scholarly journals Protein interactions and consensus clustering analysis uncover insights into herpesvirus virion structure and function relationships

PLoS Biology ◽  
2019 ◽  
Vol 17 (6) ◽  
pp. e3000316 ◽  
Author(s):  
Anna Hernández Durán ◽  
Todd M. Greco ◽  
Benjamin Vollmer ◽  
Ileana M. Cristea ◽  
Kay Grünewald ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Clustering Analysis ◽  
Structure And Function ◽  
Consensus Clustering ◽  
Virion Structure ◽  
And Function

scholarly journals Calculating glycoprotein similarities from mass spectrometric data

2020 ◽  
pp. mcp.R120.002223
Author(s):  
William Edwin Hackett ◽  
Joseph Zaia
Keyword(s):  
Protein Interactions ◽  
Secretory Pathway ◽  
Biological Effects ◽  
Life Forms ◽  
Structure And Function ◽  
Mass Spectrometric ◽  
Protein Quantification ◽  
Protein Glycosylation ◽  
Spectrometric Data ◽  
And Function

Complex protein glycosylation occurs through biosynthetic steps in the secretory pathway that create macro- and microheterogeneity of structure and function.  Required for all life forms, glycosylation diversifies and adapts protein interactions with binding partners that underpin interactions at cell surfaces and pericellular and extracellular environments. Because these biological effects arise from heterogeneity of structure and function, it is necessary to measure their changes as part of the quest to understand nature.  Quite often, however, the assumption behind proteomics that post-translational modifications are discrete additions that can be modeled using the genome as a template does not apply to protein glycosylation.  Rather, it is necessary to quantify the glycosylation distribution at each glycosite and to aggregate this information into a population of mature glycoproteins that exist in a given biological system.  To date, mass spectrometric methods for assigning singly glycosylated peptides are well-established.  But it is necessary to quantify glycosylation heterogeneity accurately in order to gauge the alterations that occur during biological processes.  The task is to quantify the glycosylated peptide forms as accurately as possible and then apply appropriate bioinformatics algorithms to the calculation of micro- and macro-similarities.  In this review, we summarize current approaches for protein quantification as they apply to this glycoprotein similarity problem.

scholarly journals The Role of Meningococcal Porin B in Protein-Protein Interactions with Host Cells

2018 ◽  
Vol 62 (1) ◽  
pp. 52-58
Author(s):  
E. Káňová ◽  
I. Jiménez-Munguía ◽  
Ľ. Čomor ◽  
Z. Tkáčová ◽  
I. Širochmanová ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Cell Signalling ◽  
Structure And Function ◽  
Host Cells ◽  
Protein Protein Interactions ◽  
Receptor Interactions ◽  
And Function ◽  
Fatal Sepsis ◽  
Porin B

Abstract Neisseria meningitidis is a Gram-negative diplococcus responsible for bacterial meningitis and fatal sepsis. Ligand-receptor interactions are one of the main steps in the development of neuroinvasion. Porin B (PorB), neisserial outer membrane protein (ligand), binds to host receptors and triggers many cell signalling cascades allowing the meningococcus to damage the host cells or induce immune cells responses via the TLR2-dependent mechanisms. In this paper, we present a brief review of the structure and function of PorB.

Nanoscale Analysis of the Effect of Pathogenic Mutations on Polycystin-1

2010 ◽  
Author(s):  
Liang Ma ◽  
Meixiang Xu ◽  
Andres F. Oberhauser
Keyword(s):  
Single Molecule ◽  
Conformational Changes ◽  
Protein Interactions ◽  
Structure And Function ◽  
Eukaryotic Cells ◽  
Mechanical Forces ◽  
Force Microscopy ◽  
Physiological Conditions ◽  
Atomic Force ◽  
And Function

The activity of proteins and their complexes often involves the conversion of chemical energy (stored or supplied) into mechanical work through conformational changes. Mechanical forces are also crucial for the regulation of the structure and function of cells and tissues. Thus, the shape of eukaryotic cells is the result of cycles of mechano-sensing, mechano-transduction, and mechano-response. Recently developed single-molecule atomic force microscopy (AFM) techniques can be used to manipulate single molecules, both in real time and under physiological conditions, and are ideally suited to directly quantify the forces involved in both intra- and intermolecular protein interactions. In combination with molecular biology and computer simulations, these techniques have been applied to characterize the unfolding and refolding reactions in a variety of proteins, such as titin (an elastic mechano-sensing protein found in muscle) and polycystin-1 (PC1, a mechanosensor found in the kidney).

scholarly journals Coevolutionary methods enable robust design of modular repressors by reestablishing intra-protein interactions

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Xian-Li Jiang ◽  
Rey P. Dimas ◽  
Clement T. Y. Chan ◽  
Faruck Morcos
Keyword(s):  
Gene Expression ◽  
Protein Structure ◽  
Ligand Binding ◽  
Protein Interactions ◽  
Dna Recognition ◽  
Design Strategy ◽  
Structure And Function ◽  
Transcriptional Repressors ◽  
And Function ◽  
Laci Family

AbstractGenetic sensors with unique combinations of DNA recognition and allosteric response can be created by hybridizing DNA-binding modules (DBMs) and ligand-binding modules (LBMs) from distinct transcriptional repressors. This module swapping approach is limited by incompatibility between DBMs and LBMs from different proteins, due to the loss of critical module-module interactions after hybridization. We determine a design strategy for restoring key interactions between DBMs and LBMs by using a computational model informed by coevolutionary traits in the LacI family. This model predicts the influence of proposed mutations on protein structure and function, quantifying the feasibility of each mutation for rescuing hybrid repressors. We accurately predict which hybrid repressors can be rescued by mutating residues to reinstall relevant module-module interactions. Experimental results confirm that dynamic ranges of gene expression induction were improved significantly in these mutants. This approach enhances the molecular and mechanistic understanding of LacI family proteins, and advances the ability to design modular genetic parts.

The structure and function of protein modules

1991 ◽  
Vol 332 (1263) ◽  
pp. 165-170 ◽  
Keyword(s):  
Protein Interactions ◽  
Serine Proteases ◽  
Extracellular Enzymes ◽  
Structural Information ◽  
Structure And Function ◽  
Factor Ix ◽  
Main Role ◽  
Factor Module ◽  
And Function ◽  
Protein Modules

Analysis of protein sequences shows that many proteins in multicellular organisms have evolved by a process of exon shuffling, deletion and duplication. These exons often correspond to autonomously folding protein modules. Many extracellular enzymes have this modular structure; for example, serine proteases involved in blood-clotting, fibrinolysis and complement. The main role of these modules is to confer specificity by protein—protein interactions. Lack of structural information about such proteins has required a new strategy for studying the structure and function of protein modules. The strategy involves the production of individual modules by protein expression techniques, determination of their structure by high resolution nuclear magnetic resonance and definition of functional patches on the modules by sitedirected mutagenesis and biological assays. The structures of the growth factor module, the fibronectin type 1 module and the complement module are briefly described. The possible functional roles of modules in various proteins, including the enzymes factor IX and tissue plasminogen activator, are discussed.

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