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T C Hodgman

Publications and source records attributed to T C Hodgman.

25 records · Page 2Linked to original sources
PubMed1986

The herpes simplex virus type 2 equivalent of the herpes simplex virus type 1 US7 gene and its flanking sequences.

Nucleotide sequencing studies (D. J. McGeoch, A. Dolan, S. Donald, and F. Rixon, 1985, J. Mol. Biol. 181, 1-14) have indicated that herpes simplex virus type 1 (HSV-1) has a coding sequence, referred to as US7, between the genes for the glycoproteins D and E (gD and gE). Northern blot analysis and nucleotide sequencing have been carried out to show that the type 2 virus (HSV-2) has an equivalent to the US7 gene. A comparison with the HSV-1 sequence has revealed some surprising similarities and differences. At the nucleotide level, HSV-2 has inserted a large sequence into the gE promoter, retained a large palindrome present in the coding sequence but not some tandem repeats, and deleted a region beside those repeats. At the amino acid level, the putative transmembrane sequence has been remarkably well conserved, and hydrophobic moment analysis indicates that it could be interacting with polar species within the plane of the membrane. Immediately after the deletion in the HSV-2 sequence, there is an N-glycosylation signal, and HSV-2 has one more such signal than HSV-1. The longest conserved sequence at the nucleotide level codes for a region of polypeptide that is strongly predicted to fold into alpha-helix. Implications of these analyses to the structure and possible function of these molecules are discussed.

Amino Acid Sequence↗
PubMed1986

The elucidation of protein function from its amino acid sequence.

This review gives an outline of how computers may be used to determine the function of a protein, when only its primary structure is known. The current programming methods are outlined in general terms before their detailed application is discussed, and the common ways of predicting protein structure are also introduced. Identification is usually by database searching and sequence alignment, though a collection of motifs relating sequence to function are also described.

Amino Acid Sequence↗
PubMed1986

An analysis of the biological properties of monoclonal antibodies against glycoprotein D of herpes simplex virus and identification of amino acid substitutions that confer resistance to neutralization.

Four monoclonal antibodies to glycoprotein D (gD) of herpes simplex virus (HSV) types 1 and 2 neutralized virus in the presence of complement but exhibited diverse activities in its absence. Amino acid substitutions that conferred resistance to neutralization by each antibody were identified by deriving the nucleotide sequence of the gD gene from resistant mutants. Each antibody selected a substitution from different parts of the molecule and mutants resistant to a single antibody always arose from the same mutation. One of the antibodies reacted with a synthetic oligopeptide corresponding to the region of the molecule in which amino acid substitution conferred resistance, but the remaining three antibodies failed to react with predicted oligopeptide targets. These antibodies may therefore react with 'discontinuous' epitopes, a view supported by the observation that two of these three antibodies competed with each other in binding assays despite the fact that substitutions conferring resistance to neutralization arose nearly 100 residues apart in the primary sequence. The four antibodies had very different biological properties. One antibody neutralized infectivity but did not inhibit cell fusion, one antibody inhibited cell fusion but did not neutralize, while a third antibody had both activities. One antibody had neither activity but enhanced the infectivity of HSV-2 in a type-specific manner. The ability of antibodies to inhibit cell fusion by syncytial virus strains correlated with an ability to prevent plaque enlargement by a non-syncytial virus strain, implying a role for gD in the intercellular spread of virus that is independent of the syncytial phenotype. We found no correlation between neutralizing activity and anti-fusion activity suggesting that, while gD is involved in cell fusion, it has at least one other function which is required for infectivity.

Amino Acid Sequence↗
PubMedDate not supplied

Structural and functional studies of a synthetic peptide mimicking a proposed membrane inserting region of a Bacillus thuringiensis delta-endotoxin.

In order to study the mechanism of action of Bacillus thuringiensis delta-endotoxins, a synthetic 31-mer peptide corresponding to the sequence of a putative pore-forming segment of the CrylA(c) toxin was characterized structurally and functionally. The peptide maps onto the central helix (alpha 5) of the six-helix bundle of domain I of the crystal structure of the CryIIIA toxin. CD and NMR spectroscopic studies indicated that the peptide exists as an alpha-helix in methanol and a random coil in water. The peptide associated with liposomes at pH 4.7 and formed discrete, characterizable channels in planar lipid bilayers at low pHs. These channels had a conductance value of 60 picosiemens (pS). It is possible that this helix is a component of the transmembrane pore formed by B. thuringiensis delta-endotoxins in vivo.

Amino Acid Sequence↗
PubMedDate not supplied

[Method SiteGA for the recognition of transcription factor binding sites].

A new approach, SiteGA, for the prediction of functional transcription factor binding sites has been developed. The approach is based on the detection of locally positioned dinucleotides by the genetic algorithm and discriminant analysis. The approach has been applied to recognize transcription factor binding sites involved in the regulation of immune responses and cell growth (AP-1, IRF1, ISGF3, NFkappaB, STAT1), obesity and lipid metabolism (HNF4, PPAR, SREBP), and the expression of steroidogenesis genes (SF-1). SiteGA is far superior in accuracy to the traditionally used method of position weight matrices. The approach was implemented in the web tool, SiteGA http://wwwmgs2. bionet.nsc.ru/mgs/programs/sitega.

Algorithms↗