scholarly journals A structural biology community assessment of AlphaFold 2 applications

2021 ◽  
Author(s):  
Mehmet Akdel ◽  
Douglas EV Pires ◽  
Eduard Porta-Pardo ◽  
Jurgen Janes ◽  
Arthur O Zalevsky ◽  
...  
Keyword(s):  
Structural Biology ◽  
Protein Complexes ◽  
Homology Modelling ◽  
Structural Data ◽  
Science Research ◽  
Structural Features ◽  
Structural Elements ◽  
Recent Developments ◽  
Transformative Impact ◽  
The Impact

Most proteins fold into 3D structures that determine how they function and orchestrate the biological processes of the cell. Recent developments in computational methods have led to protein structure predictions that have reached the accuracy of experimentally determined models. While this has been independently verified, the implementation of these methods across structural biology applications remains to be tested. Here, we evaluate the use of AlphaFold 2 (AF2) predictions in the study of characteristic structural elements; the impact of missense variants; function and ligand binding site predictions; modelling of interactions; and modelling of experimental structural data. For 11 proteomes, an average of 25% additional residues can be confidently modelled when compared to homology modelling, identifying structural features rarely seen in the PDB. AF2-based predictions of protein disorder and protein complexes surpass state-of-the-art tools and AF2 models can be used across diverse applications equally well compared to experimentally determined structures, when the confidence metrics are critically considered. In summary, we find that these advances are likely to have a transformative impact in structural biology and broader life science research.

Molecular Biology for Structural Biology

1999 ◽  
Author(s):  
P. F. Berne ◽  
S. Doublié
Keyword(s):  
Molecular Biology ◽  
Recombinant Protein ◽  
Structural Biology ◽  
Protein Complexes ◽  
Recombinant Expression ◽  
Expression System ◽  
Structural Data ◽  
Natural Source ◽  
Native Form ◽  
Number Of Publications

The number of published 3D structures has increased exponentially in the last decade and the resulting mass of structural data has contributed significantly to the understanding of mechanisms underlying the biology of living cells. However, these mechanisms are so complex that structural biologists face still greater challenges, such as the study of higher-order functional complexes. As an example, we can mention the protein complexes that assemble around activated growth factor receptors to allow the transduction of extracellular signals through the membrane and inside the cell (1). Because of their diverse intrinsic properties, proteins exhibit variable difficulty for structural biology studies. Before the rise of recombinant expression methods, only a minority of protein structures were determined, representing mainly favourable cases: proteins of high abundance in their natural source which could be purified and crystallized, in contrast to rare proteins that were often refractory to crystallization. The advent of methods for recombinant protein overexpression was a breakthrough in this area. It was followed by an increasing number of publications describing the crystallization of proteins, not under their native form, but in modified versions after sequence engineering. First we will consider the classical use of molecular biology applied to optimize the expression system for a recombinant protein for structural biology, without modification of its sequence. In the second part, we will deal with molecular biology procedures aimed at engineering the properties of a protein through sequence modifications in order to make its crystallization possible. In the last part we will give an example where molecular biology can help solve a crystallographic problem, namely that of phase determination by introducing anomalous scatterers (e.g. selenium atoms) into the protein of interest. Whenever extraction of a protein from its natural source appears unsuitable for structural studies, molecular biology resources can be brought in, initially aiming at choosing and setting up an appropriate expression system. This initial approach could involve comparing various expression hosts and vectors and deciding if the protein is to be produced as a fusion to facilitate its purification.

scholarly journals Analysis of the impact of molecular motions on the efficiency of XL-MS and the distance restraints in hybrid structural biology

2018 ◽  
Author(s):  
Vladimir Svetlov ◽  
Evgeny Nudler
Keyword(s):  
Structural Biology ◽  
Protein Complexes ◽  
Protein Docking ◽  
Protein Fold ◽  
Molecular Motions ◽  
Cross Link ◽  
Distance Restraints ◽  
Cross Links ◽  
Cross Linker ◽  
The Impact

AbstractCovalent cross-link mapping by mass spectrometry (XL-MS) is rapidly becoming the most widely used method of hybrid structural biology. We investigated the impact of incremental variations of cross-linker length have on the depth of XL-MS interrogation of protein-protein complexes, and assessed the role molecular motions in solution play in generation of cross-link-derived distance restraints. Supplementation of a popular NHS-ester cross-linker, DSS, with 2 reagents shorter or longer by CH2-CH2, increased the number of non-reductant cross-links by ~50%. Molecular dynamics simulations of these cross-linkers revealed 3 individual, partially overlapping ranges of motion, consistent with partially overlapping sets of cross-links formed by each reagent. Similar simulations elucidated protein fold-specific ranges of motions for the reactive and backbone atoms from rigid and flexible target domains. Together these findings create a quantitative framework for generation of cross-linker- and protein fold-specific distance restraints for XL-MS-guided protein-protein docking.

scholarly journals DNAproDB: an expanded database and web-based tool for structural analysis of DNA–protein complexes

2019 ◽  
Author(s):  
Jared M Sagendorf ◽  
Nicholas Markarian ◽  
Helen M Berman ◽  
Remo Rohs
Keyword(s):  
Structural Analysis ◽  
Protein Complexes ◽  
Structural Data ◽  
Data Bank ◽  
Structural Features ◽  
Analysis Tool ◽  
Web Based ◽  
Initial Release ◽  
Data Files ◽  
User Friendly

Abstract DNAproDB (https://dnaprodb.usc.edu) is a web-based database and structural analysis tool that offers a combination of data visualization, data processing and search functionality that improves the speed and ease with which researchers can analyze, access and visualize structural data of DNA–protein complexes. In this paper, we report significant improvements made to DNAproDB since its initial release. DNAproDB now supports any DNA secondary structure from typical B-form DNA to single-stranded DNA to G-quadruplexes. We have updated the structure of our data files to support complex DNA conformations, multiple DNA–protein complexes within a DNAproDB entry and model indexing for analysis of ensemble data. Support for chemically modified residues and nucleotides has been significantly improved along with the addition of new structural features, improved structural moiety assignment and use of more sequence-based annotations. We have redesigned our report pages and search forms to support these enhancements, and the DNAproDB website has been improved to be more responsive and user-friendly. DNAproDB is now integrated with the Nucleic Acid Database, and we have increased our coverage of available Protein Data Bank entries. Our database now contains 95% of all available DNA–protein complexes, making our tools for analysis of these structures accessible to a broad community.

Biological small-angle neutron scattering: recent results and development

2018 ◽  
Vol 74 (8) ◽  
pp. 715-726 ◽  
Author(s):  
Emilie Mahieu ◽  
Frank Gabel
Keyword(s):  
Membrane Proteins ◽  
Neutron Scattering ◽  
Structural Biology ◽  
Small Angle ◽  
Small Angle Neutron Scattering ◽  
Protein Complexes ◽  
Limited Range ◽  
Density Variation ◽  
Deuterium Labelling ◽  
Recent Developments

Small-angle neutron scattering (SANS) has increasingly been used by the structural biology community in recent years to obtain low-resolution information on solubilized biomacromolecular complexes in solution. In combination with deuterium labelling and solvent-contrast variation (H2O/D2O exchange), SANS provides unique information on individual components in large heterogeneous complexes that is perfectly complementary to the structural restraints provided by crystallography, nuclear magnetic resonance and electron microscopy. Typical systems studied include multi-protein or protein–DNA/RNA complexes and solubilized membrane proteins. The internal features of these systems are less accessible to the more broadly used small-angle X-ray scattering (SAXS) technique owing to a limited range of intra-complex and solvent electron-density variation. Here, the progress and developments of biological applications of SANS in the past decade are reviewed. The review covers scientific results from selected biological systems, including protein–protein complexes, protein–RNA/DNA complexes and membrane proteins. Moreover, an overview of recent developments in instruments, sample environment, deuterium labelling and software is presented. Finally, the perspectives for biological SANS in the context of integrated structural biology approaches are discussed.

scholarly journals A quantitative mapping approach to identify direct interactions within complexomes

2021 ◽  
Author(s):  
Philipp Trepte ◽  
Christopher Secker ◽  
Soon Gang Choi ◽  
Julien Olivet ◽  
Eduardo Silva Ramos ◽  
...  
Keyword(s):  
Structural Biology ◽  
Protein Complexes ◽  
Affinity Purification ◽  
3D Structure ◽  
Binary Interaction ◽  
Live Cells ◽  
Distance Measurements ◽  
Polyglutamine Expansion ◽  
Multiprotein Complexes ◽  
The Impact

ABSTRACTComplementary methods are required to fully characterize all protein complexes, or the complexome, of a cell. Affinity purification coupled to mass-spectrometry (AP-MS) can identify the composition of complexes at proteome-scale. However, information on direct contacts between subunits is often lacking. In contrast, solving the 3D structure of protein complexes can provide this information, but structural biology techniques are not yet scalable for systematic, proteome-wide efforts. Here, we optimally combine two orthogonal high-throughput binary interaction assays, LuTHy and N2H, and demonstrate that their quantitative readouts can be used to differentiate direct interactions from indirect associations within multiprotein complexes. We also show that LuTHy allows accurate distance measurements between proteins in live cells and apply these findings to study the impact of the polyglutamine expansion mutation on the structurally unresolved N-terminal domain of Huntingtin. Thus, we present a new framework based on quantitative interaction assays to complement structural biology and AP-MS techniques, which should help to provide first-approximation contact maps of multiprotein complexes at proteome-scale.Graphical Abstract

Mass Spectrometry for Structural Biology: Determining the Composition and Architecture of Protein Complexes

2011 ◽  
Vol 64 (6) ◽  
pp. 681 ◽  
Author(s):  
Tara L. Pukala
Keyword(s):  
Mass Spectrometry ◽  
Structural Biology ◽  
Protein Interactions ◽  
Structural Investigation ◽  
Protein Complexes ◽  
Individual Species ◽  
Protein Protein Interactions ◽  
Identify Protein Complex ◽  
Technological Advances ◽  
Recent Developments

Knowledge of protein structure and protein–protein interactions is vital for appreciating the elaborate biochemical pathways that underlie cellular function. While many techniques exist to probe the structure and complex interplay between functional proteins, none currently offer a complete picture. Mass spectrometry and associated methods provide complementary information to established structural biology tools, and with rapidly evolving technological advances, can in some cases even exceed other techniques by its diversity in application and information content. This is primarily because of the ability of mass spectrometry to precisely identify protein complex stoichiometry, detect individual species present in a mixture, and concomitantly offer conformational information. This review describes the attributes of mass spectrometry for the structural investigation of multiprotein assemblies in the context of recent developments and highlights in the field.

scholarly journals Analysing structural data to explore the function of an essential bacterial protein foldase

2021 ◽  
Author(s):  
Samuel F. Haysom
Keyword(s):  
Structural Biology ◽  
Protein Structures ◽  
Structural Data ◽  
Science Research ◽  
Gram Negative Bacteria ◽  
Bacterial Protein ◽  
Outer Membranes ◽  
Fundamental Part ◽  
3D Data ◽  
Shape Changes

Structural biology, or the study of how protein structures dictate their function, is a fundamental part of life science research, allowing the mechanisms underpinning life to be unravelled at the molecular level. Due to the complexity of 3D data, researchers often use special visualization methods to extract useful information from protein structures. This article uses the most common of these visualisation methods to examine different structures of the β-barrel assembly machinery complex (BAM), an essential protein that folds other proteins into the outer-membranes of Gram-negative bacteria. By exploring how BAM’s 3D shape changes as it interacts with its substrates throughout the folding process, it is possible to reconstruct a potential mechanism for this molecular machine that can be used to drive further research.

Influence of the distribution of the shear walls on the seismic response of the buildings

2020 ◽  
Vol 15 (1) ◽  
pp. 37-44
Author(s):  
El Mehdi Echebba ◽  
Hasnae Boubel ◽  
Oumnia Elmrabet ◽  
Mohamed Rougui
Keyword(s):  
Structural Analysis ◽  
Seismic Response ◽  
Natural Frequency ◽  
Structural Design ◽  
Structural Response ◽  
Shear Walls ◽  
Structural Elements ◽  
Analysis Software ◽  
Ansys Apdl ◽  
The Impact

Abstract In this paper, an evaluation was tried for the impact of structural design on structural response. Several situations are foreseen as the possibilities of changing the distribution of the structural elements (sails, columns, etc.), the width of the structure and the number of floors indicates the adapted type of bracing for a given structure by referring only to its Geometric dimensions. This was done by studying the effect of the technical design of the building on the natural frequency of the structure with the study of the influence of the distribution of the structural elements on the seismic response of the building, taking into account of the requirements of the Moroccan earthquake regulations 2000/2011 and using the ANSYS APDL and Robot Structural Analysis software.

Rapid Online Buffer Exchange: A Method for Screening of Proteins, Protein Complexes, and Cell Lysates by Native Mass Spectrometry

2019 ◽  
Author(s):  
Zachary VanAernum ◽  
Florian Busch ◽  
Benjamin J. Jones ◽  
Mengxuan Jia ◽  
Zibo Chen ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
High Speed ◽  
Structural Information ◽  
Protein Complexes ◽  
High Sensitivity ◽  
Native Mass Spectrometry ◽  
Structural Features ◽  
Consumer Products ◽  
Cell Lysates ◽  
Protein Expression And Purification

It is important to assess the identity and purity of proteins and protein complexes during and after protein purification to ensure that samples are of sufficient quality for further biochemical and structural characterization, as well as for use in consumer products, chemical processes, and therapeutics. Native mass spectrometry (nMS) has become an important tool in protein analysis due to its ability to retain non-covalent interactions during measurements, making it possible to obtain protein structural information with high sensitivity and at high speed. Interferences from the presence of non-volatiles are typically alleviated by offline buffer exchange, which is timeconsuming and difficult to automate. We provide a protocol for rapid online buffer exchange (OBE) nMS to directly screen structural features of pre-purified proteins, protein complexes, or clarified cell lysates. Information obtained by OBE nMS can be used for fast (<5 min) quality control and can further guide protein expression and purification optimization.

Protein Interaction Domains and Post-Translational Modifications: Structural Features and Drug Discovery Applications

2020 ◽  
Vol 27 (37) ◽  
pp. 6306-6355 ◽  
Author(s):  
Marian Vincenzi ◽  
Flavia Anna Mercurio ◽  
Marilisa Leone
Keyword(s):  
Drug Discovery ◽  
Protein Interaction ◽  
Protein Interactions ◽  
Structural Information ◽  
Protein Complexes ◽  
Structural Features ◽  
Protein Protein Interactions ◽  
Modular Architecture ◽  
Post Translational Modifications ◽  
Interaction Domains

Background:: Many pathways regarding healthy cells and/or linked to diseases onset and progression depend on large assemblies including multi-protein complexes. Protein-protein interactions may occur through a vast array of modules known as protein interaction domains (PIDs). Objective:: This review concerns with PIDs recognizing post-translationally modified peptide sequences and intends to provide the scientific community with state of art knowledge on their 3D structures, binding topologies and potential applications in the drug discovery field. Method:: Several databases, such as the Pfam (Protein family), the SMART (Simple Modular Architecture Research Tool) and the PDB (Protein Data Bank), were searched to look for different domain families and gain structural information on protein complexes in which particular PIDs are involved. Recent literature on PIDs and related drug discovery campaigns was retrieved through Pubmed and analyzed. Results and Conclusion:: PIDs are rather versatile as concerning their binding preferences. Many of them recognize specifically only determined amino acid stretches with post-translational modifications, a few others are able to interact with several post-translationally modified sequences or with unmodified ones. Many PIDs can be linked to different diseases including cancer. The tremendous amount of available structural data led to the structure-based design of several molecules targeting protein-protein interactions mediated by PIDs, including peptides, peptidomimetics and small compounds. More studies are needed to fully role out, among different families, PIDs that can be considered reliable therapeutic targets, however, attacking PIDs rather than catalytic domains of a particular protein may represent a route to obtain selective inhibitors.

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