US 5,856,928 A · Gene and protein representation, characterization and interpretation process

Abstract

Natural numbers are assigned to represent DNA and mRNA nucleotide bases (n-numbers 0, 1, 2, 3), base pairing numbers in RNA (p-numbers 0, 1, 2, 3), and amino acids in protein (z-numbers with seventeen prime numbers and odd numbers 1, 25, 45; all smaller than 64). These numbers reflect intrinsic properties of the nucleotide bases, their triplet-base codon combinatorics and chemical bonding properties (hydrogen bonds, hydrophobicity, codon positions, and molecular sizes). Gene and protein sequences may be represented, characterized and interpreted by their specific n-sums and z-sums. Base dimers/oligomers and dipeptides/oligopeptides are found to correspond to their sums, as verified by using statistical and other methods. Utility rules are devised for applications in base dimers distribution, RNA base pairing, oligomer repeats and the encoded oligopeptide repeats. Conserved base pairs in four stems of a given mitochondrial tRNA correlate well with the z-number in the encoded hydrophobic amino acid. Conserved protein segments are mostly prime peptides (oligopeptides with prime number z-sums) except those with strict repeats (collagen Gly-3 repeats, leucine zipper Leu-7 repeats, etc.). This representational scheme is also capable of inferring protein folding and cross linking. Sequence alphabets (nucleotide bases and amino acids) in existing and future data banks can be converted to such numbers to facilitate computation and characterization.

Claims14

Dependent claims

A process for evaluating a nucleotide sequence, comprising:

(a) determining by conventional means the nucleotide sequence of an oligomer consisting essentially of nucleotides;
(b) assigning each nucleotide an n-number, wherein Adenine (A) equals zero (0), Cytosine (C) equals one (1), both Thymine (T) and Uracil (U) equal two (2), and Guanine (G) equals three (3) to derive an n-number sequence representative of the nucleotide sequence;
(c) entering said n-number sequence into a database to derive an n-number library;
(d) specifying a property of a nucleotide sequence derivable from n-numbers;
(e) scanning the n-number library for all possible n-number sequences which satisfy the specification;
and
(f) displaying the resultant n-number sequences.

4 more elements

A process for evaluating an amino acid sequence, comprising:

(a) determining by conventional means the amino acid sequence of a polypeptide or its precursor DNA or RNA sequences;
(b) assigning each amino acid or codon a z-number, wherein a stop codon equals zero (0), tryptophan (Trp) equals the non-prime odd number one (1), isoleucine (Ile) equals the prime number two (2), methionine (Met) equals the prime number three (3), threonine (Thr) equals the prime number five (5), lysine (Lys) equals the prime number seven (7), asparagine (Asn) equals the prime number eleven (11), proline (Pro) equals the prime number thirteen (13), leucine (Leu) equals the prime number seventeen (17), glutamine (Gln) equals the prime number nineteen (19), serine (Ser) equals the prime number twenty-nine (29), aspartate (Asp) equals the prime number thirty-one (31), arginine (Arg) equals the prime number thirty-seven (37), valine (Val) equals the prime number forty-one (41), tyrosine (Tyr) equals the prime number forty-three (43), histidine (His) equals the prime number forty-seven (47), alanine (Ala) equals the prime number fifty-three (53), glutamate (Glu) equals the prime number fifty-nine (59), glycine (Gly) equals the prime number sixty-one (61), phenylalanine equals the non-prime odd number twenty-five (25), and cysteine equals the non-prime odd number forty-five (45) to derive a z-number sequence representative of the amino acid sequence;
(c) entering said z-number sequence into a database to derive a z-number library;
(d) specifying a property of a polypeptide sequence derivable from z-numbers;
(e) scanning the z-number library for all possible z-number sequences which satisfy the specification;
and
(f) displaying the resultant z-number sequences.

4 more elements

A method of determining secondary and/or tertiary structural properties of a protein or peptide comprising the following steps:

(a) determining the amino acid sequence of said protein or peptide;
(b) assigning each amino acid a z-number wherein tryptophan (Trp) is assigned non-prime odd number one (1), isoleucine (Ile) is assigned prime number two (2), methionine (Met) is assigned prime number three (3), threonine (Thr) is assigned prime number five (5), lysine (Lys) is assigned prime number seven (7), asparagine (Asn) is assigned prime number eleven (11), proline (Pro) is assigned prime number thirteen (13), leucine (Leu) is assigned prime number seventeen (17), glutamine (Gln) is assigned prime number nineteen (19), serine (Ser) is assigned prime number twenty-nine (29), aspartate (Asp) is assigned prime number thirty-one (31), arginine (Arg) is assigned prime number thirty-seven (37), valine (Val) is assigned prime number forty-one (41), tyrosine (Tyr) is assigned prime number forty-three (43), histidine (His) is assigned prime number forty-seven (47), alanine (Ala) is assigned prime number fifty-three (53), glutamate (Glu) is assigned prime number fifty-nine (59), glycine (Gly) is assigned prime number sixty-one (61), phenylalanine is assigned non-prime odd number twenty-five (25), and cysteine (Cys) is assigned non-prime odd number forty-five (45);
(c) delineating Met and/or Ile headed prime amino acid sequences by determining the length of sequences which begin with Met or Ile, wherein the sum of the z-numbers for the amino acids in such sequences is a prime number, and wherein the shortest sequence of such amino acids whose sum of z-numbers equal a prime number is determined;
(d) determining whether the Met and/or Ile headed prime amino acid sequences delineated in step (c) have a Cys or Phe in a center position;
(e) delineate Cys and/or Phe centered prime amino acid sequences by determining whether the sum of the z-numbers of the amino acid sequences immediately surrounding Cys and/or Phe are prime numbers, wherein such Cys and/or Phe are not in a center position of a Met or Ile headed prime amino acid sequence;
(f) delineate Cys and/or Phe residues present in the protein or polypeptide of step (a) wherein such Cys and/or Phe residues are not Cys and/or Phe residues according to steps (d) or (e);
(g) determining the length of the Met and/or Ile headed prime amino acid sequences of step (d) having a Cys and/or Phe in a center position;
(h) determining the length of the Cys and/or Phe centered prime amino acid sequences of step (e);
(i) delineating prime amino acid sequences according to step (e) wherein said amino acid sequence overlaps with a prime amino acid sequence according to step (c), and determining said prime amino acid sequences of step (e), which overlap, to be non-prime amino acid sequences;
j) identifying the crosslinking propensity, the propensity for forming fibrous, regular segments without turns or bends, and the propensity for forming segments which turn or bend, so as to determine the secondary or tertiary structure of the protein or peptide of step (a) wherein amino acid sequences according to steps (g) and (h) having a length>=seven amino acid residues have a propensity to crosslink with other such amino acid sequences, and wherein amino acid sequences according to steps (g) and (h) having a length<seven amino acid residues have a propensity to crosslink with other such amino acid sequences, and wherein amino acid sequences according to steps (f) and (i) have a propensity to crosslink with other such amino acid sequences.

7 more elements

Dependencies are inferred from the claim text.

Gene and protein representation, characterization and interpretation process

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Gene and protein representation, characterization and interpretation process

Life of this patent

Abstract

Claims14