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.

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.

scholarly journals Tryptophan, an Amino-Acid Endowed with Unique Properties and Its Many Roles in Membrane Proteins

Crystals ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 1032
Author(s):  
Sonia Khemaissa ◽  
Sandrine Sagan ◽  
Astrid Walrant
Keyword(s):  
Amino Acid ◽  
Membrane Proteins ◽  
Hydrogen Bonds ◽  
Membrane Protein ◽  
Lipid Bilayers ◽  
Noncovalent Interactions ◽  
Chemical Properties ◽  
Protein Stabilization ◽  
Physico Chemical

Tryptophan is an aromatic amino acid with unique physico-chemical properties. It is often encountered in membrane proteins, especially at the level of the water/bilayer interface. It plays a role in membrane protein stabilization, anchoring and orientation in lipid bilayers. It has a hydrophobic character but can also engage in many types of interactions, such as π–cation or hydrogen bonds. In this review, we give an overview of the role of tryptophan in membrane proteins and a more detailed description of the underlying noncovalent interactions it can engage in with membrane partners.

scholarly journals GeTFEP: A general transfer free energy profile of transmembrane proteins

2017 ◽  
Author(s):  
Wei Tian ◽  
Hammad Naveed ◽  
Meishan Lin ◽  
Jie Liang
Keyword(s):  
Free Energy ◽  
Amino Acid ◽  
Membrane Proteins ◽  
Lipid Bilayers ◽  
Aqueous Environment ◽  
Energy Profile ◽  
General Applicability ◽  
Transfer Free Energy ◽  
Free Energy Profile ◽  
Important Amino Acid

AbstractFree energy of transferring amino acid side–chains from aqueous environment into lipid bilayers, known as transfer free energy (TFE), provides important information on the thermodynamic stability of membrane proteins. In this study, we derived a TFE profile named General Transfer Free Energy Profile (GeTFEP) based on computation of the TFEs of 58 β–barrel membrane proteins (βMPs). The GeTFEP agrees well with experimentally measured and computationally derived TFEs. Analysis based on the GeTFEP shows that residues in different regions of the TM segments of βMPs have different roles during the membrane insertion process. Results further reveal the importance of the sequence pattern of transmembrane strands in stabilizing βMPs in the membrane environment. In addition, we show that GeTFEP can be used to predict the positioning and the orientation of βMPs in the membrane. We also show that GeTFEP can be used to identify structurally or functionally important amino acid residue sites of βMPs. Furthermore, the TM segments of α–helical membrane proteins can be accurately predicted with GeTFEP, suggesting that the GeTFEP captures fundamental thermodynamic properties of amino acid residues inside membrane, and is of general applicability in studying membrane protein.

scholarly journals Recombinant Miltenberger I and II human blood group antigens: the role of glycosylation in cell surface expression and antigenicity of glycophorin A

Blood ◽  
1993 ◽  
Vol 82 (6) ◽  
pp. 1913-1920 ◽  
Author(s):  
M Ugorski ◽  
DP Blackall ◽  
P Pahlsson ◽  
SH Shakin-Eshleman ◽  
J Moore ◽  
...  
Keyword(s):  
Amino Acid ◽  
Cell Surface ◽  
Blood Group ◽  
Cho Cells ◽  
Surface Expression ◽  
Cell Surface Expression ◽  
Glycophorin A ◽  
Blood Group Antigens ◽  
Wild Type

Abstract Glycophorin A is a heavily glycosylated glycoprotein (1 N-linked and 15 O-linked oligosaccharides) and is highly expressed on the surface of human red blood cells. It is important in transfusion medicine because it carries several clinically relevant human blood group antigens. To study further the role of glycosylation in surface expression of this protein, four mutations were separately introduced into glycophorin A cDNA by site-directed mutagenesis. Each of these mutations blocks N- linked glycosylation at Asn26 of this glycoprotein by affecting the Asn- X-Ser/Thr acceptor sequence. Two of these mutations are identical to the amino acid polymorphisms found at position 28 in the Mi.I and Mi.II Miltenberger blood group antigens. The mutated recombinant glycoproteins were expressed in transfected wild-type and glycosylation- deficient Chinese hamster ovary (CHO) cells. When expressed in wild- type CHO cells and analyzed on Western blots, each of the four mutants had a faster electrophoretic mobility than wild-type glycophorin A, corresponding to a difference of approximately 4 Kd. This change is consistent with the absence of the N-linked oligosaccharide at Asn26. Each of the four mutants was highly expressed on the surface of CHO cells, confirming that, in the presence of normal O-linked glycosylation, the N-linked oligosaccharide is not necessary for cell surface expression of this glycoprotein. To examine the role of O- linked glycosylation in this process, the Mi.I mutant cDNA was transfected into the IdlD glycosylation-deficient CHO cell line. When the transfected IdlD cells were cultured in the presence of N- acetylgalactosamine alone, only intermediate levels of cell surface expression were seen for Mi.I mutant glycophorin A containing truncated O-linked oligosaccharides. In contrast, when cultured in the presence of galactose alone, or in the absence of both galactose and N- acetylgalactosamine, Mi.I mutant glycophorin A lacking both N-linked and O-linked oligosaccharides was not expressed at the cell surface. This extends previous results (Remaley et al, J Biol Chem 266:24176, 1991) showing that, in the absence of O-linked glycosylation, some types of N-linked glycosylation can support cell surface expression of glycophorin A. The glycophorin A mutants were also used for serologic testing with defined human antisera. These studies showed that the recombinant Mi.I and Mi.II glycoproteins appropriately bound anti-Vw and anti-Hut, respectively. They also demonstrated that these antibodies recognized the amino acid polymorphisms encoded by Mi.I and Mi.II rather than cryptic peptide antigens uncovered by the lack of N- linked glycosylation.

scholarly journals Recombinant Miltenberger I and II human blood group antigens: the role of glycosylation in cell surface expression and antigenicity of glycophorin A

Blood ◽  
1993 ◽  
Vol 82 (6) ◽  
pp. 1913-1920 ◽  
Author(s):  
M Ugorski ◽  
DP Blackall ◽  
P Pahlsson ◽  
SH Shakin-Eshleman ◽  
J Moore ◽  
...  
Keyword(s):  
Amino Acid ◽  
Cell Surface ◽  
Blood Group ◽  
Cho Cells ◽  
Surface Expression ◽  
Cell Surface Expression ◽  
Glycophorin A ◽  
Blood Group Antigens ◽  
Wild Type

Glycophorin A is a heavily glycosylated glycoprotein (1 N-linked and 15 O-linked oligosaccharides) and is highly expressed on the surface of human red blood cells. It is important in transfusion medicine because it carries several clinically relevant human blood group antigens. To study further the role of glycosylation in surface expression of this protein, four mutations were separately introduced into glycophorin A cDNA by site-directed mutagenesis. Each of these mutations blocks N- linked glycosylation at Asn26 of this glycoprotein by affecting the Asn- X-Ser/Thr acceptor sequence. Two of these mutations are identical to the amino acid polymorphisms found at position 28 in the Mi.I and Mi.II Miltenberger blood group antigens. The mutated recombinant glycoproteins were expressed in transfected wild-type and glycosylation- deficient Chinese hamster ovary (CHO) cells. When expressed in wild- type CHO cells and analyzed on Western blots, each of the four mutants had a faster electrophoretic mobility than wild-type glycophorin A, corresponding to a difference of approximately 4 Kd. This change is consistent with the absence of the N-linked oligosaccharide at Asn26. Each of the four mutants was highly expressed on the surface of CHO cells, confirming that, in the presence of normal O-linked glycosylation, the N-linked oligosaccharide is not necessary for cell surface expression of this glycoprotein. To examine the role of O- linked glycosylation in this process, the Mi.I mutant cDNA was transfected into the IdlD glycosylation-deficient CHO cell line. When the transfected IdlD cells were cultured in the presence of N- acetylgalactosamine alone, only intermediate levels of cell surface expression were seen for Mi.I mutant glycophorin A containing truncated O-linked oligosaccharides. In contrast, when cultured in the presence of galactose alone, or in the absence of both galactose and N- acetylgalactosamine, Mi.I mutant glycophorin A lacking both N-linked and O-linked oligosaccharides was not expressed at the cell surface. This extends previous results (Remaley et al, J Biol Chem 266:24176, 1991) showing that, in the absence of O-linked glycosylation, some types of N-linked glycosylation can support cell surface expression of glycophorin A. The glycophorin A mutants were also used for serologic testing with defined human antisera. These studies showed that the recombinant Mi.I and Mi.II glycoproteins appropriately bound anti-Vw and anti-Hut, respectively. They also demonstrated that these antibodies recognized the amino acid polymorphisms encoded by Mi.I and Mi.II rather than cryptic peptide antigens uncovered by the lack of N- linked glycosylation.

scholarly journals Free-energy changes of bacteriorhodopsin point mutants measured by single-molecule force spectroscopy

2021 ◽  
Vol 118 (13) ◽  
pp. e2020083118
Author(s):  
David R. Jacobson ◽  
Thomas T. Perkins
Keyword(s):  
Free Energy ◽  
Amino Acid ◽  
Membrane Protein ◽  
Single Molecule ◽  
Point Mutations ◽  
Single Amino Acid ◽  
Chemical Denaturation ◽  
Amino Acid Region ◽  
Amino Acid Mutations ◽  
Lipid Environment

Single amino acid mutations provide quantitative insight into the energetics that underlie the dynamics and folding of membrane proteins. Chemical denaturation is the most widely used assay and yields the change in unfolding free energy (ΔΔG). It has been applied to >80 different residues of bacteriorhodopsin (bR), a model membrane protein. However, such experiments have several key limitations: 1) a nonnative lipid environment, 2) a denatured state with significant secondary structure, 3) error introduced by extrapolation to zero denaturant, and 4) the requirement of globally reversible refolding. We overcame these limitations by reversibly unfolding local regions of an individual protein with mechanical force using an atomic-force-microscope assay optimized for 2 μs time resolution and 1 pN force stability. In this assay, bR was unfolded from its native bilayer into a well-defined, stretched state. To measure ΔΔG, we introduced two alanine point mutations into an 8-amino-acid region at the C-terminal end of bR’s G helix. For each, we reversibly unfolded and refolded this region hundreds of times while the rest of the protein remained folded. Our single-molecule–derived ΔΔG for mutant L223A (−2.3 ± 0.6 kcal/mol) quantitatively agreed with past chemical denaturation results while our ΔΔG for mutant V217A was 2.2-fold larger (−2.4 ± 0.6 kcal/mol). We attribute the latter result, in part, to contact between Val217 and a natively bound squalene lipid, highlighting the contribution of membrane protein–lipid contacts not present in chemical denaturation assays. More generally, we established a platform for determining ΔΔG for a fully folded membrane protein embedded in its native bilayer.

Chronic Pain: Fundamental Scientific Considerations, Specifically for Legal Claims

2013 ◽  
Vol 18 (1) ◽  
pp. 1-18 ◽  
Author(s):  
Robert J. Barth
Keyword(s):  
Health Outcomes ◽  
Pain Perception ◽  
Driving Forces ◽  
Psychological Treatment ◽  
Dominant Role ◽  
Meta Analysis ◽  
General Medicine ◽  
Pain Syndrome ◽  
Problematic Relationship

Abstract Scientific findings have indicated that psychological and social factors are the driving forces behind most chronic benign pain presentations, especially in a claim context, and are relevant to at least three of the AMA Guides publications: AMA Guides to Evaluation of Disease and Injury Causation, AMA Guides to Work Ability and Return to Work, and AMA Guides to the Evaluation of Permanent Impairment. The author reviews and summarizes studies that have identified the dominant role of financial, psychological, and other non–general medicine factors in patients who report low back pain. For example, one meta-analysis found that compensation results in an increase in pain perception and a reduction in the ability to benefit from medical and psychological treatment. Other studies have found a correlation between the level of compensation and health outcomes (greater compensation is associated with worse outcomes), and legal systems that discourage compensation for pain produce better health outcomes. One study found that, among persons with carpal tunnel syndrome, claimants had worse outcomes than nonclaimants despite receiving more treatment; another examined the problematic relationship between complex regional pain syndrome (CRPS) and compensation and found that cases of CRPS are dominated by legal claims, a disparity that highlights the dominant role of compensation. Workers’ compensation claimants are almost never evaluated for personality disorders or mental illness. The article concludes with recommendations that evaluators can consider in individual cases.

Effect of High Salt Concentration on Ion Clustering and Transport in Polymer Solid Electrolytes: a Molecular Dynamics Study of PEO-LiTFSI

2018 ◽  
Author(s):  
Nicola Molinari ◽  
Jonathan P. Mailoa ◽  
Boris Kozinsky
Keyword(s):  
Polymer Electrolyte ◽  
Salt Concentration ◽  
Rational Design ◽  
Material System ◽  
Ion Dynamics ◽  
High Concentration ◽  
Anion Clusters ◽  
Poly Ethylene Oxide ◽  
Poly Ethylene

<div> <div> <div> <p>The model and analysis methods developed in this work are generally applicable to any polymer electrolyte/cation-anion combination, but we focus on the currently most prominent polymer electrolyte material system: poly(ethylene) oxide/Li- bis(trifluoromethane) sulfonamide (PEO + LiTFSI). The obtained results are surprising and challenge the conventional understanding of ionic transport in polymer electrolytes: the investigation of a technologically relevant salt concentration range (1 - 4 M) revealed the central role of the anion in coordinating and hindering Li ion movement. Our results provide insights into correlated ion dynamics, at the same time enabling rational design of better PEO-based electrolytes. In particular, we report the following novel observations. 1. Strong binding of the Li cation with the polymer competes with significant correlation of the cation with the salt anion. 2. The appearance of cation-anion clusters, especially at high concentration. 3. The asymmetry in the composition (and therefore charge) of such clusters; specifically, we find the tendency for clusters to have a higher number of anions than cations.</p> </div> </div> </div>

Sign in / Sign up

Export Citation Format

Share Document