Search PubMed⌕ Search

Biomedical subjects

H R Guy

Publications and source records attributed to H R Guy.

At least 37 records · Page 2Linked to original sources
PubMed1995

Structural models of Na+, Ca2+, and K+ channels.

The structure determination of voltage-gated channels by the combination of molecular modeling and mutagenesis experiments is a long term, iterative process. As such, the models should be considered as a work in progress, with changes expected as more data becomes available. The primary role of the models is that they assimilate the known data and provide ideas for further experiments to elucidate the real structures. Although the models presented here have already gone through two or three cycles of development and testing, many aspects remain tentative. Perhaps the most significant result so far is that the P segment was experimentally confirmed to form the ion-selective part of the channel. In a subsequent cycle of testing and modeling, the specific residues responsibility for Na+ and Ca2+ selectivity have been identified and the selectivity filter of K+ channels is now predicted to be formed by the side chains, but rather by the carbonyl oxygens of the conserved Gly-Tyr-Gly sequence backbone. As another example, the 9p residue of the P segment of K+ channels was originally modeled as either being buried in the protein or accessible channels was originally modeled as either being buried in the protein or accessible from inside the cell only. However, once mutation of this residue to histidine was found to affect blockade by extracellular TEA, protons, Zn2+ and histidine reagents (DeBiasi et al., 1993), the models were updated to have this and the hydrophilic residues in the first part of P form a helix that comprises part of the extracellular, outer vestibular of the pore. While this motif was used also for Na+ and Ca2+ pore models (see Fig. 2) where the putative helices are amphipathic, it remains to be verified. Modeling of the size and shape of the outer vestibule of K+ channels was also aided by the data for the binding of CTX in the extracellular entrance to the pore. Similarly, experiments with peptide toxins such as mu and omega conotoxins may prove useful in modeling the outer vestibules of the Na+ and/or Ca2+ channels. While important advances have been made, it is important to realize that these approaches are still very new. In the future we are likely to see improvements on both the theoretical and experimental sides which will greatly advance the process.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗
PubMed1994

Theoretical models of the ion channel structure of amyloid beta-protein.

Theoretical methods are used to develop models for the ion channel structure of the membrane-bound amyloid beta-protein. This follows recent observations that the beta-protein forms cation-selective channels in lipid bilayers in vitro. Amyloid beta-protein is the main component of the extracellular plaques in the brain that are characteristic of Alzheimer's disease. Based on the amino acid sequence and the unique environment of the membrane, the secondary structure of the 40-residue beta-protein is predicted to form a beta-hairpin followed by a helix-turn-helix motif. The channel structures were-designed as aggregates of peptide subunits in identical conformations. Three types of models were developed that are distinguished by whether the pore is formed by the beta-hairpins, the middle helices, or by the more hydrophobic C-terminal helices. The latter two types can be converted back and forth by a simple conformational change, which would explain the variable conduction states observed for a single channel. It is also demonstrated how lipid headgroups could be incorporated into the pore lining, and thus affect the ion selectivity. The atomic-scale detail of the models make them useful for designing experiments to determine the real structure of the channel, and thus further the understanding of peptide channels in general. In addition, if beta-protein-induced channel activity is found to be the cause of cell death in Alzheimer's disease, then the models may be helpful in designing counteracting drugs.

Alzheimer Disease↗
PubMed1994

Using sequence homology to analyze the structure and function of voltage-gated ion channel proteins.

Molecular modeling and mutagenesis analysis of voltage-gated channels have succeeded in identifying much of the topology of the proteins and in identifying which sequential segments are involved in functional mechanisms such as activation gating, inactivation gating, ion selectivity, and ligand binding. Efforts are currently underway to use these methods to model the protein structure and functional mechanisms more precisely. The experimental and theoretical efforts are dependent to a considerable extent upon information obtained by comparing homologous sequences. Although the fine details of models developed in this manner are unlikely to be as correct as models developed from x-ray crystallography and NMR, they still may contribute substantially to our understanding of the structure and function of these important proteins.

Amino Acid Sequence↗
PubMed1992

Magainin 2, a natural antibiotic from frog skin, forms ion channels in lipid bilayer membranes.

We have examined the ion channel forming properties of magainin 2 by incorporating the peptide into artificial lipid bilayers held under voltage clamp. Magainin 2 increased lipid bilayer conductance in a concentration dependent manner with a Hill coefficient of 1.7. The magainin 2 conductance was selective for monovalent cations over anions with a ratio of 5:1 and had both voltage-sensitive and -insensitive components. Two structurally related but antibiotically less potent analogues, magainin 1 and Z-12, also increased lipid bilayer conductance with a similar ion selectivity but these peptides were less potent than magainin 2. We propose that the weak cation selectivity of the magainin channels can be accounted for by the inclusion of negatively charged lipids in the channel complex and suggest two possible structures for such a channel. The ionophoric properties of these peptides are likely to be proximal to their antibiotic activities.

Animals↗
PubMed1992

Modeling the ion channel structure of cecropin.

Atomic-scale computer models were developed for how cecropin peptides may assemble in membranes to form two types of ion channels. The models are based on experimental data and physiochemical principles. Initially, cecropin peptides, in a helix-bend-helix motif, were arranged as antiparallel dimers to position conserved residues of adjacent monomers in contact. The dimers were postulated to bind to the membrane with the NH2-terminal helices sunken into the head-group layer and the COOH-terminal helices spanning the hydrophobic core. This causes a thinning of the top lipid layer of the membrane. A collection of the membrane bound dimers were then used to form the type I channel structure, with the pore formed by the transmembrane COOH-terminal helices. Type I channels were then assembled into a hexagonal lattice to explain the large number of peptides that bind to the bacterium. A concerted conformational change of a type I channel leads to the larger type II channel, in which the pore is formed by the NH2-terminal helices. By having the dimers move together, the NH2-terminal helices are inserted into the hydrophobic core without having to desolvate the charged residues. It is also shown how this could bring lipid head-groups into the pore lining.

Amino Acid Sequence↗
PubMed1992

Atomic scale structure and functional models of voltage-gated potassium channels.

Recent mutagenesis experiments have confirmed our hypothesis that a segment between S5 and S6 forms the ion selective portion of voltage-gated ion channels. Based on these and other new data, we have revised previous models of the general folding pattern of voltage-gated channel proteins and have developed atomic scale models of the entire transmembrane region of the Shaker A K+ channel. In these models, the ion selective region is a beta-barrel that spans the outer half of the membrane. The inner half of the pore is larger. The voltage-dependent conformational changes of activation gating are modeled to occur by the "helical screw" mechanism, in which the four S4 segments move along and rotate about their axes. These changes are followed by a voltage-independent conformational change, in which the segments linking S4 to S5 move from blocking the intracellular entrance of the pore to forming part of the lining of the large inner portion of the pore. The NH2-terminal of the protein was modeled as an alpha-helix that plugs the intracellular half of the pore to inactivate the channel.

Amino Acid Sequence↗
PubMed1991

A novel endopeptidase from Xenopus that recognizes alpha-helical secondary structure.

The magainin peptides of Xenopus laevis are broad-spectrum antimicrobial agents. Upon discharge from the skin glands, these basic, amphipathic peptides are each further processed at a single Xaa-Lys bond into half-peptides by a cosecreted protease. We describe the characterization and purification to homogeneity of this endopeptidase from Xenopus skin. The enzyme is a metalloprotease 110 kd in size. Analyses of substrate specificity revealed that the endopeptidase recognizes peptides that share the ability to adopt an amphipathic, alpha-helical motif composed of at least 12 residues, with one face strongly hydrophobic. Cleavage occurs on the amino side of a specific lysine that must be precisely positioned relative to the hydrophobic face of the alpha helix. This enzyme, which we propose to call "magaininase," represents a novel class of endopeptidases that hydrolyzes peptides on the basis of specific secondary structure rather than primary amino acid sequence.

Amino Acid Sequence↗
PubMed1990

Models of delta-hemolysin membrane channels and crystal structures.

Molecular modeling and energy calculations have been used to study how delta-hemolysin and melittin helices may aggregate on membrane surfaces and insert through membranes to form channels. In these models adjacent antiparallel amphipathic helices form planar "raft" structures, in which one surface is hydrophobic and the other hydrophilic. Models of delta-hemolysin crystal structure were developed using these "rafts." These models are based on the unit cell constants and the crystal symmetry obtained from the preliminary crystal data. Energy calculations favor channel models of delta-hemolysin with six or eight monomers per channel.

Amino Acids↗
PubMed1990

Pursuing the structure and function of voltage-gated channels.

A cyclical process of experimentation and theoretical analysis is being used to develop increasingly precise models of the structure and functional mechanisms of membrane proteins. Nucleic acid sequences have been determined for several voltage-gated sodium, calcium and potassium channels from invertebrates and vertebrates and from nerve and muscle tissues. Some of these sequences have been altered using site-directed mutagenesis. Properties of channels expressed after injection of normal and altered mRNA into Xenopus oocytes have been analysed by a variety of patch-clamp techniques. Preliminary structural models based on the first sequence information on sodium channels need to be modified to account for a large amount of new data. Here, Robert Guy and Franco Conti present their current view of the activation mechanism and ion selectivity of the voltage-gated channels.

Amino Acid Sequence↗
PubMed1989

Three dimensional structure of a functional internal image.

An anti-idiotypic antibody has been characterized that forms a functional internal image of the cell-attachment site of reovirus type 3. This antibody shares sequence similarity with the reovirus type 3 cell attachment protein. Studies utilizing synthetic peptides have shown that the region of sequence similarity corresponds to the cell-attachment site of the virus and the antibody. Studies are described demonstrating that these peptides possess biological activity similar to that of the virus and the antibody. Three-dimensional models of the cell-attachment site of the virus are presented and compared to a similar model for the antibody. These studies indicate that anti-idiotypic antibodies can be utilized to understand the three-dimensional basis of ligand - receptor interactions, and can lead to the development of novel biologically active substances.

Amino Acid Sequence↗
PubMed1988

Sequences of the cell-attachment sites of reovirus type 3 and its anti-idiotypic/antireceptor antibody: modeling of their three-dimensional structures.

Previous studies have identified an area of amino acid sequence similarity shared by the reovirus type 3 cell-attachment protein sigma 1 and an anti-idiotypic/antireceptor monoclonal antibody (mAb) 87.92.6 that mimics reovirus type 3 by attaching to the same cell-surface receptor. We found that synthetic peptides corresponding to this area of primary sequence similarity bind a neutralizing mAb 9BG5 against which the mAb 87.92.6 is directed. The synthetic peptides compete with mAb 87.92.6 and reovirus type 3 for binding by mAb 9BG5 and displace mAb 87.92.6 and reovirus type 3 from binding to the cell-surface reovirus type 3 receptor. Such observations show that the shared primary structure between reovirus type 3 sigma 1 polypeptide and antireceptor mAb 87.92.6 defines the oligopeptide neutralizing/cell-attachment epitope of reovirus type 3. Computer modeling of this epitope, by use of sequence similarities of known immunoglobulin hypervariable loop conformations, permits an examination of the rudimentary three-dimensional structure of this epitope.

Amino Acid Sequence↗
PubMed1987

Strong conformational propensities enhance T cell antigenicity.

The ability to predict T cell antigenic peptides would have important implications for the development of artificial vaccines. As a first step towards prediction, this report uses a new statistical technique to discover and evaluate peptide properties correlating with T cell antigenicity. This technique employs Monte Carlo computer experiments and is applicable to many problems involving protein or DNA. The technique is used to evaluate the contribution of various peptide properties to helper T cell antigenicity. The properties investigated include amphipathicities (alpha and beta), conformational propensities (alpha, beta, turn and coil), and the correlates of alpha-helices, such as the absence of helix-breakers and the positioning of the residues which stabilize alpha-helical dipoles. We also investigate segmental amphipathicity. (A peptide has this property when it contains at least two disjoint subpeptides, one hydrophobic, one hydrophilic.) Statistical correlations and stratifications assessed independent contributions to T cell antigenicity. The findings presented here have important implications for the manufacture of peptide vaccines. These implications are as follows: if possible, peptide vaccines should probably be those protein segments which have a propensity to form amphipathic alpha-helices, which do not have regions with a propensity to coil conformations, and which have a lysine at their COOH-terminus. The last two observations are of particular use in manufacturing peptides vaccines: they indicate where the synthetic peptides should be terminated. These implications are supported by the findings given below. The significances (p values) support the following statistical generalites about antigenic conformations: most helper T cell antigenic sites are amphipathic alpha-helices; alpha-helical amphipathicity and propensity to an alpha-helical conformation contribute independently to T cell antigenicity; there is evidence that some T cell antigenic sites are beta conformations instead of alpha-helices; T cell antigenic sites avoid random coiled conformations; and T cell antigenic sites are usually not segmentally amphipathic. alpha-Helical amphipathicity was significant, but segmental amphipathicity was not. This has implications for the dimensions of the structure interacting with the hydrophobic portion of an amphipathic T cell antigenic site. Lysines are unusually frequent at the COOH-terminal of T cell antigenic sites, even after accounting for tryptic digests. These lysines can stabilize alpha-helical peptides by a favorable interaction with alpha-helical dipoles.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗