Recent progress in protein structure prediction significantly enhanced integrative structure modeling of large macromolecular assemblies by providing improved structural coverage for individual proteins and protein-protein interactions. However, direct prediction of large protein assemblies remains a challenge. I will introduce CombFold, a hierarchical and combinatorial assembly algorithm...
To perform their functions, proteins frequently interact with other proteins and nucleic acids. Detailed information on these interactions can be obtained from the three-dimensional structures of the corresponding protein-protein or protein-nucleic acid complexes. Since the experimental structure determination is often tedious and expensive, computational structure prediction methods are...
Studying specificity in protein–glycosaminoglycan recognition with umbrella sampling
Abstract
Glycosaminoglycans (GAGs) with repeating disaccharide units intricately engage with proteins, playing a crucial role in the spatial organization of the extracellular matrix and the transduction of biological signals in...
Molecular visualization is a critical task usually performed by structural biologists and bioinformaticians to aid three processes that are essential in science and fundamental to understand structural molecular biology: synthesis, analysis and communication [1].
Here we present VTX, a molecular visualization software that includes a real-time high-performance molecular graphics engine...
Given a molecular structure, it can be represented as a set of atomic balls, each ball having a van der Waals radius corresponding to the atom type. A ball can be assigned a region of space that contains all the points that are closer (or equally close) to that ball than to any other. Such a region is called a Voronoi cell and the partitioning of space into Voronoi cells is called Voronoi...
The number of known folds is limited to a few thousand and this number is surprisingly low, several orders of magnitude lower than the number of sequences in the biosphere. Biological or physical constraints may considerably limit the repertoire of folds. In this case, structural convergence should be frequent. However, several studies showed that distribution in proteomes may be a global...
The elucidation of different conformations of biomolecular complexes is the key to understand the molecular mechanisms behind the biological functions of the complexes and the key to novel drug discovery. Single-particle cryo electron microscopy (cryo-EM) allows 3D reconstruction of multiple conformations of purified biomolecular complexes from their 2D images. Cryo electron tomography...
Peripheral membrane proteins (PMPs) are soluble proteins that bind transiently to the surface of cell membranes. Having the ability to exist in both a soluble and a membrane-bound form their membrane-binding region is constrained to retain a fine balance of polar and hydrophobic character, which makes it difficult to distinguish it from the rest of their surface. As a result peripheral...
Histone chaperones play a crucial role in regulating the assembly and disassembly of chromatin. Our lab recently reported a novel chaperone binding mode in which histone chaperone APLF single-handedly assembled the histone complexes H2A-H2B and H3-H4 into the histone octamer. The chaperone domain of APLF consists of a short (~60 aa) intrinsically disordered, highly acidic domain (AD). As we...
The continuous development of the methods for the protein structure prediction was taking advantage from the precious experimental information obtained by structural biology as well as by sequencing of multiple organisms. Indeed, the general developed pipeline is based on determining conformations of protein fragments, and then using multiple sequence alignments to obtain long-range distances...
The Nuclear Pore Complex (NPC) is one of the larger macromolecular complexes in eukaryotic cells. The NPC facilitates rapid and selective transport between the cytoplasm and the nucleus. Existing models of transport do not provide quantitative mechanistic explanations of how some key emergent properties such as the rapid transport rates of molecules as large as ribosomal units and viral...
Protein oligomers can modify their overall architecture in response to changes in the environment, such as ion concentration and composition, the presence of small ligands or mechanic stress. These changes may involve small variations in the subunit-subunit interface which can lead to important changes in the overall shape due to multiplication effect. They may also involve large interface...
Rotary ATPases are multisubunit enzyme complexes that couple synthesis or hydrolysis of ATP molecules with transport of ions across a membrane. Their transmembrane part includes a homo- or a heterooligomer of c subunits called a c-ring, with a patch of several lipids confined inside it. Little is known about this patch; it is usually not well resolved in experimental structures, but it is...
AlphaFold2 predictions for the human proteome reveal that the great majority of all human proteins contain intrinsically disordered regions (IDRs) or do not cotnain a folded domain at all. The structure of such proteins must be represented by an ensemble of conformers. However, most experimental techniques provide ensemble-average restraints, which do not contain direct information on width of...
Bacterial infections remain a major public concern due to the accelerated increase in the appearance of antibiotic resistance. Among the different mechanisms used by bacteria to resist to antibiotics, the active efflux plays a major role. In Gram-negative bacteria, this is achieved by tripartite efflux pumps that form a macromolecular assembly spanning both membranes of the cellular wall, the...
Cryo-Electron Microscopy (cryo-EM) allows conformational studies of macromolecular complexes in their close-to-native state, essential for understanding their working mechanisms and for structure-based drug development. However, deciphering continuous conformational transitions of macromolecules, through the main cryo-EM processing techniques, Single Particle Analysis (SPA) and cryo-Electron...
Over the past five years, structural biology has undergone a significant progress. The Nobel Prize in Chemistry awarded in 2017 to the developers of cryo-electron microscopy (cryo-EM) marked a milestone, and the rapid progress and widespread adoption of this technique have demonstrated that the precise structural analysis of biomacromolecules is not limited to crystallography or solution...
Life has adapted to extreme conditions on Earth. One of the most striking evidences of adaptation to extreme environments are bacteria that are capable of thriving in a vast temperature range, from below 0° C in glacial waters to above 100° C in deep-sea hydrothermal vents. It is known that the individual molecular components of these organisms, exhibit enhanced stability and resistance to the...
Integrative structural biology of cell extracts bridges the gap between the high resolution structural characterisation of highly purified, isolated biomolecules and in situ electron tomography. This booming technique combines mass spectrometry (MS)-based proteomics and cryo-electron microscopy (cryo-EM) of fractionated cell extracts to quantitatively and structurally characterise endogenous...
Intrinsically disordered proteins (IDPs) lack clearly defined structure and are therefore highly flexible and easily adaptable to different binding partners. This makes them important players in many biological processes, often with vital regulatory functions. Their dynamic features and broad range of interaction modes, however, render them difficult to study and analyzing their complexes...
Unraveling the mysteries of Intrinsically Disordered Proteins (IDPs) and Regions (IDRs) is one of the greatest challenges in the 21st century. The flexibility of these regions allow proteins to adopt vastly different conformations, allowing them to facilitate the binding and unbinding of vital activation sites. These regions, even in well-studied proteins such as the tumor...
Respiratory complexes located in the internal membranes of our mitochondria are true macromolecular batteries: they couple the flow of electrons through clusters of metals and cofactors with a transfer of protons to create a gradient that provides the energy necessary for the ATP production and therefore to the nourishment of essential life processes. The first complex in the respiratory...
Homorepeats, repetitive sequences inserted in disordered proteins, play fundamental roles in biology and mutations in these low-complexity regions are linked to several neurodegenerative and developmental diseases. Despite their relevance, the structural characterization and modelling of these proteins remain challenging. From an experimental perspective, the severe signal overlap of their NMR...
Our group, Kiharalab, participated in both the prediction and scoring stages for complex targets. We combined three components in our pipeline, DistPepFold [1], AFSample [2], and a consensus-based score called ranksum we developed for our LZerD protein docking program [3]. For peptide docking, we used our new approach, DistPepFold. DistPepFold improves protein-peptide complex docking using an...
We have participated, both as predictors and as scorers, in all proposed targets of the 8th CAPRI edition. Here we will focus on the 11 purely CAPRI targets, that is, excluding the CASP-CAPRI joint rounds 46, 50 and 54, already evaluated and discussed in the respective CASP meetings, and the 4 targets in round 51 related to COVID19, with no available structure for evaluation. These 11 targets...
In the latest CAPRI round our group used a combination of Alphafold-Multimer (AFM), the ClusPro webserver for docking, and Molecular Dynamics based sampling to refine models for small targets. Assembly prediction was based on a two-stage methodology, in which we first generate an ensemble of initial models using AlphaFold-Multimer using standard protocol for MSA generation. We stop the...
Massive sampling with AlphaFold-multimer(1,2) showed impressive results for structural prediction of macromolecular assemblies at CASP15-CAPRI(3). Generating a very large number of predictions (>1000) and pushing their diversity by playing with the neural network model versions, the number of recycle steps, the use of templates or not and the activation of the dropout in the Evoformer and in...
In the field of structural biology, predicting protein interactions and designing sequences based on backbone scaffolds remain pivotal yet challenging tasks. Built on the same deep learning architectural framework, Protein Structure Transformer (PeSTo) and its derivative, CARBonAra, address these challenges. PeSTo employs geometric transformers to proficiently predict diverse protein binding...
In CASP15, 87 predictors submitted around 11,000 models on 41 assembly targets. The community demonstrated exceptional performance in overall fold and interface contact prediction, achieving an impressive success rate of 90% (compared to 31% in CASP14). This remarkable accomplishment is largely due to the incorporation of DeepMind’s AF2-Multimer approach into custom-built prediction pipelines....
Since the last CAPRI meeting, much has happened in the modeling field. Deep Learning (DL) has revolutionized structure prediction, and we are only beginning to grasp the fruits, as well as the new challenges uncovered in this new era.
I will describe different approaches that we developed and applied to address CAPRI challenges, and how they helped us shape and improve our ability to model,...
The HADDOCK team have participated as human and webserver predictor and/or scorer in last CAPRI rounds (47-55), mainly relying on the use of our integrative modelling software HADDOCK[1] which is able to use user-provided information to guide the docking process. An important element of HADDOCK is its scoring function, computed from the weighted sum of 4 energetical terms (VdW, Electrostatics,...
Protein-RNA interactions and recognition are essential in gene expression, regulation of transcription, and other biological processes. Prediction of protein and RNA is also a new challenge category for CAPRI and CASP. In this work, we proposed a multistage docking protocol called CoDockPR, which integrates the shape complementarity, knowledge-based scoring functions, and interface similarity...
Protein-DNA interactions play a significant role in biological processes and drug design owing to their prevalence. Computational methods for predicting protein-DNA complex structures serve as a valuable alternative to experimental methods, which, although more accurate, are also time-consuming and resource-intensive. The established framework for predicting protein-protein complex structures...
Understanding the functions of protein-protein and protein-nucleic acid complexes relies on the knowledge of their 3D structures that can either be solved experimentally or predicted computationally. While AlphaFold has revolutionized protein structure prediction, challenges remain, particularly in modeling antibody-antigen interactions, protein-nucleic acid complexes, and proteins lacking...
In this talk I will introduce our recent works on machine learning for protein-ligand interactions, including explainable prediction of protein-ligand binding affinity and structure-based de novo ligand design.
First, as deep learning methods for modeling protein-ligand interactions are increasingly improving their accuracy, their interpretability is often under-explored. We had...
Macromolecular complexes play a crucial role in almost all biological functions in living cells. Elucidating structural features in proteins is essential to understanding their underlying functions and binding activity. With the rapid accumulation of protein-structure data through AI methods and experimental techniques, such as cryo-electron microscopy, there is a growing demand for efficient...
Rotary ATP synthases are large enzyme complexes present in every living cell. They consist of a transmembrane and a soluble domain, each comprising multiple subunits. The transmembrane part contains an oligomeric rotor ring (c-ring), whose stoichiometry defines the ratio between the number of synthesized ATP molecules and the number of ions transported through the membrane. Here, we present...
The understanding of biochemical processes and the machinery of life hinges on comprehending the structural aspects of macromolecular interactions. This requires a systematic approach to analysing the vast manifold of macromolecular associations, or complexes, typically determined from crystallographic or electron microscopy experiments. Specific points of interest include similarity...
The Pierce group has utilized a combination of AlphaFold and traditional docking methods, including Rosetta and ZDOCK, to model protein complexes in recent CAPRI and CASP/CAPRI rounds. This has led to success for several challenging targets, as well as useful lessons learned for prospective modeling efforts. Our group has been particularly focused on the utilization and adaptation of AlphaFold...
Macromolecular complexes are key functional components in nearly all biological processes, and achieving an atomic-level understanding of them is crucial for unravelling their molecular mechanisms. The Protein Data Bank (PDB) is the primary worldwide repository of experimentally determined macromolecular structures, offering valuable insights into the dynamics, conformations, and functional...
Computational design of peptides that can (a) recognize/bind to specific protein interfaces and (b) self-assemble into nano-scale architectures such as β-sheet-based fibrils (amyloid) have potential applications in healthcare and advanced biomaterial fabrication. Screening sequence space via experiments to discover peptides that bind to proteins and self-assemble is challenging, although some...
Traditional protein-protein docking algorithms often rely on extensive candidate sampling and subsequent re-ranking. However, these steps are time-consuming, limiting their applicability in scenarios requiring high-throughput complex structure prediction, such as structure-based virtual screening. The advent of deep learning methods has brought acceleration to the docking process, leveraging...
Sac7d is a 7kDa protein belonging to the class of the small chromosomal proteins
from archeon Sulfolobus acidocaldarius. Sac7d was discovered in 1974 in Yellowtone
National Parks geysers, and studied extensively since then for its remarkable
stability at large pH and temperature ranges. Sac7d binds to DNA minor groove to
protect DNA from these extreme conditions by increasing its melting...
