophysics↗

bioRxiv2021

Structure of plant PSI-plastocyanin complex reveals strong hydrophobic interactions.

Photosystem I is defined as plastocyanin-ferredoxin oxidoreductase. Taking advantage of genetic engineering, kinetic analyses and cryo-EM, our data provide novel mechanistic insights into binding and electron transfer between PSI and Pc. Structural data at 2.74 [A] resolution reveals strong hydrophobic interactions in the plant PSI-Pc ternary complex, leading to exclusion of water molecules from PsaA-PsaB / Pc interface once the PSI-Pc complex forms. Upon oxidation of Pc, a slight tilt of bound oxidized Pc allows water molecules to accommodate the space between Pc and PSI to drive Pc dissociation. Such a scenario is consistent with the six times larger dissociation constant of oxidized as compared to reduced Pc and mechanistically explains how this molecular machine optimized electron transfer for fast turnover. One Sentence SummaryGenetic engineering, kinetics and cryo-EM structural data reveal a mechanism in a major step of oxygenic photosynthesis

biochemistry↗

bioRxiv2020

Bridging themes: short protein segments found in different architectures

The vast majority of theoretically possible polypeptide chains do not fold, let alone confer function. Hence, protein evolution from preexisting building blocks has clear potential advantages over ab initio emergence from random sequences. In support of this view, sequence similarities between different proteins is generally indicative of common ancestry, and we collectively refer to such homologous sequences as themes. At the domain level, sequence homology is routinely detected. However, short themes which are segments, or fragments of intact domains, are particularly interesting because they may provide hints about the emergence of domains, as opposed to divergence of preexisting domains, or their mixing-and-matching to form multi-domain proteins. Here we identified 525 representative short themes, comprising 20-to-80 residues, that are unexpectedly shared between domains considered to have emerged independently. Among these bridging themes are ones shared between the most ancient domains, e.g., Rossmann, P-loop NTPase, TIM-barrel, Flavodoxin, and Ferredoxin-like. We elaborate on several particularly interesting cases, where the bridging themes mediate ligand binding. Ligand binding may have contributed to the stability and the plasticity of these building blocks, and to their ability to invade preexisting domains or serve as starting points for completely new domains.

molecular biology↗

bioRxiv2020

On the Emergence of P-Loop NTPase and Rossmann Enzymes from a Beta-Alpha-Beta Ancestral Fragment

Dating back to the last universal common ancestor (LUCA), the P-loop NTPases and Rossmanns now comprise the most ubiquitous and diverse enzyme lineages. Intriguing similarities in their overall architecture and phosphate binding motifs suggest common ancestry; however, due to a lack of sequence identity and some fundamental structural differences, these families are considered independent emergences. To address this longstanding dichotomy, we systematically searched for bridge proteins with structure and sequence elements shared by both lineages. We detected homologous segments that span the first {beta}{beta} segment of both lineages and include two key functional motifs: (i) a phosphate binding loop - the Walker A motif of P-loop NTPases or the Rossmann equivalent, both residing at the N-terminus of 1; and (ii) an Asp at the tip of {beta}2. The latter comprises the Walker B aspartate that chelates the catalytic metal in P-loop NTPases, or the canonical Rossmann {beta}2-Asp that binds the cofactors ribose moiety. Tubulin, a Rossmann GTPase, demonstrates the potential of the {beta}2-Asp to take either one of these two roles. We conclude that common P-loops/Rossmann ancestry is plausible, although convergence cannot be completely ruled out. Regardless, both lineages most likely emerged from a polypeptide comprising a {beta}{beta} segment carrying the above two functional motifs, a segment that comprises the core of both enzyme families to this very day.

evolutionary biology↗

bioRxiv2018

Evolution of Environmentally-Enforced, Repeat Protein Topology in the Outer Membrane

Outer membrane beta barrels (OMBBs) are the proteins on the surface of Gram negative bacteria. These proteins have diverse functions but only a single topology, the beta barrel. It has been suggested that this common fold is a repeat protein with the repeating unit of a beta hairpin. By grouping structurally solved OMBBs by sequence, a detailed evolutionary story unfolds. A strand-number based pathway manifests with progression from a primordial 8-stranded barrel to 16-stranded and then to 18-stranded barrels. The transitions from 16- to 18-stranded barrels show mechanisms of strand number variation without domain duplication, such as a loop to hairpin transition. This indicates that repeat protein topology can be perpetuated without genetic duplication likely because the topology is being enforced by the membrane environment. Moreover, we find the evolutionary trace is particularly prominent in the C-terminal half of OMBBs which may be relevant to understanding OMBB folding pathways.

biophysics↗

bioRxiv2018

Efflux Pumps Represent Possible Evolutionary Convergence onto the Beta Barrel Fold

There are around 100 types of integral outer membrane proteins in each Gram negative bacteria. All of these proteins have the same fold--an up-down {beta}-barrel. It has been suggested that all membrane {beta}-barrels other than lysins are homologous. Here we suggest that {beta}-barrels of efflux pumps have converged on this fold as well. By grouping structurally-solved outer membrane {beta}-barrels (OMBBs) by sequence we find evidence that the membrane environment may have led to convergent evolution of the barrel fold. Specifically, the lack of sequence linkage to other barrels coupled with distinctive structural differences, such as differences in strand tilt and barrel radius, suggest that efflux pumps have evolutionarily converged on the barrel. Finally, we find a possible ancestor for the OMBB efflux pumps as they are related to periplasmic components of the same pumps.

biophysics↗