A cooperative folding unit in HIV-1 protease. Implications for protein stability and occurrence of drug-induced mutations.

We investigated the HIV-1 protease molecule for the occurrence of cooperative folding units, i.e. structural units that exhibit a relatively stronger protection against unfolding than do other parts of the molecule. Calculated unfolding penalties are used to delineate folding units. This procedure identifies a folding core in HIV-1 protease, based on an ensemble of denatured states derived from native structures, comprising a spatially close unit of residues 84-91, 74-78 and 22-32, the last of which contains the active site residues D25, T26 and G27. Observed enzyme mutations of HIV-1 protease, either naturally occurring or induced by drug therapy, are found in regions that are not structurally designed to withstand unfolding. These mutations are especially likely to occur in the flap region, a part of the protein which is not essential for the stability of the protein, but does contribute significantly to the stability of protease-drug complexes. A similar avoidance of structurally protected regions in the reverse transcriptase enzyme is also observed.

Identification of cooperative folding units in a set of native proteins.

Cooperative unfolding penalties are calculated by statistically evaluating an ensemble of denatured states derived from native structures. The ensemble of denatured states is determined by dividing the native protein into short contiguous segments and defining all possible combinations of native, i.e., interacting, and non-native, i.e., non-interacting, segments. We use a novel knowledge-based scoring function, derived from a set of non-homologous proteins in the Protein Data Bank, to describe the interactions among residues. This procedure is used for the structural identification of cooperative folding cores for four globular proteins: bovine pancreatic trypsin inhibitor, horse heart cytochrome c, French bean plastocyanin, and staphylococcal nuclease. The theoretical folding units are shown to correspond to regions that exhibit enhanced stability against denaturation as determined from experimental hydrogen exchange protection factors. Using a sequence similarity score for related sequences, we show that, in addition to residues necessary for enzymatic function, those amino acids comprising structurally important folding cores are also preferentially conserved during evolution. This implies that the identified folding cores may be part of an array of fundamental structural folding units.

Analysis of hydrophobicity in the alpha and beta chemokine families and its relevance to dimerization.

The chemokine family of chemotactic cytokines plays a key role in orchestrating the immune response. The family has been divided into 2 subfamilies, alpha and beta, based on the spacing of the first 2 cysteine residues, function, and chromosomal location. Members within each subfamily have 25-70% sequence identity, whereas the amino acid identity between members of the 2 subfamilies ranges from 20 to 40%. A quantitative analysis of the hydrophobic properties of 11 alpha and 9 beta chemokine sequences, based on the coordinates of the prototypic alpha and beta chemokines, interleukin-8 (IL-8), and human macrophage inflammatory protein-1 beta (hMIP-1 beta), respectively, is presented. The monomers of the alpha and beta chemokines have their strongest core hydrophobic cluster at equivalent positions, consistent with their similar tertiary structures. In contrast, the pattern of monomer surface hydrophobicity between the alpha and beta chemokines differs in a manner that is fully consistent with the observed differences in quaternary structure. The most hydrophobic surface clusters on the monomer subunits are located in very different regions of the alpha and beta chemokines and comprise in each case the amino acids that are buried at the interface of their respective dimers. The theoretical analysis of hydrophobicity strongly supports the hypothesis that the distinct dimers observed for IL-8 and hMIP-1 beta are preserved for all the alpha and beta chemokines, respectively. This provides a rational explanation for the lack of receptor crossbinding and reactivity between the alpha and beta chemokine subfamilies.

The lymphoproliferative disease virus of turkeys represents a distinct class of avian type-C retrovirus.

The lymphoproliferative disease virus of turkeys (LPDV) is the etiological agent of a rapidly developing lymphoproliferative process in turkeys. To better understand the genetic relationships of LPDV to other retroviruses we determined the nucleotide sequence of its pol gene. Comparative computer analyses of the deduced amino acid sequences of the reverse transcriptase and integrase domains within pol established that LPDV represents a distinct class of avian retroviruses that is most closely related to the avian leukemia-sarcoma viruses.

A pseudoreceptor docking study of 4,5-alpha-epoxymorphinans with a range of dielectric constants.

Thirteen 4,5-epoxymorphinan mu agonists with established analgesic action were docked into an Asp-Lys-His-Phe pseudoreceptor complex under a range of distance-dependent dielectric conditions. The number of compounds with potential energies of the docked complexes that agreed in rank order with corresponding analgesic potencies was determined for each condition. Two dielectric conditions, n-decane (1.991) and ethanol (24.3), enabled the greatest number of compounds to relate to their pseudoreceptors with each having 9 and 8 successes respectively. Both of these conditions demonstrated unique influences on the types of structures that were successfully docked. For example, the morphine stereoisomer alpha-isomorphine, the geometric isomer B/C trans-morphine, and the 8-position-substituted gamma-isomorphine were successes in the n-decane condition, whereas the ethanol condition produced the substituted codeine derivatives dihydrocodeinone and dihydroxycodeinone. These findings emphasize the importance of dielectric influence when developing force-field modeled quantitative structure-activity relationships for a closely related homologous series.

Strong patterns in homooligomer tracts occurrences in non-coding and in potential regulatory sites in eukaryotic genomes.

Previous studies of the dinucleotides flanking both the 5' and 3' ends of homooligomer tracts have shown that some flanks are consistently preferred over others (1,2). In the first preferred group, the homooligomer tracts are flanked by the same nucleotide and/or the complementary nucleotides, e.g.,ATAn,TTAn,CCGn, where n = 2-5. Runs flanked by nucleotides with which they cannot base pair are distinctly disfavored. (In this group An/Tn are flanked by C and/or G; Gn/Cn are flanked by A/T, e.g.,CGAn,TnGG,GnAT). The frequencies of runs flanked by A or T, and G or C ("mixed"group) are as expected. Here we seek the origin of this effect and its relevance to protein-DNA interactions. Surprisingly, within the first group, runs flanked by their complements with a pyrimidine-purine junction (e.g.,TTAn,CnGG) are greatly preferred. The frequencies of their purine-pyrimidine junction mirror-images is just as expected. This effect, as well as additional ones enumerated below, is seen universally in eukaryotes and in prokaryotes, although it is stronger in the former. Detailed analysis of regulatory regions shows these strong trends, particularly in GC sequences. The potential relationship to DNA conformation and DNA-protein interaction is discussed.

Distinct patterns in homooligomer tract sequence context in prokaryotic and eukaryotic DNA.

The distributions of the junction sequences of homooligomer tracts of various lengths have been examined in prokaryotic DNA sequences and compared with those of eukaryotes. The general trends in the nearest and next to nearest neighbors to the tracts are similar for both groups. In both prokaryotes and eukaryotes A/T runs are preferentially flanked on either the 5' or the 3' ends by A and/or T. G/C runs are preferentially flanked by G and/or C. There is discrimination against A/T runs flanked by G or C and G/C runs flanked by A or T. However, whereas the distribution of prokaryotic homooligomer tract junction sequences was quite homogeneous, large variations were observed in the 5-fold larger eukaryotic database, increasing in magnitude from tracts of length 2 to 3 to 4 base pairs long. Possible DNA conformational implications and in particular DNA curvature and packaging aspects of prokaryotes and eukaryotes are discussed.

Sequence context of oligomer tracts in eukaryotic DNA: biological and conformational implications.

Recent studies of homooligomer tracts suggest different characteristics from random sequence DNA (dA).(dT) and (dG).(dC) tracts are frequent in upstream regions and in some cases have been shown to be essential for regulation. Here we examine homooligomer occurrences in non-coding and coding eukaryotic sequences, focusing on the context in which the homooligomers occur. This analysis of sequences in the junction areas yields distinct and consistent characteristics. In particular, the nucleotide interrupting a run is most frequently complementary to the run. The base next to it is most frequently identical to the one constituting the run. For A or T runs the least frequent nearest and next to nearest neighbors are G or C. For G or C tracts the least frequent are A or T. Complementary oligomers behave similarly. These and additional trends are strongest for run lengths greater than or equal to 3. The computations are carried out on the whole eukaryotic database of greater than 4 x 10(6) nucleotides, separately for coding and non-coding regions. These same trends are evident for both groups, but are somewhat stronger for the non-coding regions. The context in which the homooligomers occur may yield some clues to DNA conformation and its biological implications.

DISTAN--a program which detects significant distances between short oligonucleotides.

We present an algorithm to detect distances between oligonucleotides in large collections of nucleic acids sequences. The ratios of actual frequencies of occurrence of short oligonucleotides at a given distance to the corresponding expected frequencies were analyzed in four categories of DNA sequences leukaryotic exons, bacterial genes, introns and non-Alu repeated DNAs). Three base periodic occurrences (independent of the reading frame) of all combinations of mononucleotides and repeats of all dinucleotides was characteristic for protein coding regions. This was also the case with the majority of trinucleotides (including translational stop signals) in these regions. Mirror-symmetric trinucleotides (except GCG and CGC) displayed a strong tendency to be two base periodically repeated in introns. Some two and three base periodic motifs were also observed in repeated DNAs. The possible biological implications of outstanding three base periodicities in bacterial genes and eukaryotic exons are discussed.

Distance analysis helps to establish characteristic motifs in intron sequences.

Computer-assisted sequence analysis was applied to detect the most apparent nonrandom sequence motifs in eukaryotic introns. We describe in detail a method, which we call distance analysis, that we applied to the extensive study of 405 eukaryotic intron sequences. We observed very strong two-base periodicities for almost all tetranucleotides that are tandem repeats of nonhomopolymeric dinucleotides (the exception was GCGC and CGCG). We also observed, by using a fixed-point alignment method, that these periodic sequence motifs belong to large clusters of dinucleotides repeated tandemly as many as 15-35 times, which corresponds to the cluster lengths of 30-70 bases. We did not observe two-base periodicity of tetranucleotides in the collections of either 262 spliced eukaryotic exons or 107 bacterial genes. Instead, these sequences displayed strong three-base periodicity of some other tetranucleotides. These findings suggest that introns and exons display distinct sequence properties that can be used for mapping purposes.

Chemical and immunological characterizations of equine infectious anemia virus gag-encoded proteins.

The viral core proteins (p15, p26, p11, and p9) of equine infectious anemia virus (EIAV) (Wyoming strain) were purified by reverse-phase high-pressure liquid chromatography. Each purified protein was analyzed for amino acid content, N-terminal amino acid sequence, C-terminal amino acid sequence, and phosphoamino acid content. The results of N- and C-terminal amino acid sequence analysis of each gag protein, taken together with the nucleotide sequence of the EIAV gag gene (R. M. Stephens, J. W. Casey, and N. R. Rice, Science 231:589-594, 1986), show that the order of the proteins in the precursor is p15-p26-*-p11-p9, where a pentapeptide also found in the virus is represented by the asterisk. The data are in complete agreement with the predicted structure of the gag polyprotein and show the peptide bonds cleaved during proteolytic processing. The N-terminus of p15 is blocked to Edman degradation. The p11 protein is identical to the nucleic acid-binding protein of EIAV previously isolated (C. W. Long, L. E. Henderson, and S. Oroszlan, Virology 104:491-496, 1980). High-titer rabbit antiserum was prepared against each purified protein. These antisera were used to detect the putative gag precursor (Pr55gag) and intermediate cleavage products designated Pr49 (p15-p26-*-p11), Pr40 (p15-p26), and Pr35 (p26-*-p11) in the virus and in virus-infected cells. High-titer antisera to EIAV p15 and p26 showed cross-reactivity with the homologous protein of human T-cell lymphotropic virus type III/lymphadenopathy-associated virus.

Bovine leukemia virus protease: purification, chemical analysis, and in vitro processing of gag precursor polyproteins.

Bovine leukemia virus protease was purified to homogeneity and assayed by using murine leukemia virus Pr65gag, a polyprotein precursor of the viral core structural proteins, as the substrate. A chemical analysis of the protease, including an amino acid composition and NH2- and COOH-terminal amino acid sequence analysis, revealed that it has an Mr of 14,000 and is encoded by a segment of the viral RNA located between the gag gene and the putative reverse transcriptase gene. As expected from the nucleotide sequence data (Rice et al., Virology 142:357-377, 1985), the reading frame for the protease is different from both the gag and reverse transcriptase reading frames. The 5' end of the protease open reading frame extends 38 codons upstream from the codon for the NH2-terminal residue of the mature viral protease and overlaps the gag open reading frame by 7 codons. The 3' end of the protease open reading frame extends 26 codons beyond the codon for the COOH-terminal residue of the mature protease and overlaps 8 codons of the reverse transcriptase open reading frame. Several lines of evidence, such as protein mapping of the gag polyprotein precursor, the characteristic structure of the mRNA, and promotion of the synthesis of a gag polyprotein precursor by lysine tRNA in vitro, suggest that the protease could be translated by frameshift suppression of the gag termination codon. In vitro synthesized bovine leukemia virus gag-related polyproteins were cleaved by the protease into fragments which were the same size as the known components of bovine leukemia virus, suggesting that the specificity of cleavage catalyzed in vitro by the purified protease is the same as the specificity of cleavage found in the virus.

In vitro cleavage of Pr65gag by the Moloney murine leukaemia virus proteolytic activity yields p30 whose NH2-terminal sequence is identical to virion p30.

In vitro cleavage of Gazdar murine sarcoma virus Pr65gag, which has all of the antigenic determinants of Moloney murine leukaemia virus Pr65gag, i.e. p15, p12, p30 and p10, by the Moloney murine leukaemia virus proteolytic activity yielded a p30 whose partial NH2-terminal sequence was identical to Moloney murine leukaemia virus. Both [3H]leucine-labelled and unlabelled Pr65gag were used to generate the cleaved p30.

Isolation and sequence analysis of cDNA clones coding for rat skeletal muscle creatine kinase.

A series of cDNA clones corresponding to 1494 bases of rat muscle creatine kinase mRNA has been isolated and characterized. The identity of these clones has been confirmed by DNA sequence analysis and by comparison of the predicted amino acid sequence with that determined for the purified protein. The cDNA sequence accounts for the entire coding sequence of the creatine kinase protein in addition to the complete 3' untranslated region and 68 bases of 5' noncoding region. Sequences corresponding to the active site region of the protein, the initiation codon, the termination codon, and poly(A) addition signal have been identified.

Structural and antigenic characterization of the proteins of human T-cell leukemia viruses and their relationships to the gene products of other retroviruses.

The primary structure analysis of the gag gene products of human T-cell leukemia virus (HTLV)-ICR has been nearly completed. A comparison of the amino acid sequences with the published nucleotide sequence of HTLV-IATK established that i) p19 which is known to share antigenic determinants with a protein present in normal thymic epithelium, is nevertheless virally coded. ii) The gene order and complete primary structure of the gag precursor (Pr55) which has been shown to be myristylated (My) at its N-terminus is My-p19-p24-p15-OH; and iii) the Pr55gag amino acid sequences of HTLV-ICR and HTLV-IATK are nearly identical showing only a single residue difference in the C-terminal region of p15. Antibodies to synthetic peptides inferred from the nucleotide sequence of the env gene of HTLV-IATK were also raised and used to identify and purify env precursor gPr62-68, surface glycoprotein gp46-51 and transmembrane protein p21. While most of the peptide sera were shown to be subgroup specific some of them detected antigenic determinants shared between protein homologs of viruses of subgroups I and II. Partial or complete amino acid sequences of both the gag and env gene coded proteins of bovine leukemia virus (BLV) structural proteins have also been determined. These extensive protein data together with nucleotide sequences confirm and extend our initial finding that HTLV and BLV are structurally and antigenically related and may have originated from common ancestor. The structural and immunological studies revealed also relationships between HTLV and a number of type C and type D retroviruses studied. One of the highly conserved sequences is shared by the transmembrane proteins of these retroviruses which have been implicated in immunosuppression. It is conceivable that these common regions have common biological function. Two previously unidentified proteins of BLV have also been purified and structurally characterized. Nucleotide sequences capable of coding for related products are present in HTLV. The nature and possible biological functions of these new BLV proteins and the putative HTLV gene products will be discussed. The size and complexity of the genome of the replication competent retroviruses are similar but not identical. The 35S RNA of all replication competent helper viruses is divided into three genes encoding the viral structural proteins: the gag (group-specific antigen) gene codes for the internal structural proteins, the pol (polymerase) gene codes for the enzymes protease, reverse transcriptase and endonuclease and the env (envelope) gene codes for the proteins of the viral envelope.(ABSTRACT TRUNCATED AT 400 WORDS)

Characterization of the phosphorylation sites and the surrounding amino acid sequences of the p21 transforming proteins coded for by the Harvey and Kirsten strains of murine sarcoma viruses.

The transforming protein coded for by the onc gene (v-rasHa) of Harvey murine sarcoma virus (Ha-MuSV) is the 21,000-dalton protein (p21) which is the immediate agent responsible for the virus-induced malignant transformation of normal cells. The p21 proteins of Ha-MuSV and the closely related Kirsten murine sarcoma virus are heavily phosphorylated in vivo. In the partially purified Ha-MuSV p21, the protein shows a guanine nucleotide-binding activity and, in addition, a very unique autophosphorylating activity at a threonine residue using as phosphoryl donor GTP but not ATP. In the present study, we compared the tryptic peptide maps of the Ha-MuSV p21 phosphorylated in vivo and in vitro. The results show that the major phosphorylation site is identical. Since the GTP-specific phosphorylation is very unique and distinct from all other known protein kinases, the present observation suggests that the in vitro enzymatic activity is responsible for the p21 phosphorylation in vivo. We have analyzed the amino acid sequence surrounding the major phosphorylation site of the Ha-MuSV p21 by automated Edman degradations of the tryptic phosphopeptides. Threonine residue 59 from the initiator methionine residue 1 of the p21 protein is the phosphorylated amino acid residue, and the surrounding amino acid sequence is NH2...-Thr-Cys-Leu-Leu-Asp-Ile-Leu-Asp-Thr-Thr(P)-Gly-Gln-Glu-Glu-Tyr-...COOH. The p21 proteins of both the Ha-MuSV and the closely related Kirsten murine sarcoma virus share the same phosphopeptide. The amino acid sequence of the phosphorylation site is distinct from all other known protein kinases.

Primary structure of the low molecular weight nucleic acid-binding proteins of murine leukemia viruses.

Murine leukemia viruses contain a low molecular weight basic protein, designated p10, which binds to single-stranded nucleic acids. The complete amino acid sequence of p10 from the Rauscher strain of virus has been determined. The partial amino acid sequences of p10s from Moloney, Friend, AKR, Gross, radiation leukemia, and BALB/2 viral strains have also been determined using microsequencing techniques. Rauscher p10 is composed of 56 amino acid residues; the other p10s are similar in size but differ from Rauscher by a few conservative amino acid substitutions. The structure of Rauscher p10 was compared to the structure of a functionally homologous protein from Rous avian sarcoma virus. The comparison revealed regions of amino acid sequence homologies which indicate a phylogenetic relationship between the murine and avian viral strains. The analyses revealed a periodic placement of three Cys residues and a Gly-His sequence. A structure involving these residues is found once in the murine protein and twice in the avian protein. A similar structure is seen in the single stranded nucleic acid binding protein of bacteriophage T4. However, in the latter case, the order of amino acid residues is inverted.