Toward Revealing Protein Function: Identifying Biologically Relevant Clusters With Graph Spectral Methods

2019 ◽  
pp. 375-409 ◽  
Author(s):  
Robin Davies ◽  
Urmi Ghosh-Dastidar ◽  
Jeff Knisley ◽  
Widodo Samyono
Keyword(s):  
Spectral Methods ◽  
Protein Function ◽  
Biologically Relevant

scholarly journals Impact of fluorescent protein fusions on the bacterial flagellar motor

2017 ◽  
Author(s):  
M Heo ◽  
AL Nord ◽  
D Chamousset ◽  
E van Rijn ◽  
HJE Beaumont ◽  
...  
Keyword(s):  
Side Effects ◽  
Protein Function ◽  
Fusion Proteins ◽  
Fluorescent Proteins ◽  
Protein Complexes ◽  
Switching Frequency ◽  
Flagellar Motor ◽  
Internal Dynamics ◽  
Biologically Relevant ◽  
Bacterial Flagellar Motor

AbstractFluorescent fusion proteins open a direct and unique window onto protein function. However, they also introduce the risk of perturbation of the function of the native protein. Successful applications of fluorescent fusions therefore rely on a careful assessment and minimization of the side effects. Such insight, however, is still lacking for many applications of fluorescent fusions. This is particularly relevant in the study of the internal dynamics of motor protein complexes, where both the chemical and mechanical reaction coordinates can be affected. Fluorescent proteins fused to thestatorof the bacterial flagellar motor (BFM) complex have previously been used to successfully unveil the internal subunit dynamics of the motor. Here we report the effects of three different fluorescent proteins fused to the stator, all of which altered BFM behavior. The torque generated by individual stators was reduced while their stoichiometry in the complex remained unaffected. MotB fusions decreased the rotation-direction switching frequency of single motors and induced a novel BFM behavior: a bias-dependent asymmetry in the speed attained in the two rotation directions. All these effects could be mitigated by the insertion of a linker at the fusion point. These findings provide a quantitative account of the effects of fluorescent fusions on BFM dynamics and their alleviation—new insights that advance the use of fluorescent fusions to probe the dynamics of protein complexes.Author summaryMuch of what is known about the biology of proteins was discovered by fusing them to fluorescent proteins that allow detection of their location. But the label comes at a cost: the presence of the tag can alter the behavior of the protein of interest in unforeseen, yet biologically relevant ways. These side effects limit the depth to which fluorescent proteins can be used to probe protein function. One of the systems that has been successfully studied with fluorescent fusions for which these effects have not been addressed are dynamic protein complexes that carry out mechanical work. We examined how fluorescent proteins fused to a component of the bacterial flagellar motor complex impacts its function. Our findings show that the fusion proteins altered biologically relevant dynamical properties of the motor, including induction of a novel mechanical behavior, and demonstrate an approach to alleviate this. These results advance our ability to dissect the bacterial flagellar motor, and the internal dynamics of protein complexes in general, with fluorescent fusion proteins while causing minimal perturbation.

scholarly journals From residue coevolution to protein conformational ensembles and functional dynamics

2015 ◽  
Vol 112 (44) ◽  
pp. 13567-13572 ◽  
Author(s):  
Ludovico Sutto ◽  
Simone Marsili ◽  
Alfonso Valencia ◽  
Francesco Luigi Gervasio
Keyword(s):  
Protein Function ◽  
Structure Prediction ◽  
De Novo ◽  
Learning Algorithm ◽  
Coarse Grained ◽  
Static Structure ◽  
Biologically Relevant ◽  
Alternative Structures ◽  
Functional Dynamics ◽  
Dynamics Simulations

The analysis of evolutionary amino acid correlations has recently attracted a surge of renewed interest, also due to their successful use in de novo protein native structure prediction. However, many aspects of protein function, such as substrate binding and product release in enzymatic activity, can be fully understood only in terms of an equilibrium ensemble of alternative structures, rather than a single static structure. In this paper we combine coevolutionary data and molecular dynamics simulations to study protein conformational heterogeneity. To that end, we adapt the Boltzmann-learning algorithm to the analysis of homologous protein sequences and develop a coarse-grained protein model specifically tailored to convert the resulting contact predictions to a protein structural ensemble. By means of exhaustive sampling simulations, we analyze the set of conformations that are consistent with the observed residue correlations for a set of representative protein domains, showing that (i) the most representative structure is consistent with the experimental fold and (ii) the various regions of the sequence display different stability, related to multiple biologically relevant conformations and to the cooperativity of the coevolving pairs. Moreover, we show that the proposed protocol is able to reproduce the essential features of a protein folding mechanism as well as to account for regions involved in conformational transitions through the correct sampling of the involved conformers.

Attempting to rewrite History: challenges with the analysis of histidine-phosphorylated peptides

2013 ◽  
Vol 41 (4) ◽  
pp. 1089-1095 ◽  
Author(s):  
Maria-Belen Gonzalez-Sanchez ◽  
Francesco Lanucara ◽  
Matthew Helm ◽  
Claire E. Eyers
Keyword(s):  
Amino Acids ◽  
Protein Function ◽  
Biologically Relevant ◽  
Phosphorylated Peptides ◽  
Higher Eukaryotes ◽  
Histidine Phosphorylation ◽  
Rapid Hydrolysis ◽  
Hydrolysis Of ◽  
Acid Labile

A significant number of proteins in both eukaryotes and prokaryotes are known to be post-translationally modified by the addition of phosphate, serving as a means of rapidly regulating protein function. Phosphorylation of the amino acids serine, threonine and tyrosine are the focus of the vast majority of studies aimed at elucidating the extent and roles of such modification, yet other amino acids, including histidine and aspartate, are also phosphorylated. Although histidine phosphorylation is known to play extensive roles in signalling in eukaryotes, plants and fungi, roles for phosphohistidine are poorly defined in higher eukaryotes. Characterization of histidine phosphorylation aimed at elucidating such information is problematic due to the acid-labile nature of the phosphoramidate bond, essential for many of its biological functions. Although MS-based strategies have proven extremely useful in the analysis of other types of phosphorylated peptides, the chromatographic procedures essential for such approaches promote rapid hydrolysis of phosphohistidine-containing peptides. Phosphate transfer to non-biologically relevant aspartate residues during MS analysis further complicates the scenario.

scholarly journals Ensembles from ordered and disordered proteins reveal similar structural constraints during evolution

2018 ◽  
Author(s):  
Julia Marchetti ◽  
Alexander Miguel Monzon ◽  
Silvio C.E. Tosatto ◽  
Gustavo Parisi ◽  
María Silvina Fornasari
Keyword(s):  
Protein Function ◽  
Relevant Information ◽  
Biological Information ◽  
Disordered Proteins ◽  
Evolutionary Information ◽  
Structural Constraints ◽  
Biologically Relevant ◽  
Conformational Ensembles ◽  
Residue Contacts ◽  
Constrained Model

AbstractInter-residue contacts determine the structural properties for each conformer in the ensembles describing the native state of proteins. Structural constraints during evolution could then provide biologically relevant information about the conformational ensembles and their relationship with protein function. Here, we studied the proportion of sites evolving under structural constraints in two very different types of ensembles, those coming from ordered or disordered proteins. Using a structurally constrained model of protein evolution we found that both types of ensembles show comparable, near 40%, number of positions evolving under structural constraints. Among these sites, ~68% are in disordered regions and ~57% of them show long-range inter-residue contacts. Also, we found that disordered ensembles are redundant in reference to their structurally constrained evolutionary information and could be described on average with ~11 conformers. Despite the different complexity of the studied ensembles and proteins, the similar constraints reveal a comparable level of selective pressure to maintain their biological functions. These results highlight the importance of the evolutionary information to recover meaningful biological information to further characterize conformational ensembles.

scholarly journals Experimental and bioinformatic approaches for interrogating protein–protein interactions to determine protein function

2005 ◽  
Vol 34 (2) ◽  
pp. 263-280 ◽  
Author(s):  
Arnaud Droit ◽  
Guy G Poirier ◽  
Joanna M Hunter
Keyword(s):  
Protein Interactions ◽  
Protein Function ◽  
Large Scale ◽  
Protein Protein Interactions ◽  
Biologically Relevant ◽  
Protein Protein Interaction ◽  
Bioinformatic Approaches ◽  
Disparate Data ◽  
Protein Protein Interaction Networks ◽  
Novel Protein

An ambitious goal of proteomics is to elucidate the structure, interactions and functions of all proteins within cells and organisms. One strategy to determine protein function is to identify the protein–protein interactions. The increasing use of high-throughput and large-scale bioinformatics-based studies has generated a massive amount of data stored in a number of different databases. A challenge for bioinformatics is to explore this disparate data and to uncover biologically relevant interactions and pathways. In parallel, there is clearly a need for the development of approaches that can predict novel protein–protein interaction networks in silico. Here, we present an overview of different experimental and bioinformatic methods to elucidate protein–protein interactions.

scholarly journals Multi-PAS domain-mediated protein oligomerization of PpsR fromRhodobacter sphaeroides

2014 ◽  
Vol 70 (3) ◽  
pp. 863-876 ◽  
Author(s):  
Udo Heintz ◽  
Anton Meinhart ◽  
Andreas Winkler
Keyword(s):  
Protein Function ◽  
Binding Motif ◽  
Protein Oligomerization ◽  
Pas Domain ◽  
Biologically Relevant ◽  
Domain Structures ◽  
Dimerization Interface ◽  
Single Polypeptide ◽  
And Function ◽  
Polypeptide Chains

Per–ARNT–Sim (PAS) domains are essential modules of many multi-domain signalling proteins that mediate protein interaction and/or sense environmental stimuli. Frequently, multiple PAS domains are present within single polypeptide chains, where their interplay is required for protein function. Although many isolated PAS domain structures have been reported over the last decades, only a few structures of multi-PAS proteins are known. Therefore, the molecular mechanism of multi-PAS domain-mediated protein oligomerization and function is poorly understood. The transcription factor PpsR fromRhodobacter sphaeroidesis such a multi-PAS domain protein that, in addition to its three PAS domains, contains a glutamine-rich linker and a C-terminal helix–turn–helix DNA-binding motif. Here, crystal structures of two N-terminally and C-terminally truncated PpsR variants that comprise a single (PpsRQ-PAS1) and two (PpsRN-Q-PAS1) PAS domains, respectively, are presented and the multi-step strategy required for the phasing of a triple PAS domain construct (PpsRΔHTH) is illustrated. While parts of the biologically relevant dimerization interface can already be observed in the two shorter constructs, the PpsRΔHTHstructure reveals how three PAS domains enable the formation of multiple oligomeric states (dimer, tetramer and octamer), highlighting that not only the PAS cores but also their α-helical extensions are essential for protein oligomerization. The results demonstrate that the long helical glutamine-rich linker of PpsR results from a direct fusion of the N-cap of the PAS1 domain with the C-terminal extension of the N-domain that plays an important role in signal transduction.

Investigation of thin sections of biological standards by EDX, EELS, and Auger electron spectroscopy

1990 ◽  
Vol 48 (2) ◽  
pp. 184-185
Author(s):  
S. Lehner ◽  
H.E. Bauer ◽  
R. Wurster ◽  
H. Seiler
Keyword(s):  
Processing System ◽  
Beam Current ◽  
Beam Diameter ◽  
Thin Sections ◽  
Biologically Relevant ◽  
Energy Filtering ◽  
Low Viscosity ◽  
Carbon Foils ◽  
Electron Microscopical ◽  
Exchange Membrane

In order to compare different microanalytical techniques commercially available cation exchange membrane SC-1 (Stantech Inc, Palo Alto), was loaded with biologically relevant elements as Na, Mg, K, and Ca, respectively, each to its highest possible concentration, given by the number concentration of exchangeable binding sites (4 % wt. for Ca). Washing in distilled water, dehydration through a graded series of ethanol, infiltration and embedding in Spurr’s low viscosity epoxy resin was followed by thin sectioning. The thin sections (thickness of about 50 nm) were prepared on carbon foils and mounted on electron microscopical finder grids.The samples were analyzed with electron microprobe JXA 50A with transmitted electron device, EDX system TN 5400, and on line operating image processing system SEM-IPS, energy filtering electron microscope CEM 902 with EELS/ESI and Auger spectrometer 545 Perkin Elmer.With EDX, a beam current of some 10-10 A and a beam diameter of about 10 nm, a minimum-detectable mass of 10-20 g Ca seems within reach.

Quantification of cell-surface expressed antigenic sites with 5-nm gold markers: Getting close to biologically relevant data

1989 ◽  
Vol 47 ◽  
pp. 1050-1051
Author(s):  
Etienne de Harven ◽  
Hilary Christensen ◽  
Richard Leung ◽  
Cameron Ackerley
Keyword(s):  
Cell Surface ◽  
Human Peripheral Blood ◽  
Contour Length ◽  
Thin Sections ◽  
Gold Particles ◽  
Biologically Relevant ◽  
Transmission Electron ◽  
Entire Cell ◽  
Electron Imaging ◽  
Cell Contour

The T-derived subset of human peripheral blood normal lymphocytes has been selected as a model system to study the usefulness of 5 nm gold markers for quantification of single epitopes expressed on cell surfaces. The chosen epitopes are parts of the CD3 and CD5 molecules and can be specifically identified by hybridoma produced monoclonal antibodies (MoAbs; LEU-4 and LEU-1; Becton-Dick- inson, Mountain view, CA) . An indirect immunolabeling procedure, with goat anti-murine IgG adsorbed on the surface of 5 nm colloidal gold particles (GAM-G5, Janssen Pharmaceutica, Beerse, Belgium) has been used. Backscattered Electron Imaging (BEI) in a field emission scanning electronmicroscope (SEM) and transmission electron microscopy of thin sections of lymphocytes labeled before plastic embedding, were both used to identify and quantitate gold labeled cell surface sites, Estimating that the thickness of “silver” sections is approximately 60 nm and counting the number of gold particles on the entire cell perimeter, we calculated that, for LEU-4, the number of markers per um2 of cell surface is in the 140-160 range (Fig.l). Cell contour length measurements indicated that the surface of one lymphocyte is approximately 130-160 um2 that of a smooth sphere of identical diameter, reflecting the role of microvilli in expanding the surface area. The total number of gold labeled sites on the surface of one lymphocyte averages, therefore between 20,000 and 24,000 per cell.

Reading the phosphorylation code: binding of the 14-3-3 protein to multivalent client phosphoproteins

2020 ◽  
Vol 477 (7) ◽  
pp. 1219-1225 ◽  
Author(s):  
Nikolai N. Sluchanko
Keyword(s):  
Protein Function ◽  
Intrinsically Disordered Protein ◽  
Structural Basis ◽  
Major Protein ◽  
Post Translational Modifications ◽  
Protein Protein Interaction ◽  
Intrinsically Disordered ◽  
Biochemical Journal ◽  
Multiple Binding ◽  
And Control

Many major protein–protein interaction networks are maintained by ‘hub’ proteins with multiple binding partners, where interactions are often facilitated by intrinsically disordered protein regions that undergo post-translational modifications, such as phosphorylation. Phosphorylation can directly affect protein function and control recognition by proteins that ‘read’ the phosphorylation code, re-wiring the interactome. The eukaryotic 14-3-3 proteins recognizing multiple phosphoproteins nicely exemplify these concepts. Although recent studies established the biochemical and structural basis for the interaction of the 14-3-3 dimers with several phosphorylated clients, understanding their assembly with partners phosphorylated at multiple sites represents a challenge. Suboptimal sequence context around the phosphorylated residue may reduce binding affinity, resulting in quantitative differences for distinct phosphorylation sites, making hierarchy and priority in their binding rather uncertain. Recently, Stevers et al. [Biochemical Journal (2017) 474: 1273–1287] undertook a remarkable attempt to untangle the mechanism of 14-3-3 dimer binding to leucine-rich repeat kinase 2 (LRRK2) that contains multiple candidate 14-3-3-binding sites and is mutated in Parkinson's disease. By using the protein-peptide binding approach, the authors systematically analyzed affinities for a set of LRRK2 phosphopeptides, alone or in combination, to a 14-3-3 protein and determined crystal structures for 14-3-3 complexes with selected phosphopeptides. This study addresses a long-standing question in the 14-3-3 biology, unearthing a range of important details that are relevant for understanding binding mechanisms of other polyvalent proteins.

The challenge of detecting modifications on proteins

2020 ◽  
Vol 64 (1) ◽  
pp. 135-153 ◽  
Author(s):  
Lauren Elizabeth Smith ◽  
Adelina Rogowska-Wrzesinska
Keyword(s):  
Mass Spectrometry ◽  
Protein Function ◽  
Chemical Properties ◽  
Lysine Acetylation ◽  
Mass Determination ◽  
Post Translational Modifications ◽  
Site Specific ◽  
The Common

Abstract Post-translational modifications (PTMs) are integral to the regulation of protein function, characterising their role in this process is vital to understanding how cells work in both healthy and diseased states. Mass spectrometry (MS) facilitates the mass determination and sequencing of peptides, and thereby also the detection of site-specific PTMs. However, numerous challenges in this field continue to persist. The diverse chemical properties, low abundance, labile nature and instability of many PTMs, in combination with the more practical issues of compatibility with MS and bioinformatics challenges, contribute to the arduous nature of their analysis. In this review, we present an overview of the established MS-based approaches for analysing PTMs and the common complications associated with their investigation, including examples of specific challenges focusing on phosphorylation, lysine acetylation and redox modifications.

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