Biomedical subjects

A Kister

Publications and source records attributed to A Kister.

6 recordsLinked to original sources

PubMed1996

The IgG binding site of human FcgammaRIIIB receptor involves CC' and FG loops of the membrane-proximal domain.

Fc gamma receptors for the Fc part of IgG are the mediators for antibody effector functions. FcgammaRIII and FcgammaRII are low affinity receptors that, through the interaction with immune complexes, initiate a variety of immunological responses, such as phagocytosis, antibody-dependent cellular cytotoxicity, and release of inflammatory mediators. We set out to define the IgG binding site on human FcgammaRIII. We assumed that potential beta-turns in Ig-like domains are the most probable determinants for ligand binding, and chimeric FcgammaRIIIB/FcepsilonRI receptors as well as single residue mutants were constructed in these regions of FcgammaRIIIB. Substitution of four amino acids in the membrane-proximal domain (Gln126, Arg156, Lys162, Val164) resulted in decreased binding of human IgG1. Lys162 and Val164 were found also to be crucial for the interaction with the IgG-binding inhibitory monoclonal antibody 3G8. In a putative three-dimensional model constructed in this study, these residues map on the CC loop (Gln126), on F beta-sheet (Arg156), and on the FG loop (Lys162, Val164). Our data are consistent with the study about human FcgammaRII (Hulett, M. D., Witort, E., Brinkworth, R. I., McKenzie, I. F. C., and Hogarth, P. M. (1994) J. Biol. Chem. 269, 15287-15293), suggesting that common structural determinants, i.e. FG loop or the GFC surface of the membrane-proximal domain, can be involved in interactions with IgG by both low affinity receptor classes FcgammaRII and FcgammaRIII.

Amino Acid Sequence↗

PubMed1994

Interaction between human CD2 and CD58 involves the major beta sheet surface of each of their respective adhesion domains.

The CD58 binding site on human CD2 was recently shown by nuclear magnetic resonance structural data in conjunction with site-directed mutagenesis to be a highly charged surface area covering approximately 770A2 on the major AGFCC'C" face of the CD2 immunoglobulin-like (Ig-like) NH2-terminal domain. Here we have identified the other binding surface of the CD2-CD58 adhesion pair by mutating charged residues shared among CD2 ligands (human CD58, sheep CD58, and human CD48) that are predicted to be solvent exposed on a molecular model of the Ig-like adhesion domain of human CD58. This site includes beta strand residues along the C strand (E25, K29, and K30), in the middle of the C' strand (E37) and in the G strand (K87). In addition, several residues on the CC' loop (K32, D33, and K34) form this site. Thus, the interaction between CD2 and CD58 involves the major beta sheet surface of each adhesion domain. Possible docking orientations for the CD2-CD58 molecular complex are offered. Strict conservation of human and sheep CD58 residues within the involved C and C' strands and CC' loop suggests that this region is particularly important for stable formation of the CD2-CD58 complex. The analysis of this complex offers molecular insight into the nature of a receptor-ligand pair involving two Ig family members.

Amino Acid Sequence↗

PubMed1993

The CD58 (LFA-3) binding site is a localized and highly charged surface area on the AGFCC'C" face of the human CD2 adhesion domain.

Using site-directed mutagenesis in conjunction with NMR structural data on the adhesion domain of human CD2, we have defined the binding region for CD58. Previous structural studies of rat and human CD2 indicate that this adhesion domain is immunoglobulin-like. Here we report that the CD58 binding site is a well-circumscribed, charged surface area covering approximately 770 A2 on the AGFCC'C" face of the CD2 beta barrel. This site contains beta-strand residues in the carboxyl-terminal half of the F strand (including Lys-82 and Tyr-86), the top of the C strand (Asp-32 and Lys-34), and the C' strand (Gln-46), which are all solvent exposed. In addition, several exposed residues on the FG loop (Gly-90, Lys-91, Asn-92, and Val-93), the CC' loop (Lys-41 and Lys-43), and the C'C" loop (Arg-48 and Lys-51) form this site. In contrast, neither residues on the more peripheral G and C" strands of the same CD2 surface nor residues on B, E, and D strands of the opposite face are involved in CD58 binding. This CD58 binding site is predicted to lie most distal to the T-lymphocyte surface membrane, with ready access to CD58 on the surface of the opposing antigen-presenting cell.

Amino Acid Sequence↗

PubMed1993

The theoretical analysis of the process of RNA molecule self-assembly.

The Kinetic approach to the problem of the RNA structure prediction based on the analysis of the molecule self-formation is proposed. Re-structurization that occurs during processing is described in terms of Markov processes. A new formalism designating nucleotides by complex numbers is proposed, leading to the complex unitary space of nucleic vectors. Properties of structure and transition matrices are discussed in relation to the analysis of RNA structural formation processes. The non-linear dynamic behavior of secondary structure transition is analyzed. Soliton-like oscillations of RNA and DNA tertiary structures are predicted. The Monte-Carlo simulation of the RNA structure self-formation is used to calculate the ensemble of the secondary structures of the tRNA(Ala) precursor from Bombix mori formed during processing.

Animals↗

PubMed1993

Efficient pattern comparative method for selecting functionally important motifs in protein sequences: application to zinc enzymes.

We have developed a pattern comparative method for identifying functionally important motifs in protein sequences. The essence of most standard pattern comparative methods is a comparison of patterns occurring in different sequences using an optimized weight matrix. In contrast, our approach is based on a measure of similarity among all the candidate motifs within the same sequence. This method may prove to be particularly efficient for proteins encoding the same biochemical function, but with different primary sequences, and when tertiary structure information from one or more sequences is available. We have applied this method to a special class of zinc-binding enzymes known as endopeptidases.

Amino Acid Sequence↗

PubMed1986

RNA secondary structure formation during transcription.

A new approach has been proposed for predicting the kinetic ensemble of the RNA secondary structures during chain growth. It is based on an analysis of time intervals in structural reconstruction. The Markov chain employed for describing structural reconstruction was modelled on the Monte Carlo method. A calculation was made of possible secondary structures formed during transcription. An algorithm has also been suggested for the search of a helix with a bulge type defect in which a cooperative effect is retained. Kinetic ensembles of the SD-sites and initiation regions of the polycistronic mRNA transcribed from ATP operon E. coli were calculated. A correlation between the secondary structures of these mRNA regions and the relative cistronic expression was established.

Base Sequence↗