, a bio/informatics shared resource is still "open for business" - Visit the CDS website


Other search tools

About this data

The publication data currently available has been vetted by Vanderbilt faculty, staff, administrators and trainees. The data itself is retrieved directly from NCBI's PubMed and is automatically updated on a weekly basis to ensure accuracy and completeness.

If you have any questions or comments, please contact us.

Results: 1 to 10 of 65

Publication Record

Connections

Peripheral myelin protein 22 alters membrane architecture.
Mittendorf KF, Marinko JT, Hampton CM, Ke Z, Hadziselimovic A, Schlebach JP, Law CL, Li J, Wright ER, Sanders CR, Ohi MD
(2017) Sci Adv 3: e1700220
MeSH Terms: Cell Membrane, Charcot-Marie-Tooth Disease, Cysteine, Humans, Lipid Bilayers, Lipids, Liposomes, Mutation, Myelin Proteins, Recombinant Proteins
Show Abstract · Added November 21, 2018
Peripheral myelin protein 22 (PMP22) is highly expressed in myelinating Schwann cells of the peripheral nervous system. genetic alterations cause the most common forms of Charcot-Marie-Tooth disease (CMTD), which is characterized by severe dysmyelination in the peripheral nerves. However, the functions of PMP22 in Schwann cell membranes remain unclear. We demonstrate that reconstitution of purified PMP22 into lipid vesicles results in the formation of compressed and cylindrically wrapped protein-lipid vesicles that share common organizational traits with compact myelin of peripheral nerves in vivo. The formation of these myelin-like assemblies depends on the lipid-to-PMP22 ratio, as well as on the PMP22 extracellular loops. Formation of the myelin-like assemblies is disrupted by a CMTD-causing mutation. This study provides both a biochemical assay for PMP22 function and evidence that PMP22 directly contributes to membrane organization in compact myelin.
0 Communities
2 Members
0 Resources
10 MeSH Terms
Gβγ directly modulates vesicle fusion by competing with synaptotagmin for binding to neuronal SNARE proteins embedded in membranes.
Zurawski Z, Page B, Chicka MC, Brindley RL, Wells CA, Preininger AM, Hyde K, Gilbert JA, Cruz-Rodriguez O, Currie KPM, Chapman ER, Alford S, Hamm HE
(2017) J Biol Chem 292: 12165-12177
MeSH Terms: Animals, Binding, Competitive, Calcium Signaling, Cattle, Cell Line, GTP-Binding Protein beta Subunits, GTP-Binding Protein gamma Subunits, Humans, Lipid Bilayers, Liposomes, Membrane Fusion, Models, Molecular, Mutation, Nerve Tissue Proteins, Peptide Fragments, Protein Conformation, Protein Interaction Domains and Motifs, Protein Multimerization, Rats, Recombinant Fusion Proteins, Recombinant Proteins, Synaptosomal-Associated Protein 25, Synaptotagmin I, Syntaxin 1
Show Abstract · Added July 12, 2017
G-coupled G protein-coupled receptors can inhibit neurotransmitter release at synapses via multiple mechanisms. In addition to Gβγ-mediated modulation of voltage-gated calcium channels (VGCC), inhibition can also be mediated through the direct interaction of Gβγ subunits with the soluble -ethylmaleimide attachment protein receptor (SNARE) complex of the vesicle fusion apparatus. Binding studies with soluble SNARE complexes have shown that Gβγ binds to both ternary SNARE complexes, t-SNARE heterodimers, and monomeric SNAREs, competing with synaptotagmin 1(syt1) for binding sites on t-SNARE. However, in secretory cells, Gβγ, SNAREs, and synaptotagmin interact in the lipid environment of a vesicle at the plasma membrane. To approximate this environment, we show that fluorescently labeled Gβγ interacts specifically with lipid-embedded t-SNAREs consisting of full-length syntaxin 1 and SNAP-25B at the membrane, as measured by fluorescence polarization. Fluorescently labeled syt1 undergoes competition with Gβγ for SNARE-binding sites in lipid environments. Mutant Gβγ subunits that were previously shown to be more efficacious at inhibiting Ca-triggered exocytotic release than wild-type Gβγ were also shown to bind SNAREs at a higher affinity than wild type in a lipid environment. These mutant Gβγ subunits were unable to inhibit VGCC currents. Specific peptides corresponding to regions on Gβ and Gγ shown to be important for the interaction disrupt the interaction in a concentration-dependent manner. In fusion assays using full-length t- and v-SNAREs embedded in liposomes, Gβγ inhibited Ca/synaptotagmin-dependent fusion. Together, these studies demonstrate the importance of these regions for the Gβγ-SNARE interaction and show that the target of Gβγ, downstream of VGCC, is the membrane-embedded SNARE complex.
© 2017 by The American Society for Biochemistry and Molecular Biology, Inc.
0 Communities
2 Members
0 Resources
24 MeSH Terms
Investigating the Structure of Multicomponent Gel-Phase Lipid Bilayers.
Hartkamp R, Moore TC, Iacovella CR, Thompson MA, Bulsara PA, Moore DJ, McCabe C
(2016) Biophys J 111: 813-823
MeSH Terms: Gels, Hydrogen Bonding, Lipid Bilayers, Models, Molecular, Molecular Conformation, Water
Show Abstract · Added May 3, 2017
Single- and multicomponent lipid bilayers of 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine (DPPC), 1,2-distearoyl-sn-glycero-3-phosphatidylcholine (DSPC), isostearyl isostearate, and heptadecanoyl heptadecanoate in the gel phase are studied via molecular dynamics simulations. It is shown that the structural properties of multicomponent bilayers can deviate strongly from the structures of their single-component counterparts. Specifically, the lipid mixtures are shown to adopt a compact packing by offsetting the positioning depths at which different lipid species are located in the bilayer. This packing mechanism affects the area per lipid, the bilayer height, and the chain tilt angles and has important consequences for other bilayer properties, such as interfacial hydrogen bonding and bilayer permeability. In particular, the simulations suggest that bilayers containing isostearyl isostearate or heptadecanoyl heptadecanoate are less permeable than pure 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine or DSPC bilayers. Furthermore, hydrogen-bond analysis shows that the residence times of lipid-water hydrogen bonds depend strongly on the bilayer composition, with longer residence times for bilayers that have a higher DSPC content. The findings illustrate and explain the fundamental differences between the properties of single- and multicomponent bilayers.
Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.
0 Communities
1 Members
0 Resources
6 MeSH Terms
Structural organization of membrane-inserted hexamers formed by Helicobacter pylori VacA toxin.
Pyburn TM, Foegeding NJ, González-Rivera C, McDonald NA, Gould KL, Cover TL, Ohi MD
(2016) Mol Microbiol 102: 22-36
MeSH Terms: Bacterial Proteins, Cytotoxins, HeLa Cells, Helicobacter pylori, Humans, Lipid Bilayers, Membrane Proteins, Protein Conformation, Protein Domains, Structure-Activity Relationship, Vacuoles
Show Abstract · Added September 29, 2016
Helicobacter pylori colonizes the human stomach and is a potential cause of peptic ulceration or gastric adenocarcinoma. H. pylori secretes a pore-forming toxin known as vacuolating cytotoxin A (VacA). The 88 kDa secreted VacA protein, composed of an N-terminal p33 domain and a C-terminal p55 domain, assembles into water-soluble oligomers. The structural organization of membrane-bound VacA has not been characterized in any detail and the role(s) of specific VacA domains in membrane binding and insertion are unclear. We show that membrane-bound VacA organizes into hexameric oligomers. Comparison of the two-dimensional averages of membrane-bound and soluble VacA hexamers generated using single particle electron microscopy reveals a structural difference in the central region of the oligomers (corresponding to the p33 domain), suggesting that membrane association triggers a structural change in the p33 domain. Analyses of the isolated p55 domain and VacA variants demonstrate that while the p55 domain can bind membranes, the p33 domain is required for membrane insertion. Surprisingly, neither VacA oligomerization nor the presence of putative transmembrane GXXXG repeats in the p33 domain is required for membrane insertion. These findings provide new insights into the process by which VacA binds and inserts into the lipid bilayer to form membrane channels.
© 2016 John Wiley & Sons Ltd.
0 Communities
3 Members
0 Resources
11 MeSH Terms
Probing Structural Dynamics and Topology of the KCNE1 Membrane Protein in Lipid Bilayers via Site-Directed Spin Labeling and Electron Paramagnetic Resonance Spectroscopy.
Sahu ID, Craig AF, Dunagan MM, Troxel KR, Zhang R, Meiberg AG, Harmon CN, McCarrick RM, Kroncke BM, Sanders CR, Lorigan GA
(2015) Biochemistry 54: 6402-12
MeSH Terms: Amino Acid Sequence, Electron Spin Resonance Spectroscopy, Lipid Bilayers, Molecular Dynamics Simulation, Molecular Sequence Data, Mutagenesis, Site-Directed, Potassium Channels, Voltage-Gated, Protein Conformation
Show Abstract · Added November 21, 2018
KCNE1 is a single transmembrane protein that modulates the function of voltage-gated potassium channels, including KCNQ1. Hereditary mutations in the genes encoding either protein can result in diseases such as congenital deafness, long QT syndrome, ventricular tachyarrhythmia, syncope, and sudden cardiac death. Despite the biological significance of KCNE1, the structure and dynamic properties of its physiologically relevant native membrane-bound state are not fully understood. In this study, the structural dynamics and topology of KCNE1 in bilayered lipid vesicles was investigated using site-directed spin labeling (SDSL) and electron paramagnetic resonance (EPR) spectroscopy. A 53-residue nitroxide EPR scan of the KCNE1 protein sequence including all 27 residues of the transmembrane domain (45-71) and 26 residues of the N- and C-termini of KCNE1 in lipid bilayered vesicles was analyzed in terms of nitroxide side-chain motion. Continuous wave-EPR spectral line shape analysis indicated the nitroxide spin label side-chains located in the KCNE1 TMD are less mobile when compared to the extracellular region of KCNE1. The EPR data also revealed that the C-terminus of KCNE1 is more mobile when compared to the N-terminus. EPR power saturation experiments were performed on 41 sites including 18 residues previously proposed to reside in the transmembrane domain (TMD) and 23 residues of the N- and C-termini to determine the topology of KCNE1 with respect to the 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)/1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (POPG) lipid bilayers. The results indicated that the transmembrane domain is indeed buried within the membrane, spanning the width of the lipid bilayer. Power saturation data also revealed that the extracellular region of KCNE1 is solvent-exposed with some of the portions partially or weakly interacting with the membrane surface. These results are consistent with the previously published solution NMR structure of KCNE1 in micelles.
0 Communities
3 Members
0 Resources
MeSH Terms
Development of electron spin echo envelope modulation spectroscopy to probe the secondary structure of recombinant membrane proteins in a lipid bilayer.
Zhang R, Sahu ID, Gibson KR, Muhammad NB, Bali AP, Comer RG, Liu L, Craig AF, Mccarrick RM, Dabney-Smith C, Sanders CR, Lorigan GA
(2015) Protein Sci 24: 1707-13
MeSH Terms: Electron Spin Resonance Spectroscopy, Humans, Lipid Bilayers, Membrane Proteins, Models, Molecular, Potassium Channels, Voltage-Gated, Protein Structure, Secondary
Show Abstract · Added November 21, 2018
Membrane proteins conduct many important biological functions essential to the survival of organisms. However, due to their inherent hydrophobic nature, it is very difficult to obtain structural information on membrane-bound proteins using traditional biophysical techniques. We are developing a new approach to probe the secondary structure of membrane proteins using the pulsed EPR technique of Electron Spin Echo Envelope Modulation (ESEEM) Spectroscopy. This method has been successfully applied to model peptides made synthetically. However, in order for this ESEEM technique to be widely applicable to larger membrane protein systems with no size limitations, protein samples with deuterated residues need to be prepared via protein expression methods. For the first time, this study shows that the ESEEM approach can be used to probe the local secondary structure of a (2) H-labeled d8 -Val overexpressed membrane protein in a membrane mimetic environment. The membrane-bound human KCNE1 protein was used with a known solution NMR structure to demonstrate the applicability of this methodology. Three different α-helical regions of KCNE1 were probed: the extracellular domain (Val21), transmembrane domain (Val50), and cytoplasmic domain (Val95). These results indicated α-helical structures in all three segments, consistent with the micelle structure of KCNE1. Furthermore, KCNE1 was incorporated into a lipid bilayer and the secondary structure of the transmembrane domain (Val50) was shown to be α-helical in a more native-like environment. This study extends the application of this ESEEM approach to much larger membrane protein systems that are difficult to study with X-ray crystallography and/or NMR spectroscopy.
© 2015 The Protein Society.
0 Communities
1 Members
0 Resources
MeSH Terms
Notch Transmembrane Domain: Secondary Structure and Topology.
Deatherage CL, Lu Z, Kim JH, Sanders CR
(2015) Biochemistry 54: 3565-8
MeSH Terms: Humans, Lipid Bilayers, Lysophosphatidylcholines, Models, Molecular, Nuclear Magnetic Resonance, Biomolecular, Peptide Fragments, Phosphatidylcholines, Protein Conformation, Protein Structure, Secondary, Protein Structure, Tertiary, Receptor, Notch1, Recombinant Proteins, Surface Properties
Show Abstract · Added February 5, 2016
The Notch signaling pathway is critical in development, neuronal maintenance, and hematopoiesis. An obligate step in the activation of this pathway is cleavage of its transmembrane (TM) domain by γ-secretase. While the soluble domains have been extensively studied, little has been done to characterize its TM and flanking juxtamembrane (JM) segments. Here, we present the results of nuclear magnetic resonance (NMR) studies of the human Notch1 TM/JM domain. The TM domain is largely α-helical. While the flanking JM segments do not adopt regular secondary structure, they interact with the membrane surface, suggesting membrane interactions may play a role in modulating its cleavage by γ-secretase and subsequent NOTCH signaling function.
1 Communities
1 Members
0 Resources
13 MeSH Terms
Functional stability of rhodopsin in a bicelle system: evaluating G protein activation by rhodopsin in bicelles.
Kaya AI, Iverson TM, Hamm HE
(2015) Methods Mol Biol 1271: 67-76
MeSH Terms: Cell Membrane, GTP-Binding Proteins, Lipid Bilayers, Phospholipids, Rhodopsin
Show Abstract · Added March 24, 2020
Rhodopsin is a prototypical member of the G protein-coupled receptors (GPCRs). This photoreceptor is responsible for initiating the visual signaling transduction cascade upon interaction with its heterotrimeric G protein, transducin (Gt), after light activation. Like all transmembrane proteins, rhodopsin is embedded within a phospholipid bilayer. Many studies have proposed that the membrane composition of this bilayer is an important factor for receptor function during the activation process. Here we describe the methods and assays used to evaluate the function of purified and reconstituted rhodopsin in bicelles.
0 Communities
1 Members
0 Resources
MeSH Terms
Structural investigation of the transmembrane domain of KCNE1 in proteoliposomes.
Sahu ID, Kroncke BM, Zhang R, Dunagan MM, Smith HJ, Craig A, McCarrick RM, Sanders CR, Lorigan GA
(2014) Biochemistry 53: 6392-401
MeSH Terms: Amino Acid Substitution, Humans, Lipid Bilayers, Liposomes, Molecular Dynamics Simulation, Phosphatidylcholines, Phosphatidylglycerols, Potassium Channels, Voltage-Gated, Protein Structure, Secondary, Protein Structure, Tertiary, Thermodynamics
Show Abstract · Added November 21, 2018
KCNE1 is a single-transmembrane protein of the KCNE family that modulates the function of voltage-gated potassium channels, including KCNQ1. Hereditary mutations in KCNE1 have been linked to diseases such as long QT syndrome (LQTS), atrial fibrillation, sudden infant death syndrome, and deafness. The transmembrane domain (TMD) of KCNE1 plays a key role in mediating the physical association with KCNQ1 and in subsequent modulation of channel gating kinetics and conductance. However, the mechanisms associated with these roles for the TMD remain poorly understood, highlighting a need for experimental structural studies. A previous solution NMR study of KCNE1 in LMPG micelles revealed a curved transmembrane domain, a structural feature proposed to be critical to KCNE1 function. However, this curvature potentially reflects an artifact of working in detergent micelles. Double electron electron resonance (DEER) measurements were conducted on KCNE1 in LMPG micelles, POPC/POPG proteoliposomes, and POPC/POPG lipodisq nanoparticles to directly compare the structure of the TMD in a variety of different membrane environments. Experimentally derived DEER distances coupled with simulated annealing molecular dynamic simulations were used to probe the bilayer structure of the TMD of KCNE1. The results indicate that the structure is helical in proteoliposomes and is slightly curved, which is consistent with the previously determined solution NMR structure in micelles. The evident resilience of the curvature in the KCNE1 TMD leads us to hypothesize that the curvature is likely to be maintained upon binding of the protein to the KCNQ1 channel.
0 Communities
1 Members
0 Resources
MeSH Terms
Influence of Pathogenic Mutations on the Energetics of Translocon-Mediated Bilayer Integration of Transmembrane Helices.
Schlebach JP, Sanders CR
(2015) J Membr Biol 248: 371-81
MeSH Terms: Amino Acid Sequence, Animals, Cattle, Conserved Sequence, Cystic Fibrosis Transmembrane Conductance Regulator, Humans, KCNQ1 Potassium Channel, Lipid Bilayers, Mutation, Mutation, Missense, Myelin Proteins, Protein Structure, Secondary, Protein Transport, Receptors, Vasopressin, Rhodopsin, Thermodynamics
Show Abstract · Added November 21, 2018
Aberrant protein folding and assembly contribute to a number of diseases, and efforts to rationalize how pathogenic mutations cause this phenomenon represent an important imperative in biochemical research. However, for α-helical membrane proteins, this task is complicated by the fact that membrane proteins require intricate machinery to achieve structural and functional maturity under cellular conditions. In this work, we utilized the ΔG predictor algorithm ( www.dgpred.cbr.su.se ) to survey 470 known pathogenic mutations occurring in five misfolding-prone α-helical membrane proteins for their predicted effects on the translocon-mediated membrane integration of transmembrane helices, a critical step in biosynthesis and folding of nascent membrane proteins. The results suggest that about 10 % of these mutations are likely to have adverse effects on the topogenesis of nascent membrane proteins. These results suggest that the misfolding of a modest but nonetheless significant subset of pathogenic variants may begin at the translocon. Potential implications for therapeutic design and personalized medicine are discussed.
0 Communities
1 Members
0 Resources
MeSH Terms