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K C Chou

Publications and source records attributed to K C Chou.

At least 73 records · Page 4Linked to original sources
PubMed1995

Analysis of the loop-helix interaction in bundle motif protein structures.

Molecular dynamics simulations and energy analysis have been carried out to study the structural mobility and stability of the four alpha-helix bundle motifs. The simulation results as well as the X-ray data show that the atomic RMS fluctuation is larger at the loop region for four representative proteins investigated: methemerythrin, cytochrome b-562, cytochrome c', and bovine somatotropin. The loop-loop, helix-helix, and loop-helix interactions are computed for the unfolded and folded proteins. In the folded and solvated protein structures the loop-helix interaction is stronger than the helix-helix interaction, especially in the electrostatic component. But the stabilization energies of both the loop-helix and the helix-helix interactions relative to those of an unfolded structure are of the same order of magnitude. The stabilization due to protein-solvent interaction is greater in the helix region than in the loop region. The percentage of hydrophilic solvent accessible area for the four proteins studied was calculated with the method of Eisenberg and McLachlan. The percentage of the hydrophilic area is greater in the loops than in the helices. A Poisson-Boltzmann calculation shows that the potential from the loops acting on a helix is generally more negative than that from other helices.

Animals↗
PubMed1995

An analysis of protein folding type prediction by seed-propagated sampling and jackknife test.

In the development of methodology for statistical prediction of protein folding types, how to test the predicted results is a crucial problem. In addition to the resubstitution test in which the folding type of each protein from a training set is predicted based on the rules derived from the same set, cross-validation tests are needed. Among them, the single-test-set method seems to be least reliable due to the arbitrariness in selecting the test set. Although the leaving-one-out (or jackknife) test is more objective and hence more reliable, it may cause a severe information loss by leaving a protein in turn out of the training set when its size is not large enough. In order to overcome the above drawback, a seed-propagated sampling approach is proposed that can be used to generate any number of simulated proteins with a desired type based on a given training set database. There is no need to make any predetermined assumption about the statistical distribution function of the amino acid frequencies. Combined with the existing cross-validation methods, the new technique may provide a more objective estimation for various protein-folding-type prediction methods.

Amino Acids↗
PubMed1995

Predicting protein structural classes from amino acid composition: application of fuzzy clustering.

Most globular proteins can be classified into one of four structural classes--all-alpha, all-beta, alpha + beta and alpha/beta--depending upon the type, amount and arrangement of secondary structures present. In this work a new method, based upon fuzzy clustering, is proposed for predicting the structural class of a protein from its amino acid composition. Here, each of the structural classes is described by a fuzzy cluster and each protein is characterized by its membership degree, a number between zero and one in each of the four clusters, with the constraint that the sum of the membership degrees equals unity. A given protein is then classified as belonging to that structural class corresponding to the fuzzy cluster with maximum membership degree. Calculation of membership degrees is carried out using the fuzzy c-means algorithm on a training set of 64 proteins. Results obtained for the training set show that the fuzzy clustering approach produces results comparable with or better than those obtained by other methods. A test set of 27 proteins also produced comparable results to those obtained with the training set. The success of the present preliminary work on protein structure class prediction suggests that further refinements of method may lead to improved predictions and this is currently being investigated.

Algorithms↗
PubMed1995

Prediction of protein structural classes.

A protein is usually classified into one of the following five structural classes: alpha, beta, alpha + beta, alpha/beta, and zeta (irregular). The structural class of a protein is correlated with its amino acid composition. However, given the amino acid composition of a protein, how may one predict its structural class? Various efforts have been made in addressing this problem. This review addresses the progress in this field, with the focus on the state of the art, which is featured by a novel prediction algorithm and a recently developed database. The novel algorithm is characterized by a covariance matrix that takes into account the coupling effect among different amino acid components of a protein. The new database was established based on the requirement that the classes should have (1) as many nonhomologous structures as possible, (2) good quality structure, and (3) typical or distinguishable features for each of the structural classes concerned. The very high success rate for both the training-set proteins and the testing-set proteins, which has been further validated by a simulated analysis and a jackknife analysis, indicates that it is possible to predict the structural class of a protein according to its amino acid composition if an ideal and complete database can be established. It also suggests that the overall fold of a protein is basically determined by its amino acid composition.

Algorithms↗
PubMed1994

Predicting protein folding types by distance functions that make allowances for amino acid interactions.

Given the amino acid composition of a protein, how may one predict its folding type? Although around this problem a number of methods have been proposed, none of them has taken into account the correlative effect among different amino acids, and hence the accuracy of prediction could not be improved to the extent that it should have. In view of this, a new method has been developed in which the similarity between two protein molecules is based on the scale of Mahalanobis distance rather than on the ordinary intuitive geometric distances, such as Minkowski's distance and Euclidian distance. By introducing the Mahalanobis distance, the correlative effect among different amino acids can be automatically incorporated. Predictions have been performed for 131 real proteins consisting of alpha, beta, alpha+beta, and alpha/beta proteins. The results indicate that the rates of correct prediction for both alpha and beta proteins are 100%, and those for alpha+beta and alpha/beta are 88.9 and 89.7%, respectively, with an average accuracy of 94.7%. Predictions have also been performed for 10,000 simulated proteins generated by Monte Carlo sampling for each of the above four folding types, yielding an average accuracy of 95.9%. The accuracy thus obtained for the simulated proteins can avoid the bias due to the limited number of testing proteins selected arbitrarily by different investigators and hence can be regarded as an objective accuracy. It is anticipated that a method with such a high objective accuracy should become a reliable tool in predicting the protein folding type and a useful tool for improving the prediction of secondary structure as well.

Models, Chemical↗
PubMed1994

Kinetic studies with the non-nucleoside human immunodeficiency virus type-1 reverse transcriptase inhibitor U-90152E.

The bisheteroarylpiperazine U-90152E is a potent inhibitor of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) and possesses excellent anti-HIV activity in HIV-1-infected lymphocytes grown in tissue culture. The compound inhibits both the RNA- and DNA-directed DNA polymerase functions of HIV-1 RT. Kinetic studies were carried out to elucidate the mechanism of RT inhibition by U-90152E. Michaelis-Menten kinetics, which are based on the establishment of a rapid equilibrium between the enzyme and its substrates, proved inadequate for the analysis of the experimental data. The data were thus analyzed using Briggs-Haldane kinetics, assuming that the reaction is ordered in that the template:primer binds to the enzyme first, followed by the addition of dNTP and that the polymerase is a processive enzyme. Based on these assumptions, a velocity equation was derived, which allows the calculation of all the essential forward and backward rate constants for the reactions occurring between the enzyme, its substrates and the inhibitor. The results obtained indicate that U-90152E acts exclusively as a mixed inhibitor with respect to the template: primer and dNTP binding sites for both the RNA- and DNA-directed DNA polymerase domains of the enzyme. The inhibitor shows a significantly higher binding affinity for the enzyme-substrate complexes than for the free enzyme and consequently does not directly impair the functions of the substrate binding sites. Therefore, U-90152E appears to impair an event occurring after the formation of the enzyme-substrate complexes, which involves either inhibition of the phosphoester bond formation or translocation of the enzyme relative to its template:primer following the formation of the ester bond.

Antiviral Agents↗
PubMed1994

A graphic approach to analyzing codon usage in 1562 Escherichia coli protein coding sequences.

The occurrence frequencies of the four bases (adenine, cytosine, guanine and thymine) at each of the three codon positions for 1562 Escherichia coli protein coding sequences have been calculated. The 1562 x 4 x 3 = 18,744 data thus obtained have been analyzed by a graphic method in which the four base occurrence frequencies at each codon position for each coding sequence are represented by a point in a three-dimensional space. Thus, the 18,744 data, which would otherwise occupy several printed pages, can be intuitively displayed by a graphy. The point distribution pattern for each of the three codon positions has been analyzed. The results of our analysis indicate that the patterns for the first two codon positions reflect the origin for producing native folding structures of proteins. We thus come to the conclusion that the distribution patterns for the first two codon positions should be basically species-independent, as confirmed by studies for a number of other species. However, the distribution pattern for the third codon position is species-dependent. Based on the point distribution of the third codon position, six collective parameters have been defined to describe the overall feature of the pattern concerned. These collective parameters can be generally used to classify different species, and hence would be a useful vehicle for studies in taxonomy. In addition to E. coli, the collective parameters for a number of other species have been calculated and analyzed.

Animals↗
PubMed1994

Steady-state kinetic studies with the polysulfonate U-9843, an HIV reverse transcriptase inhibitor.

The tetramer of ethylenesulfonic acid (U-9843) is a potent inhibitor of HIV-1 RT* and possesses excellent antiviral activity at nontoxic doses in HIV-1 infected lymphocytes grown in tissue culture. Kinetic studies of the HIV-1 RT-catalyzed RNA-directed DNA polymerase activity were carried out in order to determine if the inhibitor interacts with the template primer or the deoxyribonucleotide triphosphate (dNTP) binding sites of the polymerase. Michaelis-Menten kinetics, which are based on the establishment of a rapid equilibrium between the enzyme and its substrates, proved inadequate for the analysis of the experimental data. The data were thus analyzed using steady-state Briggs-Haldane kinetics assuming that the template: primer binds to the enzyme first, followed by the binding of the dNTP and that the polymerase is a processive enzyme. Based on these assumptions, a velocity equation was derived which allows the calculation of all the specific forward and backward rate constants for the reactions occurring between the enzyme, its substrates and the inhibitor. The calculated rate constants are in agreement with this model and the results indicated that U-9843 acts as a noncompetitive inhibitor with respect to both the template:primer and dNTP binding sites. Hence, U-9843 exhibits the same binding affinity for the free enzyme as for the enzyme-substrate complexes and must inhibit the RT polymerase by interacting with a site distinct from the substrate binding sites. Thus, U-9843 appears to impair an event occurring after the formation of the enzyme-substrate complexes, which involves either an event leading up to the formation of the phosphoester bond, the formation of the ester bond itself or translocation of the enzyme relative to its template:primer following the formation of the ester bond.

Binding Sites↗
PubMed1994

Solitary wave dynamics as a mechanism for explaining the internal motion during microtubule growth.

Microtubules, which play many diverse and important roles in biological systems, are usually made up of 13 nearly axial protofilaments formed from individual tubulin molecules. In this paper, a nonlinear dynamic model has been developed to elucidate the mechanism of the internal motion occurring during the assembly of microtubules. The results derived from the model indicate that such internal motion is associated with a solitary wave, or kink, excited by the energy released from the hydrolysis of GTP-->GDP in microtubular solutions. As the kink moves forward, the individual tubulin molecules involved in the kink undergo motions that can be likened to the dislocation of atoms within the crystal lattice. Thus, the dynamic instability of microtubules may be characterized by a series of dislocation motions of the tubulin molecules. An energy estimate shows that a kink in the system possesses about 0.36-0.44 eV, which is quite close to but smaller than the 0.49 eV of energy released from the hydrolysis of GTP. Therefore, the relevant energy derived from our model is fully consistent with experimental observations; this finding also suggests that the hydrolysis energy may be responsible for exciting the solitary wave, or kink, leading to tubulin dislocation in microtubules. Our model, and its intrinsic properties, i.e., dynamic nonlinearity, thermodynamic irreversibility, as well as an energy input from a sustained source, implies that the growth of microtubules is a typical dissipative process and that their structure in vivo is typical of dissipative structures.

Energy Metabolism↗
PubMed1994

An alternate-subsite-coupled model for predicting HIV protease cleavage sites in proteins.

A 2-4-6 subsite-coupled model is proposed to predict the cleavability of peptide sequences by HIV protease. For an enzyme with eight extended specificity subsites, such as HIV protease, the coupling effects of the second subsite with the fourth one and the fourth with the sixth subsite are much more important than those of the others. Accordingly, in establishing a model for predicting whether a given peptide can be cleaved by HIV protease, the 2-4-6 subsite-coupled effect must be incorporated. The model leads to an algorithm for predicting protease-susceptible sites from primary structure. The high rate of correct prediction for both HIV-1 and HIV-2 proteases has borne out that this kind of alternation-coupled mechanism does exist along the extended subsites of HIV protease. The principle of the new method can be used for analyzing the specificity of any multisubsite enzyme. In particular, the new method can serve as a supplementary means for finding effective inhibitors of HIV protease, which is one of the targets in designing potential drugs for AIDS therapy.

Algorithms↗
PubMed1994

Protein folding classes: a geometric interpretation of the amino acid composition of globular proteins.

The amino acid composition of globular proteins of known tertiary structures is analyzed for the classification of the folding classes of protein structures and for a description of their relationship which can be useful in the determination of the folding type of a protein. For each of the folding classes, an ellipsoid in the multidimensional space was constructed from the 20-D vectors of amino acid composition of its member proteins according to standard analytical geometry methods. From this representation, an ellipsoid-based scheme is then presented for determining the folding type of a protein on the basis of its elliptically scaled radial distances from ellipsoid centroids (rather than the conventional Euclidean distances) in a definitive and analytical manner. Among the 132 basis set proteins from which the ellipsoid representations were derived, locations of their individual vectors give correct assignment of the folding type for 127 proteins; this success rate of 96%, though better than those in previous studies, is established to be the theoretical upper limit only for the basis set proteins. Moreover, the geometrical description of the relationship between amino acid composition and protein folding types derived from this analytical (rather than statistical) method indicates that amino acid composition alone cannot determine the protein folding type in all cases. The high success rate for the basis set proteins nevertheless suggests that the ellipsoid representation and the elliptically scaled distances can be more successful in determining the folding type of a protein from its amino acid composition than other analytical approaches reported previously.

Amino Acids↗
PubMed1993

A vectorized sequence-coupling model for predicting HIV protease cleavage sites in proteins.

What kind of peptide sequences can be cleaved by HIV protease, and what kind cannot be? This is a crucially important problem in designing effective inhibitors against HIV protease as potential drugs for AIDS therapy. To tackle this problem, a sequence-coupling and vectorized model is proposed for predicting the cleavability of oligopeptides by proteases with multiple and extended specificity subsites. In comparison with existing methods, the new method has proved to be an improvement in both the accuracy of the model and the rationality of the statistical treatment. Meanwhile, the Monte Carlo sampling procedure introduced here has also proved to be very useful in dealing with the situation when the experimental data are insufficiently sampled for complete statistics. Owing to its very high rate of correct prediction, it is expected that the new method can be a useful technique for helping to find effective inhibitors of HIV protease, which is one of the targets in designing potential drugs against AIDS. The principle of the new method can also be applied to analyzing the specificity of any multi-subsite enzyme.

Amino Acid Sequence↗
PubMed1993

The quinoline U-78036 is a potent inhibitor of HIV-1 reverse transcriptase.

The quinoline U-78036 represents a new class of non-nucleoside human immunodeficiency virus (HIV)-1 reverse transcriptase inhibitors. The agent possesses excellent antiviral activity at nontoxic doses in HIV-1-infected lymphocytes grown in tissue culture. Enzymatic kinetic studies of the HIV-1 reverse transcriptase (RT)-catalyzed RNA-directed DNA polymerase function were carried out in order to determine whether the inhibitor interacts with the template-primer or deoxyribonucleotide triphosphate (dNTP) binding sites of the polymerase. The data were analyzed using steady-state or Briggs-Haldane kinetics assuming that the template-primer binds to the enzyme first followed by the dNTP and that the polymerase functions processively. The calculated rate constants are in agreement with this model. The results show that the inhibitor acts as a mixed to noncompetitive inhibitor with respect to both the template-primer and the dNTP binding sites of the enzyme. Hence, U-78036 inhibits the RNA-directed DNA polymerase activity of RT by interacting with a site distinct from the template-primer and dNTP binding sites. Moreover, the potency of U-78036 is dependent on the base composition of the template-primer. The equilibrium constants for various enzyme-substrate-inhibitor complexes were at least seven times lower for the poly(rC).(dG)10-catalyzed system than the one catalyzed by poly(rA).(dT)10. In addition, the inhibitor does not impair the DNA-dependent DNA polymerase activity and the RNase H function of HIV-1 RT nor does it inhibit the RNA-directed DNA polymerase activity of the HIV-2, avian myoblastoma virus, and murine leukemia virus RT enzymes.

Antiviral Agents↗
PubMed1993

Kinetic studies with the non-nucleoside HIV-1 reverse transcriptase inhibitor U-88204E.

The bis(heteroaryl)piperazine U-88204E is a potent inhibitor of HIV-1 reverse transcriptase (RT) and possesses excellent anti-HIV activity in HIV-1-infected lymphocytes grown in tissue culture. Enzymatic kinetic studies of the RNA- and DNA-dependent DNA polymerases of RT were carried out in order to determine whether the inhibitor interacts directly with the template:primer or deoxyribonucleotide triphosphate (dNTP) binding sites of the polymerase. The experimental results were analyzed using steady-state or Briggs-Haldane kinetics, by assuming that the template:primer binds to the enzyme first followed by the dNTP and that the polymerase functions processively. The results of the analysis show that the inhibitor acts as a mixed to noncompetitive inhibitor with respect to both the template:primer and the dNTP binding sites. The potency of U-88204E on the RNA-directed DNA polymerase activity depends on the base composition of the template:primer. The Ki values for the poly(rC):(dG)10-directed reactions were at least 7 times lower than the ones for reactions directed by poly(rA):(dT)10. The inhibitor did not inhibit the RNase H function of HIV-1 RT nor did it impair the RNA-directed DNA polymerase activity of HIV-2 RT. These data thus demonstrate the unique specificity of U-88204E for HIV-1 RT.

HIV Reverse Transcriptase↗
PubMed1993

Steady-state kinetic studies with the non-nucleoside HIV-1 reverse transcriptase inhibitor U-87201E.

The multifunctional HIV-1 RT (human immunodeficiency virus type 1-reverse transcriptase) enzyme possesses three main functions including the RNA- and DNA-directed DNA polymerases and the RNase H. The bisheteroarylpiperazine U-87201E inhibits the two polymerase functions but not the RNase H. Enzymatic kinetic studies of the HIV-1 RT-catalyzed RNA- and DNA-directed DNA polymerase activities were carried out in order to determine if the inhibitor interferes with either the template:primer or the deoxyribonucleotide triphosphate (dNTP)-binding sites of the enzyme. The data were analyzed using steady-state kinetics, considering that the polymerase reaction is ordered in that the template:primer is added first, followed by the dNTP and that the enzyme functions processively. The data were consistent with the model. The steady-state rate constants for the forward and backward reactions were of similar magnitude for both the RNA- and DNA-catalyzed DNA polymerases and suggest that both functions share the same substrate-binding sites. The dissociation constants for the enzyme-inhibitor and enzyme-substrate-inhibitor complexes were somewhat higher for the DNA-directed DNA polymerase function as compared to the RNA directed one. This indicates that U-87201E is a more potent inhibitor for the RNA-directed DNA polymerase than the DNA-directed DNA polymerase. The pattern of inhibition exerted by U-87201E was noncompetitive with respect to both the nucleic acid and nucleotide-binding sites of the RT enzyme for both the RNA- and DNA-directed DNA polymerases. Hence, U-87201E inhibits these functions by interacting with a site distinct from the template:primer and dNTP-binding sites. HIV-2 RT was insensitive to U-87201E, demonstrating the unique sensitivity of HIV-1 RT to this inhibitor.

DNA, Viral↗
PubMed1993

A vector projection approach to predicting HIV protease cleavage sites in proteins.

A vector projection method is proposed to predict the cleavability of oligopeptides by extended-specificity site proteases. For an enzyme with eight specificity subsites the substrate octapeptide can be uniquely expressed as a vector in an 8-dimensional space, whose eight bases correspond to the amino acids at the eight subsites, P4, P3, P2, P1, P1', P2', P3', and P4', respectively. The component of such a characteristic vector on each of the eight bases is defined as the frequency of an amino acid occurring at a given site. These frequencies were derived from a set of octapeptides known to be cleaved by HIV protease. The cleavability of an octapeptide can then be estimated from the projection of its characteristic vector on an idealized, optimally cleavable vector. The high ratio of correct prediction vs. total prediction for the data in both the training and the testing sets indicates that the new method is self-consistent and efficient. It provides a rapid and accurate algorithm for analyzing the specificity of any multi-subsite enzyme for which there is no coupling between subsites. In particular, it is useful for predicting the cleavability of an oligopeptide by either HIV-1 or HIV-2 protease, and hence offers a supplementary means for finding effective inhibitors of HIV protease as potential drugs against AIDS.

Amino Acid Sequence↗