scholarly journals Improving integrative 3D modeling into low- to medium- resolution EM structures with evolutionary couplings

2021 ◽  
Author(s):  
Caitlyn L. McCafferty ◽  
David W. Taylor ◽  
Edward M. Marcotte
Keyword(s):  
Conformational Changes ◽  
Spatial Data ◽  
Sequence Data ◽  
Protein Complexes ◽  
Three Dimensional ◽  
Distance Restraint ◽  
Evolutionary Information ◽  
Additional Information ◽  
Integrative Modeling ◽  
Medium Resolution

AbstractElectron microscopy (EM) continues to provide near-atomic resolution structures for well-behaved proteins and protein complexes. Unfortunately, structures of some complexes are limited to low- to medium-resolution due to biochemical or conformational heterogeneity. Thus, the application of unbiased systematic methods for fitting individual structures into EM maps is important. A method that employs co-evolutionary information obtained solely from sequence data could prove invaluable for quick, confident localization of subunits within these structures. Here, we incorporate the co-evolution of intermolecular amino acids as a new type of distance restraint in the Integrative Modeling Platform (IMP) in order to build three-dimensional models of atomic structures into EM maps ranging from 10-14 Å in resolution. We validate this method using four complexes of known structure, where we highlight the conservation of intermolecular couplings despite dynamic conformational changes using the BAM complex. Finally, we use this method to assemble the subunits of the bacterial holo-translocon into a model that agrees with previous biochemical data. The use of evolutionary couplings in integrative modeling improves systematic, unbiased fitting of atomic models into medium- to low-resolution EM maps, providing additional information to integrative models lacking in spatial data.

scholarly journals Three-Dimensional Graph Matching to Identify Secondary Structure Correspondence of Medium-Resolution Cryo-EM Density Maps

Biomolecules ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 1773
Author(s):  
Bahareh Behkamal ◽  
Mahmoud Naghibzadeh ◽  
Mohammad Reza Saberi ◽  
Zeinab Amiri Tehranizadeh ◽  
Andrea Pagnani ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Graph Matching ◽  
Protein Complexes ◽  
Three Dimensional ◽  
Protein Structure Determination ◽  
Secondary Structures ◽  
Computational Method ◽  
Target Sequence ◽  
Matching Problem ◽  
Medium Resolution

Cryo-electron microscopy (cryo-EM) is a structural technique that has played a significant role in protein structure determination in recent years. Compared to the traditional methods of X-ray crystallography and NMR spectroscopy, cryo-EM is capable of producing images of much larger protein complexes. However, cryo-EM reconstructions are limited to medium-resolution (~4–10 Å) for some cases. At this resolution range, a cryo-EM density map can hardly be used to directly determine the structure of proteins at atomic level resolutions, or even at their amino acid residue backbones. At such a resolution, only the position and orientation of secondary structure elements (SSEs) such as α-helices and β-sheets are observable. Consequently, finding the mapping of the secondary structures of the modeled structure (SSEs-A) to the cryo-EM map (SSEs-C) is one of the primary concerns in cryo-EM modeling. To address this issue, this study proposes a novel automatic computational method to identify SSEs correspondence in three-dimensional (3D) space. Initially, through a modeling of the target sequence with the aid of extracting highly reliable features from a generated 3D model and map, the SSEs matching problem is formulated as a 3D vector matching problem. Afterward, the 3D vector matching problem is transformed into a 3D graph matching problem. Finally, a similarity-based voting algorithm combined with the principle of least conflict (PLC) concept is developed to obtain the SSEs correspondence. To evaluate the accuracy of the method, a testing set of 25 experimental and simulated maps with a maximum of 65 SSEs is selected. Comparative studies are also conducted to demonstrate the superiority of the proposed method over some state-of-the-art techniques. The results demonstrate that the method is efficient, robust, and works well in the presence of errors in the predicted secondary structures of the cryo-EM images.

scholarly journals Inferring interaction partners from protein sequences

2016 ◽  
Author(s):  
Anne-Florence Bitbol ◽  
Robert S. Dwyer ◽  
Lucy J. Colwell ◽  
Ned S. Wingreen
Keyword(s):  
Protein Interactions ◽  
Sequence Data ◽  
Protein Complexes ◽  
A Priori ◽  
Specific Interaction ◽  
Three Dimensional ◽  
Specific Protein ◽  
Protein Protein Interactions ◽  
Entropy Model ◽  
Interaction Partners

Specific protein-protein interactions are crucial in the cell, both to ensure the formation and stability of multi-protein complexes, and to enable signal transduction in various pathways. Functional interactions between proteins result in coevolution between the interaction partners. Hence, the sequences of interacting partners are correlated. Here we exploit these correlations to accurately identify which proteins are specific interaction partners from sequence data alone. Our general approach, which employs a pairwise maximum entropy model to infer direct couplings between residues, has been successfully used to predict the three-dimensional structures of proteins from sequences. Building on this approach, we introduce an iterative algorithm to predict specific interaction partners from among the members of two protein families. We assess the algorithm's performance on histidine kinases and response regulators from bacterial two-component signaling systems. The algorithm proves successful without any a priori knowledge of interaction partners, yielding a striking 0.93 true positive fraction on our complete dataset, and we uncover the origin of this surprising success. Finally, we discuss how our method could be used to predict novel protein-protein interactions.

scholarly journals A coarse-grained methodology identifies intrinsic mechanisms that dissociate interacting protein pairs

2020 ◽  
Author(s):  
Haleh Abdizadeh ◽  
Farzaneh Jalalypour ◽  
Ali Rana Atilgan ◽  
Canan Atilgan
Keyword(s):  
Conformational Changes ◽  
Electromechanical Coupling ◽  
Protein Complexes ◽  
Three Dimensional ◽  
Biological Significance ◽  
Local Environment ◽  
Coarse Grained ◽  
Alternative Mode ◽  
Interacting Protein ◽  
Elastic Network

AbstractWe address the problem of triggering dissociation events between proteins that have formed a complex. We have collected a set of 25 non-redundant, functionally diverse protein complexes having high-resolution three-dimensional structures in both the unbound and bound forms. We unify elastic network models with perturbation response scanning (PRS) methodology as an efficient approach for predicting residues that have the propensity to trigger dissociation of an interacting protein pair, using the three-dimensional structures of the bound and unbound proteins as input. PRS reveals that while for a group of protein pairs, residues involved in the conformational shifts are confined to regions with large motions, there are others where they originate from parts of the protein unaffected structurally by binding. Strikingly, only a few of the complexes have interface residues responsible for dissociation. We find two main modes of response: In one mode, remote control of disassociation in which disruption of the electrostatic potential distribution along protein surfaces play the major role; in the alternative mode, mechanical control of dissociation by remote residues prevail. In the former, dissociation is triggered by changes in the local environment of the protein e.g. pH or ionic strength, while in the latter, specific perturbations arriving at the controlling residues, e.g. via binding to a third interacting partner is required for decomplexation. We resolve the observations by relying on an electromechanical coupling model which reduces to the usual elastic network result in the limit of the lack of coupling. We validate the approach by illustrating the biological significance of top residues selected by PRS on select cases where we show that the residues whose perturbation leads to the observed conformational changes correspond to either functionally important or highly conserved residues in the complex.

scholarly journals Structural and energetic aspects of protein-protein recognition.

1997 ◽  
Vol 44 (3) ◽  
pp. 367-387 ◽  
Author(s):  
J Otlewski ◽  
W Apostoluk
Keyword(s):  
Conformational Changes ◽  
Growth Hormone Receptor ◽  
Structural Information ◽  
Protein Complexes ◽  
Three Dimensional ◽  
Water Structure ◽  
Human Growth ◽  
Protein Recognition ◽  
Specific Recognition ◽  
Different Types

Specific recognition between proteins plays a crucial role in a great number of vital processes. In this review different types of protein-protein complexes are analyzed on the basis of their three-dimensional structures which became available in recent years. The complexes which are analyzed include: those resulting from different types of recognition between proteinase and protein inhibitor (canonical inhibitors of serine proteinases, hirudin, inhibitors of cysteine proteinases, carboxypeptidase inhibitor), barnase-barstar, human growth hormone-receptor and antibody-antigen. It seems obvious that specific and strong protein-protein recognition is achieved in many different ways. To further explore this question, the structural information was analyzed together with kinetic and thermodynamic data available for the respective complexes. It appears that the energy and rates of specific recognition of proteins are influenced by many different factors, including: area of interacting surfaces; complementarity of shapes, charges and hydrogen bonds; water structure at the interface; conformational changes; additivity and cooperativity of individual interactions, steric effects and various (conformational, hydration) entropy changes.

scholarly journals Inferring interaction partners from protein sequences using mutual information

2018 ◽  
Author(s):  
Anne-Florence Bitbol
Keyword(s):  
Mutual Information ◽  
Protein Interactions ◽  
Sequence Data ◽  
Protein Complexes ◽  
Three Dimensional ◽  
Specific Protein ◽  
Amino Acid Residues ◽  
Protein Protein Interactions ◽  
Cellular Processes ◽  
Interaction Partners

AbstractSpecific protein-protein interactions are crucial in most cellular processes. They enable multiprotein complexes to assemble and to remain stable, and they allow signal transduction in various pathways. Functional interactions between proteins result in coevolution between the interacting partners, and thus in correlations between their sequences. Pairwise maximum-entropy based models have enabled successful inference of pairs of amino-acid residues that are in contact in the three-dimensional structure of multi-protein complexes, starting from the correlations in the sequence data of known interaction partners. Recently, algorithms inspired by these methods have been developed to identify which proteins are specific interaction partners among the paralogous proteins of two families, starting from sequence data alone. Here, we demonstrate that a slightly higher performance for partner identification can be reached by an approximate maximization of the mutual information between the sequence alignments of the two protein families. This stands in contrast with structure prediction of proteins and of multiprotein complexes from sequence data, where pairwise maximum-entropy based global statistical models substantially improve performance compared to mutual information. Our findings entail that the statistical dependences allowing interaction partner prediction from sequence data are not restricted to the residue pairs that are in direct contact at the interface between the partner proteins.Author summarySpecific protein-protein interactions are at the heart of most intra-cellular processes. Mapping these interactions is thus crucial to a systems-level understanding of cells, and has broad applications to areas such as drug targeting. Systematic experimental identification of protein interaction partners is still challenging. However, a large and rapidly growing amount of sequence data is now available. Recently, algorithms have been proposed to identify which proteins interact from their sequences alone, thanks to the co-variation of the sequences of interacting proteins. These algorithms build upon inference methods that have been used with success to predict the three-dimensional structures of proteins and multi-protein complexes, and their focus is on the amino-acid residues that are in direct contact. Here, we propose a simpler method to identify which proteins interact among the paralogous proteins of two families, starting from their sequences alone. Our method relies on an approximate maximization of mutual information between the sequences of the two families, without specifically emphasizing the contacting residue pairs. We demonstrate that this method slightly outperforms the earlier one. This result highlights that partner prediction does not only rely on the identities and interactions of directly contacting amino-acids.

scholarly journals Automatic building of protein atomic models from cryo-EM density maps using residue co-evolution

2020 ◽  
Author(s):  
Guillaume Bouvier ◽  
Benjamin Bardiaux ◽  
Riccardo Pellarin ◽  
Chiara Rapisarda ◽  
Michael Nilges
Keyword(s):  
Conformational Changes ◽  
Minimum Spanning Tree ◽  
De Novo ◽  
Three Dimensional ◽  
Weighted Graph ◽  
Atomic Resolution ◽  
Side Chain ◽  
Evolutionary Information ◽  
Atomic Models ◽  
Density Maps

AbstractElectron cryo-microscopy (cryo-EM) has emerged as a powerful method to obtain three-dimensional (3D) structures of macromolecular complexes at atomic or near-atomic resolution. However, de novo building of atomic models from near-atomic resolution (3-5 Å) cryo-EM density maps is a challenging task, in particular since poorly resolved side-chain densities hamper sequence assignment by automatic procedures at a lower resolution. Furthermore, segmentation of EM density maps into individual subunits remains a difficult problem when no three-dimensional structures of these subunits exist, or when significant conformational changes occur between the isolated and complexed form of the subunits. To tackle these issues, we have developed a graph-based method to thread most of the C-α trace of the protein backbone into the EM density map. The EM density is described as a weighted graph such that the resulting minimum spanning tree encompasses the high-density regions of the map. A pruning algorithm cleans the tree and finds the most probable positions of the C-α atoms, using side-chain density when available, as a collection of C-α trace fragments. By complementing experimental EM maps with contact predictions from sequence co-evolutionary information, we demonstrate that our approach can correctly segment EM maps into individual subunits and assign amino acids sequence to backbone traces to generate full-atom models.

Electron Microscopy and image reconstruction reveal the structural basis for spectrin's elastic properties

1992 ◽  
Vol 50 (1) ◽  
pp. 510-511
Author(s):  
Amy M. McGough ◽  
Robert Josephs
Keyword(s):  
Electron Microscopy ◽  
Elastic Properties ◽  
Conformational Changes ◽  
Quaternary Structure ◽  
Three Dimensional ◽  
Membrane Skeleton ◽  
Projection Algorithm ◽  
Structural Basis ◽  
Iterative Approximation ◽  
Membrane Skeletons

The remarkable deformability of the erythrocyte derives in large part from the elastic properties of spectrin, the major component of the membrane skeleton. It is generally accepted that spectrin's elasticity arises from marked conformational changes which include variations in its overall length (1). In this work the structure of spectrin in partially expanded membrane skeletons was studied by electron microscopy to determine the molecular basis for spectrin's elastic properties. Spectrin molecules were analysed with respect to three features: length, conformation, and quaternary structure. The results of these studies lead to a model of how spectrin mediates the elastic deformation of the erythrocyte.Membrane skeletons were isolated from erythrocyte membrane ghosts, negatively stained, and examined by transmission electron microscopy (2). Particle lengths and end-to-end distances were measured from enlarged prints using the computer program MACMEASURE. Spectrin conformation (straightness) was assessed by calculating the particles’ correlation length by iterative approximation (3). Digitised spectrin images were correlation averaged or Fourier filtered to improve their signal-to-noise ratios. Three-dimensional reconstructions were performed using a suite of programs which were based on the filtered back-projection algorithm and executed on a cluster of Microvax 3200 workstations (4).

scholarly journals Three-Dimensional Thematic Map Imaging of the Yacht Port on the Example of the Polish National Sailing Centre Marina in Gdańsk

2021 ◽  
Vol 11 (15) ◽  
pp. 7016
Author(s):  
Pawel S. Dabrowski ◽  
Cezary Specht ◽  
Mariusz Specht ◽  
Artur Makar
Keyword(s):  
Spatial Data ◽  
Convex Surface ◽  
Dimensional Space ◽  
Three Dimensional ◽  
Future Research ◽  
Two Dimensional ◽  
Thematic Maps ◽  
Research Directions ◽  
Future Research Directions ◽  
The Many

The theory of cartographic projections is a tool which can present the convex surface of the Earth on the plane. Of the many types of maps, thematic maps perform an important function due to the wide possibilities of adapting their content to current needs. The limitation of classic maps is their two-dimensional nature. In the era of rapidly growing methods of mass acquisition of spatial data, the use of flat images is often not enough to reveal the level of complexity of certain objects. In this case, it is necessary to use visualization in three-dimensional space. The motivation to conduct the study was the use of cartographic projections methods, spatial transformations, and the possibilities offered by thematic maps to create thematic three-dimensional map imaging (T3DMI). The authors presented a practical verification of the adopted methodology to create a T3DMI visualization of the marina of the National Sailing Centre of the Gdańsk University of Physical Education and Sport (Poland). The profiled characteristics of the object were used to emphasize the key elements of its function. The results confirmed the increase in the interpretative capabilities of the T3DMI method, relative to classic two-dimensional maps. Additionally, the study suggested future research directions of the presented solution.

Turbulent three-dimensional dielectric electrohydrodynamic convection between two plates

2012 ◽  
Vol 696 ◽  
pp. 228-262 ◽  
Author(s):  
A. Kourmatzis ◽  
J. S. Shrimpton
Keyword(s):  
Spatial Data ◽  
Three Dimensional ◽  
Reynolds Numbers ◽  
Two Dimensions ◽  
Three Dimensions ◽  
Energy Budgets ◽  
Turbulent Regime ◽  
Scalar Flux ◽  
Wide Range ◽  
Scalar Variance

AbstractThe fundamental mechanisms responsible for the creation of electrohydrodynamically driven roll structures in free electroconvection between two plates are analysed with reference to traditional Rayleigh–Bénard convection (RBC). Previously available knowledge limited to two dimensions is extended to three-dimensions, and a wide range of electric Reynolds numbers is analysed, extending into a fully inherently three-dimensional turbulent regime. Results reveal that structures appearing in three-dimensional electrohydrodynamics (EHD) are similar to those observed for RBC, and while two-dimensional EHD results bear some similarities with the three-dimensional results there are distinct differences. Analysis of two-point correlations and integral length scales show that full three-dimensional electroconvection is more chaotic than in two dimensions and this is also noted by qualitatively observing the roll structures that arise for both low (${\mathit{Re}}_{E} = 1$) and high electric Reynolds numbers (up to ${\mathit{Re}}_{E} = 120$). Furthermore, calculations of mean profiles and second-order moments along with energy budgets and spectra have examined the validity of neglecting the fluctuating electric field ${ E}_{i}^{\ensuremath{\prime} } $ in the Reynolds-averaged EHD equations and provide insight into the generation and transport mechanisms of turbulent EHD. Spectral and spatial data clearly indicate how fluctuating energy is transferred from electrical to hydrodynamic forms, on moving through the domain away from the charging electrode. It is shown that ${ E}_{i}^{\ensuremath{\prime} } $ is not negligible close to the walls and terms acting as sources and sinks in the turbulent kinetic energy, turbulent scalar flux and turbulent scalar variance equations are examined. Profiles of hydrodynamic terms in the budgets resemble those in the literature for RBC; however there are terms specific to EHD that are significant, indicating that the transfer of energy in EHD is also attributed to further electrodynamic terms and a strong coupling exists between the charge flux and variance, due to the ionic drift term.

Three-dimensional crystallization of membrane proteins

1988 ◽  
Vol 21 (4) ◽  
pp. 429-477 ◽  
Author(s):  
W. Kühlbrandt
Keyword(s):  
High Resolution ◽  
Membrane Proteins ◽  
Membrane Protein ◽  
Protein Complexes ◽  
Three Dimensional ◽  
Biological Macromolecules ◽  
X Ray ◽  
X Ray Crystallography ◽  
Membrane Protein Complexes ◽  
Essential Prerequisite

As recently as 10 years ago, the prospect of solving the structure of any membrane protein by X-ray crystallography seemed remote. Since then, the threedimensional (3-D) structures of two membrane protein complexes, the bacterial photosynthetic reaction centres of Rhodopseudomonas viridis (Deisenhofer et al. 1984, 1985) and of Rhodobacter sphaeroides (Allen et al. 1986, 1987 a, 6; Chang et al. 1986) have been determined at high resolution. This astonishing progress would not have been possible without the pioneering work of Michel and Garavito who first succeeded in growing 3-D crystals of the membrane proteins bacteriorhodopsin (Michel & Oesterhelt, 1980) and matrix porin (Garavito & Rosenbusch, 1980). X-ray crystallography is still the only routine method for determining the 3-D structures of biological macromolecules at high resolution and well-ordered 3-D crystals of sufficient size are the essential prerequisite.

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