Andrzej K Konopka - Academia.edu (original) (raw)
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Papers by Andrzej K Konopka
FEBS Letters, 1987
The primary amino acid sequence within a stretch of 25 residues (positions 91-116) of the middle ... more The primary amino acid sequence within a stretch of 25 residues (positions 91-116) of the middle portion of the 3'-orf protein (p27(3')-orf) of the human immunodeficiency virus (HIV) shares structural homology with a highly charged region within the intracytoplasmic phosphorylation domain of human interleukin-2 receptor (IL-2R) and the ATP-binding site of the catalytic subunit of cAMP-dependent protein kinase (cAMP-PK) and other members of the protein kinase family. Comparison of the predicted secondary structure within this region of p27(3')-orf with the phosphorylation domain of human IL-2R and the ATP-binding region of the phospho-kinase family of protein suggests that the 3'-orf protein could serve homologous function(s).
Ecology, 1997
... Others may disagree; in any case, a comprehensive overview of molecular biology requires a co... more ... Others may disagree; in any case, a comprehensive overview of molecular biology requires a competence I ... The physicalists had been right in insisting that there is no meta-physical life component ... The Middle Ages were dominated by a strict adherence to the teachings of the ...
Computational Biology and Chemistry, 2004
Computational Biology and Chemistry, 2008
Computational Biology and Chemistry, 2004
Bioinformatics, 1988
A fixed-point alignment analysis technique is presented which is designed to locate common sequen... more A fixed-point alignment analysis technique is presented which is designed to locate common sequence motifs in collections of proteins or nucleic acids. Initially a program aligns a collection of sequences by a common sequence pattern or known biological feature. The common pattern or feature (fixed-point) may be a user-specified sequence string or a known sequence position like mRNA start site, which may be taken directly from the annotated feature table of GenBank. Once all alignment markers are located, the sequences are scanned for occurrences of given oligomers within a specified span both upstream and downstream of the fixed-point. The occurrences may then be plotted as a function of the position relative to the fixed-point, displayed as an actual sequence alignment or selectively summarized via various program options. Applications of the technique are discussed.
Bioinformatics, 1987
ABSTRACT
Biochimie, 1985
In the cases of the 6-fold degenerate residues and the stop signal, selective codon usage at the ... more In the cases of the 6-fold degenerate residues and the stop signal, selective codon usage at the level of transcription can account for a 10-20% variation in their mistranslation rate. For all other residues, the mistranslation rate is dependent upon the degree of degeneracy only, but not upon the pattern of synonymous codon usage.
Computational Biology and Chemistry / Computers & Chemistry, 1993
AIDS Research and Human Retroviruses, 1996
. This observation suggests that chemical inhibitors of integrase may prevent the spread of HIV i... more . This observation suggests that chemical inhibitors of integrase may prevent the spread of HIV in infected individuals. In our search for such potential chemotherapeutic agents, we observed that -conidendrol inhibits both the sequence-dependent and sequenceindependent endonucleolytic activities of integrase with comparable potencies in vitro (50% inhibitory concentration, 500 nM). Structurally related compounds tested for their abilities to inhibit integrase generated a limited structure-activity analysis which demonstrated that potency is associated with the bis-catechol structure: two pairs of adjacent hydroxyls on separate benzene rings. -Conidendrol did not inhibit several other endonucleases and/or phosphoryltransferases. Although -conidendrol was not effective in preventing HIV-1 infection in cell culture, the in vitro data demonstrate that it is possible to identify selective agents targeted against this essential HIV-1 function.
The chapter reviews classical methods of cryptanalysis and their application to nucleic acids and... more The chapter reviews classical methods of cryptanalysis and their application to nucleic acids and protein sequence analysis.
The theory of degenerate coding is presented in a way enabling further application to molecular b... more The theory of degenerate coding is presented in a way enabling further application to molecular biology. There are two kinds of redundancy of a degenerate code. The first is due to the excess in codon length and the second to the code degeneracy. If the code is asymmetrically degenerate, the second kind of redundancy can be profitable for control of error rate. This control can be performed just by selective synonymous codon usage. Utilization of the genetic code is partially influenced by this theoretical possibility. In particular the degree of error protectivity is well correlated with deviation from equiprobability in synonymous codon usage. The biological significance of this fact is discussed.
The theory of surrogacy is briefly outlined as one of the conceptual foundations of systems biolo... more The theory of surrogacy is briefly outlined as one of the conceptual foundations of systems biology that has been developed for the last 30 years in the context of Hertz-Rosen modeling relationship. Conceptual foundations of modeling convoluted (biologically complex) systems are briefly reviewed and discussed in terms of current and future research in systems biology. New as well as older results that pertain to the concepts of modeling relationship, sequence of surrogacies, cascade of representations, complementarity, analogy, metaphor, and epistemic time are presented together with a classification of models in a cascade. Examples of anticipated future applications of surrogacy theory in life sciences are briefly discussed.
A maximum entropy principle (MEP) governing the distribution of complexity of short oligonucleoti... more A maximum entropy principle (MEP) governing the distribution of complexity of short oligonucleotides from large collections of functionally equivalent sequences is presented. The principle is seen to work well in both translated regions (exons and bacterial genes) and introns from various genomes.
1. Computational biology has been a marvelous experience for at least three generations of the br... more 1. Computational biology has been a marvelous experience for at least three generations of the brightest scientists of the second half of the twentieth century and continues to be so in the twenty-first century. Simply speaking, computational biology is the science of biology done with the use of computers. Because computers require some specialized knowledge of the cultural and technical infrastructure in which they can be used, computational biology is significantly motivated (or even inspired) by computer science and its engineering variant known as information technology. On the other hand, the kind of data and data structures that can be processed by computers provide practical constraints on the selection of computational biology research topics. For instance, it is easier to analyze sequences of biopolymers with string processing techniques and statistics than to infer unknown biological functions from the unknown three-dimensional structures of the same biopolymers by using image processing tools. Similarly, it is advisable to study systems of chemical reactions (including metabolic pathways) in terms MD: KONOPKA, JOB: 04359, PAGE: 1 1 0982-9_Konopka_Ch01_R2_070204
FEBS Letters, 1987
The primary amino acid sequence within a stretch of 25 residues (positions 91-116) of the middle ... more The primary amino acid sequence within a stretch of 25 residues (positions 91-116) of the middle portion of the 3'-orf protein (p27(3')-orf) of the human immunodeficiency virus (HIV) shares structural homology with a highly charged region within the intracytoplasmic phosphorylation domain of human interleukin-2 receptor (IL-2R) and the ATP-binding site of the catalytic subunit of cAMP-dependent protein kinase (cAMP-PK) and other members of the protein kinase family. Comparison of the predicted secondary structure within this region of p27(3')-orf with the phosphorylation domain of human IL-2R and the ATP-binding region of the phospho-kinase family of protein suggests that the 3'-orf protein could serve homologous function(s).
Ecology, 1997
... Others may disagree; in any case, a comprehensive overview of molecular biology requires a co... more ... Others may disagree; in any case, a comprehensive overview of molecular biology requires a competence I ... The physicalists had been right in insisting that there is no meta-physical life component ... The Middle Ages were dominated by a strict adherence to the teachings of the ...
Computational Biology and Chemistry, 2004
Computational Biology and Chemistry, 2008
Computational Biology and Chemistry, 2004
Bioinformatics, 1988
A fixed-point alignment analysis technique is presented which is designed to locate common sequen... more A fixed-point alignment analysis technique is presented which is designed to locate common sequence motifs in collections of proteins or nucleic acids. Initially a program aligns a collection of sequences by a common sequence pattern or known biological feature. The common pattern or feature (fixed-point) may be a user-specified sequence string or a known sequence position like mRNA start site, which may be taken directly from the annotated feature table of GenBank. Once all alignment markers are located, the sequences are scanned for occurrences of given oligomers within a specified span both upstream and downstream of the fixed-point. The occurrences may then be plotted as a function of the position relative to the fixed-point, displayed as an actual sequence alignment or selectively summarized via various program options. Applications of the technique are discussed.
Bioinformatics, 1987
ABSTRACT
Biochimie, 1985
In the cases of the 6-fold degenerate residues and the stop signal, selective codon usage at the ... more In the cases of the 6-fold degenerate residues and the stop signal, selective codon usage at the level of transcription can account for a 10-20% variation in their mistranslation rate. For all other residues, the mistranslation rate is dependent upon the degree of degeneracy only, but not upon the pattern of synonymous codon usage.
Computational Biology and Chemistry / Computers & Chemistry, 1993
AIDS Research and Human Retroviruses, 1996
. This observation suggests that chemical inhibitors of integrase may prevent the spread of HIV i... more . This observation suggests that chemical inhibitors of integrase may prevent the spread of HIV in infected individuals. In our search for such potential chemotherapeutic agents, we observed that -conidendrol inhibits both the sequence-dependent and sequenceindependent endonucleolytic activities of integrase with comparable potencies in vitro (50% inhibitory concentration, 500 nM). Structurally related compounds tested for their abilities to inhibit integrase generated a limited structure-activity analysis which demonstrated that potency is associated with the bis-catechol structure: two pairs of adjacent hydroxyls on separate benzene rings. -Conidendrol did not inhibit several other endonucleases and/or phosphoryltransferases. Although -conidendrol was not effective in preventing HIV-1 infection in cell culture, the in vitro data demonstrate that it is possible to identify selective agents targeted against this essential HIV-1 function.
The chapter reviews classical methods of cryptanalysis and their application to nucleic acids and... more The chapter reviews classical methods of cryptanalysis and their application to nucleic acids and protein sequence analysis.
The theory of degenerate coding is presented in a way enabling further application to molecular b... more The theory of degenerate coding is presented in a way enabling further application to molecular biology. There are two kinds of redundancy of a degenerate code. The first is due to the excess in codon length and the second to the code degeneracy. If the code is asymmetrically degenerate, the second kind of redundancy can be profitable for control of error rate. This control can be performed just by selective synonymous codon usage. Utilization of the genetic code is partially influenced by this theoretical possibility. In particular the degree of error protectivity is well correlated with deviation from equiprobability in synonymous codon usage. The biological significance of this fact is discussed.
The theory of surrogacy is briefly outlined as one of the conceptual foundations of systems biolo... more The theory of surrogacy is briefly outlined as one of the conceptual foundations of systems biology that has been developed for the last 30 years in the context of Hertz-Rosen modeling relationship. Conceptual foundations of modeling convoluted (biologically complex) systems are briefly reviewed and discussed in terms of current and future research in systems biology. New as well as older results that pertain to the concepts of modeling relationship, sequence of surrogacies, cascade of representations, complementarity, analogy, metaphor, and epistemic time are presented together with a classification of models in a cascade. Examples of anticipated future applications of surrogacy theory in life sciences are briefly discussed.
A maximum entropy principle (MEP) governing the distribution of complexity of short oligonucleoti... more A maximum entropy principle (MEP) governing the distribution of complexity of short oligonucleotides from large collections of functionally equivalent sequences is presented. The principle is seen to work well in both translated regions (exons and bacterial genes) and introns from various genomes.
1. Computational biology has been a marvelous experience for at least three generations of the br... more 1. Computational biology has been a marvelous experience for at least three generations of the brightest scientists of the second half of the twentieth century and continues to be so in the twenty-first century. Simply speaking, computational biology is the science of biology done with the use of computers. Because computers require some specialized knowledge of the cultural and technical infrastructure in which they can be used, computational biology is significantly motivated (or even inspired) by computer science and its engineering variant known as information technology. On the other hand, the kind of data and data structures that can be processed by computers provide practical constraints on the selection of computational biology research topics. For instance, it is easier to analyze sequences of biopolymers with string processing techniques and statistics than to infer unknown biological functions from the unknown three-dimensional structures of the same biopolymers by using image processing tools. Similarly, it is advisable to study systems of chemical reactions (including metabolic pathways) in terms MD: KONOPKA, JOB: 04359, PAGE: 1 1 0982-9_Konopka_Ch01_R2_070204