CombLabel: rational design of optimized sequence-specific combinatorial labeling schemes. Application to backbone assignment of membrane proteins with low stability

2019 ◽  
Vol 73 (10-11) ◽  
pp. 531-544 ◽  
Author(s):  
M. Yu. Myshkin ◽  
M. A. Dubinnyi ◽  
D. S. Kulbatskii ◽  
E. N. Lyukmanova ◽  
M. P. Kirpichnikov ◽  
...  
Keyword(s):  
Membrane Proteins ◽  
Rational Design ◽  
Backbone Assignment ◽  
Labeling Schemes

Cryo-Electron Microscopy: Moving Beyond X-Ray Crystal Structures for Drug Receptors and Drug Development

2020 ◽  
Vol 60 (1) ◽  
pp. 51-71 ◽  
Author(s):  
Javier García-Nafría ◽  
Christopher G. Tate
Keyword(s):  
Membrane Proteins ◽  
G Protein ◽  
Rational Design ◽  
Protein Complexes ◽  
Host Cells ◽  
X Ray ◽  
X Ray Crystallography ◽  
Receptor Modulation ◽  
Lipid Environment ◽  
Drug Receptors

Electron cryo-microscopy (cryo-EM) has revolutionized structure determination of membrane proteins and holds great potential for structure-based drug discovery. Here we discuss the potential of cryo-EM in the rational design of therapeutics for membrane proteins compared to X-ray crystallography. We also detail recent progress in the field of drug receptors, focusing on cryo-EM of two protein families with established therapeutic value, the γ-aminobutyric acid A receptors (GABAARs) and G protein–coupled receptors (GPCRs). GABAARs are pentameric ion channels, and cryo-EM structures of physiological heteromeric receptors in a lipid environment have uncovered the molecular basis of receptor modulation by drugs such as diazepam. The structures of ten GPCR–G protein complexes from three different classes of GPCRs have now been determined by cryo-EM. These structures give detailed insights into molecular interactions with drugs, GPCR–G protein selectivity, how accessory membrane proteins alter receptor–ligand pharmacology, and the mechanism by which HIV uses GPCRs to enter host cells.

Platelet membrane proteomics: a novel repository for functional research

Blood ◽  
2009 ◽  
Vol 114 (1) ◽  
pp. e10-e19 ◽  
Author(s):  
Urs Lewandrowski ◽  
Stefanie Wortelkamp ◽  
Katharina Lohrig ◽  
René P. Zahedi ◽  
Dirk A. Wolters ◽  
...  
Keyword(s):  
Membrane Proteins ◽  
Rational Design ◽  
Large Scale ◽  
Plasma Membranes ◽  
Research Field ◽  
Platelet Membrane ◽  
Complete Collection ◽  
Spectrometric Data ◽  
Major Interest ◽  
Initial Adhesion

Abstract Being central players in thrombosis and hemostasis, platelets react in manifold and complex ways to extracellular stimuli. Cell-matrix and cell-cell interactions are mandatory for initial adhesion as well as for final development of stable plugs. Primary interfaces for interactions are plasma membrane proteins, of which many have been identified over the past decades in individual studies. However, due to their enucleate structure, platelets are not accessible to large-scale genomic screens and thus a comprehensive inventory of membrane proteins is still missing. For this reason, we here present an advanced proteomic setup for the detailed analysis of enriched platelet plasma membranes and the so far most complete collection of platelet membrane proteins. In summary, 1282 proteins were identified, of which more than half are termed to be of membrane origin. This study provides a brief overview of gene ontology subcellular and functional classification, as well as interaction network analysis. In addition, the mass spectrometric data were used to assemble a first tentative relative quantification of large-scale data on the protein level. We therefore estimate the presented data to be of major interest to the platelet research field and to support rational design of functional studies.

Rational design of novel high molecular weight solubilization surfactants for membrane proteins from the peptide gemini surfactants (PG-surfactants)

Tetrahedron ◽  
2016 ◽  
Vol 72 (43) ◽  
pp. 6898-6908 ◽  
Author(s):  
Shuhei Koeda ◽  
Tomoyuki Suzuki ◽  
Tomoyasu Noji ◽  
Keisuke Kawakami ◽  
Shigeru Itoh ◽  
...  
Keyword(s):  
Molecular Weight ◽  
Membrane Proteins ◽  
High Molecular Weight ◽  
Rational Design ◽  
Gemini Surfactants

scholarly journals A Bioinformatics Analysis Reveals a Group of MocR Bacterial Transcriptional Regulators Linked to a Family of Genes Coding for Membrane Proteins

2016 ◽  
Vol 2016 ◽  
pp. 1-13 ◽  
Author(s):  
Teresa Milano ◽  
Sebastiana Angelaccio ◽  
Angela Tramonti ◽  
Martino Luigi Di Salvo ◽  
Roberto Contestabile ◽  
...  
Keyword(s):  
Membrane Proteins ◽  
Rational Design ◽  
Bioinformatics Analysis ◽  
Distinct Group ◽  
Transcriptional Regulators ◽  
Type I ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Terminal Domain ◽  
Fold Type

The MocR bacterial transcriptional regulators are characterized by an N-terminal domain, 60 residues long on average, possessing the winged-helix-turn-helix (wHTH) architecture responsible for DNA recognition and binding, linked to a large C-terminal domain (350 residues on average) that is homologous to fold type-I pyridoxal 5′-phosphate (PLP) dependent enzymes like aspartate aminotransferase (AAT). These regulators are involved in the expression of genes taking part in several metabolic pathways directly or indirectly connected to PLP chemistry, many of which are still uncharacterized. A bioinformatics analysis is here reported that studied the features of a distinct group of MocR regulators predicted to be functionally linked to a family of homologous genes coding for integral membrane proteins of unknown function. This group occurs mainly in the Actinobacteria and Gammaproteobacteria phyla. An analysis of the multiple sequence alignments of their wHTH and AAT domains suggested the presence of specificity-determining positions (SDPs). Mapping of SDPs onto a homology model of the AAT domain hinted at possible structural/functional roles in effector recognition. Likewise, SDPs in wHTH domain suggested the basis of specificity of Transcription Factor Binding Site recognition. The results reported represent a framework for rational design of experiments and for bioinformatics analysis of other MocR subgroups.

scholarly journals Synthesis and Evaluation of a Library of Alternating Amphipathic Copolymers to Solubilize and Study Membrane Proteins

2021 ◽  
Author(s):  
Adrian H. Kopf ◽  
Odette Lijding ◽  
Barend O. W. Elenbaas ◽  
Martijn C. Koorengevel ◽  
Justyna M. Dobruchowska ◽  
...  
Keyword(s):  
Membrane Proteins ◽  
Maleic Acid ◽  
Rational Design ◽  
Extraction Efficiency ◽  
Yeast Mitochondria ◽  
Electronic Effects ◽  
Alternating Copolymers ◽  
Polymer Properties

Amphipathic copolymers such as poly(styrene-maleic acid) (SMA) are promising tools for the facile extraction of membrane proteins (MPs) into native nanodiscs. Here, we designed and synthesized a library of well-defined alternating copolymers of SMA analogues in order to elucidate polymer properties that are important for MP solubilization and stability. MP extraction efficiency was determined using KcsA from E.coli membranes and general solubilization efficiency was investigated via turbidimetry experiments on membranes of E.coli, yeast mitochondria and synthetic lipids. Remarkably, halogenation of SMA copolymers dramatically improved solubilization efficiency in all systems, while substituents on the copolymer backbone improved resistance to Ca2+. Relevant polymer properties were found to include hydrophobic balance, size and positioning of substituents, rigidity and electronic effects. The library thus contributes to the rational design of copolymers for the study of MPs.

Membrane Protein Structures for Rational Antimicrobial Drug Design

2014 ◽  
Vol 67 (12) ◽  
pp. 1724 ◽  
Author(s):  
Patricia M. Walden ◽  
Roisin M. McMahon ◽  
Julia K. Archbold
Keyword(s):  
Membrane Proteins ◽  
Poor Prognosis ◽  
Rational Design ◽  
Vaccine Development ◽  
Protein Structures ◽  
Resistance Mechanisms ◽  
Bacterial Membrane ◽  
Gram Negative Bacteria ◽  
Drug Resistant

Antibiotic resistance is a major global health threat. Bacteria have developed novel resistance mechanisms to many of the latest generations of antibiotics and there is an urgent need to develop new therapies to combat these infections. Infections that are caused by multi-drug resistant Gram-negative bacteria result in poor prognosis, prolonged illness, and greater costs for health care. Recent research has pointed to several key bacterial membrane proteins as potential targets for drug and vaccine development. However, determination of the structures of these membrane proteins is not a trivial task. Here we review recent breakthroughs of the structural determination of bacterial membrane proteins and their potential for the future rational design of novel antimicrobial therapies.

scholarly journals Transmembrane segment enhanced labeling as a tool for the backbone assignment of  -helical membrane proteins

2008 ◽  
Vol 105 (24) ◽  
pp. 8262-8267 ◽  
Author(s):  
S. Reckel ◽  
S. Sobhanifar ◽  
B. Schneider ◽  
F. Junge ◽  
D. Schwarz ◽  
...  
Keyword(s):  
Membrane Proteins ◽  
Backbone Assignment ◽  
Transmembrane Segment

scholarly journals Role of the Lipid Environment in the Dimerization of Transmembrane Domains of Glycophorin A

Acta Naturae ◽  
2015 ◽  
Vol 7 (4) ◽  
pp. 122-127 ◽  
Author(s):  
A. S. Kuznetsov ◽  
P. E. Volynsky ◽  
R. G. Efremov
Keyword(s):  
Free Energy ◽  
Amino Acid ◽  
Membrane Proteins ◽  
Rational Design ◽  
Dominant Role ◽  
Detailed Balance ◽  
Glycophorin A ◽  
Negative Contribution ◽  
Lipid Environment

An efficient computational approach is developed to quantify the free energy of a spontaneous association of the -helices of proteins in the membrane environment. The approach is based on the numerical decomposition of the free energy profiles of the transmembrane (TM) helices into components corresponding to protein-protein, protein-lipid, and protein-water interactions. The method was tested for the TM segments of human glycophorin A (GpA) and two mutant forms, Gly83Ala and Thr87Val. It was shown that lipids make a significant negative contribution to the free energy of dimerization, while amino acid residues forming the interface of the helix-helix contact may be unfavorable in terms of free energy. The detailed balance between different energy contributions is highly dependent on the amino acid sequence of the TM protein segment. The results show the dominant role of the environment in the interaction of membrane proteins that is changing our notion of the driving force behind the spontaneous association of TM -helices. Adequate estimation of the contribution of the water-lipid environment thus becomes an extremely urgent task for a rational design of new molecules targeting bitopic membrane proteins, including receptor tyrosine kinases.

Efficient Strategy for the Rapid Backbone Assignment of Membrane Proteins

2005 ◽  
Vol 127 (39) ◽  
pp. 13504-13505 ◽  
Author(s):  
Nikola Trbovic ◽  
Christian Klammt ◽  
Alexander Koglin ◽  
Frank Löhr ◽  
Frank Bernhard ◽  
...  
Keyword(s):  
Membrane Proteins ◽  
Backbone Assignment ◽  
Efficient Strategy
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