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J Novotny

Publications and source records attributed to J Novotny.

At least 109 records · Page 6Linked to original sources
PubMed1991

Conformation of endothelin in aqueous ethylene glycol determined by 1H-NMR and molecular dynamics simulations.

The solution conformation of a 21-residue vasoconstrictor peptide endothelin-1 (ET-1) in water-ethylene glycol has been determined by two-dimensional 1H-NMR spectroscopy and constrained molecular dynamics simulations. The N-terminus (residues 1-4) appears to undergo conformational averaging and no single structure consistent with the NMR constraints could be found for this region. Residues 5-8 form a turn, and residues 9-16 exist in a helical conformation. A flexible 'hinge' between residues 8-9 allows various orientations of the turn relative to the helix. Another 'hinge' at residue 17 connects the extended C-terminus to the bicyclic core region (residues 1-15). Residues important for binding and biological activity form a contiguous surface on one side of the helix, with the two disulfides extending from the other side of the helix.

Computer Simulation↗
PubMed1991

Altered hapten recognition by two anti-digoxin hybridoma variants due to variable region point mutations.

Two spontaneous variants of the murine anti-digoxin antibody-producing hybridoma cell line 26-10 were isolated by two-color fluorescence-activated cell sorting on the basis of altered hapten binding. The variable region sequences of the antibodies produced by the mutant lines revealed that each contains a single amino acid change in the heavy chain second complementarity determining region. A Tyr to His change at position 50 leads to a 40-fold reduction in affinity for digoxin. A Ser to Phe mutation at position 52 results in a 300-fold reduction in affinity for digoxin. A competition assay involving 33 digoxin analogues was used to examine the specificity of hapten binding of 26-10 and the two mutant antibodies. The position 50 mutant has a distinct specificity change; it exhibits a preference for digoxin congeners containing a hydroxyl group at the steroid 12 position, whereas the 26-10 parent does not. The affinities of all three antibodies for hapten are progressively lowered by substitutions of increasing size at the digoxin steroid D ring 16 position. Although 26-10 binds digoxin and its genin form equally, 12 and 16 steroid position substitutions which lower affinity also confer a preference for a sugar at the steroid 3 position. These results suggest that position 50 contributes to specificity of the antibody and that alterations of the hapten can lead to differences in recognition, possibly through a shift in hapten orientation within the binding site.

Amino Acid Sequence↗
PubMed1991

The specificity properties that distinguish members of a set of homologous anti-digoxin antibodies are controlled by H chain mutations.

Five murine A/J strain anti-digoxin mAb (35-20, 40-40, 40-120, 40-140, and 40-160) have highly homologous H and L chain V regions, only differing by somatic mutation, yet differ in affinity and specificity. The availability of the VH and VL genomic clones from one hybridoma, 40-140, has now allowed studies involving in vitro mutagenesis and chain recombination among these five hybridomas. To determine the relative contributions of the mutations found in either VH or VL to the overall binding properties of these antibodies, we recombined the 40-140VH with the VL of each hybridoma. The 40-140VH gene was transfected into hybridoma variants that produce only VL. The recombinant antibodies show that the mutations present in VH, rather than in VL, affect the fine specificity properties of these antibodies, whereas, the mutations among both VH and VL chains are important in determining antigen affinity. From mutations present in VH that affect fine specificity properties, the comparison of the antibody sequences, and from the previously measured binding properties, we predicted and tested selected VH mutations for their ability to alter specificity or affinity by doing site-directed in vitro mutagenesis. The results for the somatic mutations found in this group of antibodies show: 1) VH mutations control the fine specificity properties that distinguish different members of this group; 2) in particular, VH residues 54 and 55 in CDR2 control the distinguishing characteristics of specificities between these antibodies; and 3) by mutagenesis, we had the unusual result of being able to alter Ag specificity without affecting affinity. A computer model of the 40-140 antibody binding site was generated which indicates that VH residues 54 and 55 are highly accessible.

Amino Acid Sequence↗
PubMed1991

Protein antigenicity: a thermodynamic approach.

This article summarizes computer-aided analyses of X-ray crystallographic data aimed at understanding the immunologically important aspects of the structure of antibody combining sites and protein antigens. In these calculations we use an empirical free energy potential function to estimate the atomic origin of binding specificity. By evaluating contributions of individual amino acid residues towards the Gibbs free energy of antibody-antigen complex formation, we arrive at a better understanding of the essential antigenic features of protein surfaces, as well as the inherent "binding" properties of the antibody combining sites. Such an "energetic" understanding of antigenicity may well be of practical importance in vaccine design. This article both reviews published data and discusses new results, i.e. delta G calculations on the HyHEL-10 complex with lysozyme, and an alternative treatment of the McPC 603 complex with phosphoryl choline.

Antigen-Antibody Complex↗
PubMed1991

Stabilities of leucine zipper dimers estimated by an empirical free energy method.

The leucine zipper motif is a characteristic amino acid sequence found in dimeric DNA-binding proteins. Computer-generated models for leucine zippers were constructed as alpha-helical coiled dimers with leucine repeated every seventh residue. An empirical Gibbs free energy, delta G, function which incorporates hydrophobic force, electrostatic interactions, and conformational entropy loss as the major intermolecular interactions was used to estimate the delta G of dimer formation in fos, jun, and GCN4 zipper sequences. The calculations showed that complexes known to form stable homo- or heterodimers have favorable (negative) delta G, while other less stable complexes have unfavorable (positive) delta G. Leucines in position d of the coiled coil contribute large hydrophobic stabilization energies while residues in the a position contribute less to dimer stability. Hydrophobic contributions show little sequence specificity, however, and do not contribute significantly to homo/heterodimer preference. Charged residues in the e and g positions, on the other hand, determine homo/heterodimer specificity. In GCN4 homodimers, residues GLU el, Glu b2, Lys g2, and Lys e4 greatly contribute to dimer stability. The preferential stability of fos-jun heterodimer over the jun-jun and fos-fos homodimers is primarily due to the side chains Asp b1, Glu g1, Asp b2, Glu e2, Glu g2, Glu g3, and Lys a5 of the fos helix, and Arg c1, Lys g1, Lys b2, Lys e2, Arg e4, and Glu g4 of the jun helix.

Leucine Zippers↗
PubMed1990

Computer analysis of mutations that affect antibody specificity.

The mouse hybridoma cell line 40-150 secretes antibodies with high affinity toward the cardiac glycosides digoxin and digitoxin. A spontaneous mutant, 40-150 A2.4, produces an antibody which carries a single residue mutation, Ser----Arg, in its heavy chain (H94) and has an altered specificity. A second-order mutant, 40-150 A2.4 P.10, produces two antibody molecules, one the same as 40-150 A2.4, the other lacking two residues at the N-terminus of its H chain, and having a specificity profile approaching that of 40-150 antibody. The N-terminus and the position H94 are distant from the antigen-binding site of the antibody; thus, the structural basis of the specificity changes was not immediately clear. Approximate structures of the 40-150 antibody and its mutants were constructed in the computer, based on atomic coordinates of the homologous mouse antibody McPC 603. Using the program CONGEN, the torsional space of the polypeptide backbone and side chains around position H94 was uniformly sampled, and the lowest energy conformations were analyzed in detail. The results indicate that when Arg-H94 is substituted for Ser, Arg-H94 can hydrogen bond to side chains of Asp-H101, Arg-L46, and Asp-L55. This results in a change in the surface of the combining site which may account for the affinity changes. Deletion of the two N-terminal residues increases solvent accessibility of Arg-H94. The solvation may cause a hydrogen bond between Arg-H94 and Asp-H101 to be lost, restoring the structure to one similar to that of 40-150.

Animals↗
PubMed1990

Utilization of Glycerol as a Hydrogen Acceptor by Lactobacillus reuteri: Purification of 1,3-Propanediol:NAD Oxidoreductase.

Lactobacillus reuteri utilizes exogenously added glycerol as a hydrogen acceptor during carbohydrate fermentations, resulting in higher growth rates and cell yields than those obtained during growth on carbohydrates alone. Glycerol is first converted to 3-hydroxypropionaldehyde by a coenzyme B(12)-dependent glycerol dehydratase and then reduced to 1,3-propanediol by an NAD -dependent oxidoreductase. The latter enzyme was purified and determined to have a molecular weight of 180,000; it is predicted to exist as a tetramer of identical 42,000-molecular-weight subunits.

Journal Article↗
PubMed1990

Structure-function studies of the herpes simplex virus type 1 DNA polymerase.

The analysis of the deduced amino acid sequence of the herpes simplex virus type 1 (HSV-1) DNA polymerase reported here suggests that the polymerase structure consists of domains carrying separate biological functions. The HSV-1 enzyme is known to possess 5'-3'-exonuclease (RNase H), 3'-5'-exonuclease, and DNA polymerase catalytic activities. Sequence analysis suggests an arrangement of these activities into distinct domains resembling the organization of Escherichia coli polymerase I. In order to more precisely define the structure and C-terminal limits of a putative catalytic domain responsible for the DNA polymerization activity of the HSV-1 enzyme, we have undertaken in vitro mutagenesis and computer modeling studies of the HSV-1 DNA polymerase gene. Sequence analysis predicts that the major DNA polymerization domain of the HSV-1 enzyme will be contained between residues 690 and 1100, and we present a three-dimensional model of this region, on the basis of the X-ray crystallographic structure of the E. coli polymerase I. Consistent with these structural and modeling studies, deletion analysis by in vitro mutagenesis of the HSV-1 DNA polymerase gene expressed in Saccharomyces cerevisiae has confirmed that certain amino acids from the C terminus (residues 1073 to 1144 and 1177 to 1235) can be deleted without destroying HSV-1 DNA polymerase catalytic activity and that the extreme N-terminal 227 residues are also not required for this activity.

Amino Acid Sequence↗
PubMed1989

On the attribution of binding energy in antigen-antibody complexes McPC 603, D1.3, and HyHEL-5.

Using X-ray coordinates of antigen-antibody complexes McPC 603, D1.3, and HyHEL-5, we made semiquantitative estimates of Gibbs free energy changes (delta G) accompanying noncovalent complex formation of the McPC 603 Fv fragment with phosphocholine and the D1.3 or HyHEL-5 Fv fragments with hen egg white lysozyme. Our empirical delta G function, which implicitly incorporates solvent effects, has the following components: hydrophobic force, solvent-modified electrostatics, changes in side-chain conformational entropy, translational/overall rotational entropy changes, and the dilutional (cratic) entropy term. The calculated delta G ranges matched the experimentally determined delta G of McPC 603 and D1.3 complexes and overestimated it (i.e., gave a more negative value) in the case of HyHEL-5. Relative delta G contributions of selected antibody residues, calculated for HyHEL-5 complexes, agreed with those determined independently in site-directed mutagenesis experiments. Analysis of delta G attribution in all three complexes indicated that only a small number of amino acids probably contribute actively to binding energetics. These form a subset of the total antigen-antibody contact surface. In the antibodies, the bottom part of the antigen binding cavity dominated the energetics of binding whereas in lysozyme, the energetically most important residues defined small (2.5-3 nm2) "energetic" epitopes. Thus, a concept of protein antigenicity emerges that involves the active, attractive contributions mediated by the energetic antigenic epitopes and the passive surface complementarity contributed by the surrounding contact area. The D1.3 energetic epitope of lysozyme involved Gly 22, Gly 117, and Gln 121; the HyHEL-5 epitope consisted of Arg 45 and Arg 68. These are also the essential antigenic residues determined experimentally. The above positions belong to the most protruding parts of the lysozyme surface, and their backbones are not exceptionally flexible. Least-squares analysis of six different antibody binding regions indicated that the geometry of the VH-VL interface beta-barrel is well conserved, giving no indication of significant changes in domain-domain contacts upon complex formation.

Amino Acids↗
PubMed1989

The antigenic structure of a scorpion toxin.

Scorpion toxins constitute a family of homologous proteins that exert potent pharmacological effects on ion channels. These proteins are immunogenic and constitute a good model for investigation of the molecular basis of antigenicity. In the first part of this article we summarize the results we have obtained in recent years concerning the location of the main antigenic regions of a model toxin, toxin II of the North African scorpion Androctonus australis Hector. Then, thanks to the recently available atomic coordinates of this toxin, we analyzed the relationships between the structural features of the protein and the location of the antigenic regions: we found that antigenic regions are located at exposed parts of the molecular surface, i.e. in reverse turns and the alpha-helix. These surface parts also correspond to segments of the polypeptide chain which are most accessible to a large spherical probe modelizing an antibody molecule. Finally, we obtained a general idea of what could be the main discontinuous antigenic determinants by looking for the neighboring relationships between the most exposed residues of the protein.

Animals↗
PubMed1989

On the molecular nature of "restrictive" antigenic elements present on major histocompatibility complex (MHC) proteins.

By analogy with the way in which antibodies recognize their specific antigens, it appears likely that T-cell receptors recognize peptides presented by MHC molecules as composite epitopes involving the presented peptide and portions of the MHC molecules. We extend here the analogy to attempt to define which portions of the MHC molecules are most accessible to the TcR and thereby most likely to participate in the binding. We suggest that the alpha chain segments 56-60, 73-77, 149-153 and 158-162, which are most protruding according to accessibility calculations, are likely candidates for the interaction. Again, by analogy with antibodies, we further propose that TcR recognition may involve: (1) an "active" recognition process, focussed on a few residues which provide the major contribution to the binding energy, and (2) a "passive" recognition process, in which the relatively large contact areas between TcR and the composite epitope primarily need to be compatible with one another rather than to contribute significantly to binding energy.

Binding Sites↗
PubMed1987

Trypanosoma congolense: structure and molecular organization of the surface glycoproteins of two early bloodstream variants.

The complete primary structures of two variant specific glycoproteins (VSGs) of the nannomonad Trypanosoma (N.) congolense are presented. These coat proteins subserve the function of antigenic variation. The secondary structure potentials of both VSGs have been calculated. The amino acid sequences and secondary structure potentials of these VSGs have been compared with the primary structures and secondary structure potentials of several Trypanosoma brucei complex VSGs. In homologous regions, the T. brucei complex VSGs show a pattern of sharply contrasting secondary structure potentials. It has been suggested previously that this pattern gives rise to different folding structures in different members of this polygene protein family. Thus, different short regions of the polypeptide sequence are exposed as antigenic "caps" on the solvent-exposed surface of intact trypanosomes. A sharply contrasting secondary structure potential pattern is also found in regions of the two T. congolense VSGs. However, there is little homology of primary structure between each of the two T. congolense VSGs and any member of the T. brucei complex VSG polygene family whose primary structure has been determined.

Amino Acid Sequence↗
PubMed1987

Murine and human T11 (CD2) cDNA sequences suggest a common signal transduction mechanism.

The murine equivalent of the cDNA encoding the human T11 (CD2) sheep erythrocyte-binding protein has been cloned. It codes for a putative transmembrane protein which is homologous to human T11. In contrast to immunoglobulins whose domains consist of anti-parallel beta sheets, we predict that mouse and human T11 external domains probably belong to the alpha/beta protein folding class. The cytoplasmic region of T11 is a lengthy, proline-rich segment; secondary structural analysis predicts it to have a nonglobular conformation. This elongated tail could allow for interaction with multiple other intracellular proteins and may contain a cation-binding site involved in T lineage activation.

Amino Acid Sequence↗
PubMed1987

Evolutionary relationship between the T3 chains of the T-cell receptor complex and the immunoglobulin supergene family.

Antigen receptors on the surface of the thymus-derived (T) lymphocytes are associated with small integral membrane proteins called the T3 (CD3) gamma, delta, epsilon, and zeta chains. After interaction of the T-cell receptor with antigen, the T3 proteins are believed to transfer an activation signal to the intracellular compartment. In previous studies, the human gamma, epsilon, and delta chains have been cloned along with the mouse delta chain, but a relationship between these sequences and known molecular families has not been established. We now report the molecular cloning and characterization of the murine T3-epsilon protein and a sequence and structural analysis of the relationships between all the T3 chains and the immunoglobulin superfamily. It is established that the T3 chains are immunoglobulin-related and a particular relationship to the neural cell adhesion molecule (N-CAM) is noted. This sequence relationship adds interest to previous findings that the T3 chains are genetically linked to N-CAM and Thy-1 antigen on band q23 of human chromosome 11.

Animals↗
PubMed1986

Occurrence of particular isoenzymes in fresh and cultured leukemia-lymphoma cells. II. Hexosaminidase I isoenzyme.

The isoenzyme profiles of hexosaminidase (N-acetyl-beta-D-glucosaminidase) were analyzed by isoelectric focusing on horizontal polyacrylamide thin-layer gel with special emphasis on the intermediate isoenzyme (Hex I). The expression of Hex I was examined in 87 leukemia-lymphoma cell lines, in 14 B-lymphoblastoid cell lines, in 441 cases of leukemia-lymphoma (specimens containing 80% or more tumor cells), in 22 leukemia cell lines and in 14 cases of leukemia that had been treated with phorbolesters (TPA) for induction of differentiation, and in the mononuclear cell preparations separated from peripheral blood, lymph node, thymus, bone marrow, tonsil, liver, and spleen specimens from normal donors. Hex I was detected in the leukemia cell lines arrested at early, immature or at late, mature stages of B- and T-cell differentiation, but not in cell lines blocked at intermediate stages of maturation. Most myelomonocytic leukemia cell lines and the erythroleukemia cell lines showed Hex I, whereas the B-lymphoblastoid cell lines were negative for this marker. During induction of differentiation, the expression of Hex I was lost in 13 of 15 leukemia cell lines that were originally Hex I-positive. Among the panel of the "fresh" leukemia-lymphoma cells, Hex I was found predominantly in cases of acute lymphoblastic leukemia and acute myeloblastic/monoblastic leukemia, but rarely or not at all in the mature T-, B- or myeloid malignancies. However, two out of two cases of multiple myeloma were Hex I-positive, and the Hex I expression could be induced by TPA in three of six B-cell chronic lymphocytic leukemia cases. Chronic myelocytic leukemia cells remained Hex I-negative during induction of differentiation. Hex I-positivity was not detected in the cell preparations from normal tissues, and peripheral blood indicating that the normal cellular counterpart of the Hex I-positive tumor cells are present at only low percentages within the respective cell populations. It is suggested that Hex I is a marker of early lymphoid and myeloid hematopoiesis that is no longer expressed in intermediate stages of lymphoid differentiation and in later or terminal stages of myeloid differentiation, but that is again detectable in terminally differentiated B-cells. Further studies will focus on identification and isolation of normal Hex I-positive cells.

Acetylglucosaminidase↗
PubMed1986

Speculations on sequence homologies between the fibronectin cell-attachment site, major histocompatibility antigens, and a putative AIDS virus polypeptide.

The core of the fibronectin cell-attachment site has been shown to be the tetrapeptide sequence Arg-Gly-Asp-Ser (RGDS). This peptide as well as its inverted analogue Ser-Asp-Gly-Arg (SDGR) efficiently inhibit fibronectin-mediated cell attachment in vivo and in vitro. Homology searches in protein data banks revealed the presence of the peptide SDGR in the alpha 2 domain of MHC class I antigens, and a variant of RGDS, Arg-Phe-Asp-Ser (RFDS), was found highly conserved in MHC class I (alpha 1 domain) and class II antigens (beta 1 domain). Three-dimensional models of MHC class I antigens suggested that the two tetrapeptide sequences may be located at the surface of the molecule, readily available for intermolecular contacts. We propose that fibronectin-mediated and MHC-mediated cell-cell interactions have similar molecular bases and that the RGDS-like sequences participate in specific cell adhesion between lymphoid cells. The RFDS tetrapeptide was also found in the sequence of a putative polypeptide chain encoded by the HTLVIII/LAV retrovirus family, the causative agent of AIDS. These amino acid sequence homologies suggest a common molecular basis for specific interactions between the MHC class II antigens, or the AIDS virus, and the T -cell specific T4 glycoprotein.

Amino Acid Sequence↗