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US 2003/0211538 A1Published application
CAP-Gly domain structure and uses thereof
OwnerMing Luoinventor
Life of this patent
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Abstract
The present invention relates to a polypeptide that includes amino acid sequence of the CAP-Gly domain or a portion thereof and heterologous amino acid sequence, the structure of any such polypeptide and its use in designing, identifying or validating ligands to the CAP-Gly domain or homologous structure.
Claims98
A polypeptide comprising amino acid sequence of the CAP-Gly domain and heterologous amino acid sequence.
An isolated polypeptide comprising an amino acid sequence according to amino acid residues 135 to 229 of a cytoskeletal-associated protein with structure analogous to the structure of the CAP-Gly domain of F53F4.3 protein.
A crystal of the CAP-Gly domain, wherein the space group of the crystal is P6122 and unit cell dimensions of the crystal are about a=64±3 Å, b=64±3 Å, and c=102±3 Å.
A crystal of the CAP-Gly domain, wherein the space group of the crystal is P6122 and unit cell dimensions are about a=64±2 Å, b=64±2 Å, and c=102±2Å.
A crystal of the CAP-Gly domain, wherein the space group of the crystal is P6122 and unit cell dimensions are about a=64±1 Å, b=64±1 Å, and c=102±1 Å.
A method of characterizing protein structures comprising the steps:
- (a) determining the three-dimensional structure of the CAP-Gly domain;
- (b) determining the three-dimensional structure of an experimental protein;
- (c) comparing the three-dimensional structure of the experimental protein to the three-dimensional structure of the CAP-Gly domain;
- and
- (d) recording variances between the three-dimensional structure of the CAP-Gly domain and the experimental protein.
2 more elements
A method for generating analogs of polypeptides comprising the CAP-Gly domain, comprising:
- (a) determining the structure of a CAP-Gly domain;
- (b) selecting a polypeptide comprising an amino acid sequence that maintains a CAP-Gly domain structure;
- and
- (c) generating an analog polypeptide comprising the amino acid sequence according to step (b) that maintains the CAP-Gly domain structure.
1 more element
A method for determining whether an analog of the CAP-Gly domain will have an altered three-dimensional structure as compared to the CAP-Gly domain, comprising:
- (a) determining the three-dimensional coordinates of atoms of a CAP-Gly domain;
- (b) providing a computer having a memory means, a data input means, a visual display means, the memory means containing three-dimensional molecular simulation software operable to retrieve coordinate data from the memory means and to display a three-dimensional representation of a molecule on the visual display means and being operable to produce a three-dimensional representation of an analog of the molecule responsive to operator-selected changes to the chemical structure of the molecule and to display the three-dimensional representation of the analog;
- (c) inputting three-dimensional coordinate data of the atoms of the CAP-Gly domain into the computer and storing the data in the memory means;
- (d) displaying a three-dimensional representation of the CAP-Gly domain on the visual display means;
- (e) inputting into the data input means of the computer at least one operator-selected change in chemical structure of the CAP-Gly domain;
- (f) executing the molecular simulation software to produce a modified three-dimensional molecular representation of the analog structure;
- and
- (g) displaying the three-dimensional representation of the analog on the visual display means, whereby changes in three-dimensional structure of the Cap-Gly domain consequent on changes in chemical structure can be visually determined.
5 more elements
A method for producing an analog of a CAP-Gly domain that mimics the three-dimensional structure of the CAP-Gly domain, comprising:
- (a) determining the three-dimensional coordinates of atoms of an CAP-Gly domain;
- (b) providing a computer having a memory means, a data input means, a visual display means, the memory means containing three-dimensional molecular simulation software operable to retrieve coordinate data from the memory means and to display a three-dimensional representation of a domain on the visual display means and being operable to produce a modified three-dimensional analog representation responsive to operator-selected changes to the chemical structure of the domain and to display the three-dimensional representation of the modified analog;
- (c) inputting three-dimensional co-ordinate data of atoms of the CAP-Gly domain into the computer and storing the data in the memory means;
- (d) inputting into the data input means of the computer at least one operator-selected change in chemical structure of the CAP-Gly domain;
- (e) executing the molecular simulation software to produce a modified three-dimensional molecular representation of the analog structure;
- (f) displaying the three-dimensional representation of the analog on the visual display means, whereby changes in three-dimensional structure of the CAP-Gly domain consequent on changes in chemical structure can be visually monitored;
- (g) repeating steps (d) through (f) to produce a multiplicity of analogs;
- (h) selecting an analog structure represented by a three-dimensional representation wherein the three-dimensional configuration and spatial arrangement of regions involved in function of the CAP-Gly domain remain substantially preserved;
- (i) synthesizing the selected analog by means of recombinant DNA technology;
- and
- (j) determining the CAP-Gly domain function of the synthesized CAP-Gly domain analog, whereby an analog having the activity is a mimic of the three-dimensional structure of the CAP-Gly domain.
8 more elements
A method for identifying a potential ligand of a CAP-Gly domain containing protein, comprising:
- (a) using a three-dimensional structure of the CAP-Gly domain or portions thereof as defined by atomic coordinates of F53F4.3 according to Table 2;
- (b) employing the three-dimensional structure to design or select the potential ligand;
- (c) synthesizing the potential ligand;
- (d) contacting the potential ligand with the CAP-Gly domain containing protein;
- and
- (e) determining whether the potential ligand binds to the CAP-Gly domain containing protein.
3 more elements
An analog of the CAP-Gly domain made by;
- (a) determining the structure of a CAP-Gly domain;
- (b) selecting a polypeptide comprising an amino acid sequence that maintains a CAP-Gly domain structure;
- and
- (c) generating an analog polypeptide comprising the amino acid sequence according to step (b) that maintains the CAP-Gly domain structure.
1 more element
An analog of the CAP-Gly domain made by;
- (a) determining the three-dimensional coordinates of atoms of an CAP-Gly domain;
- (b) providing a computer having a memory means, a data input means, a visual display means, the memory means containing three-dimensional molecular simulation software operable to retrieve coordinate data from the memory means and to display a three-dimensional representation of a domain on the visual display means and being operable to produce a modified three-dimensional analog representation responsive to operator-selected changes to the chemical structure of the domain and to display the three-dimensional representation of the modified analog;
- (c) inputting three-dimensional co-ordinate data of atoms of the CAP-Gly domain into the computer and storing the data in the memory means;
- (d) inputting into the data input means of the computer at least one operator-selected change in chemical structure of the CAP-Gly domain;
- (e) executing the molecular simulation software to produce a modified three-dimensional molecular representation of the analog structure;
- (f) displaying the three-dimensional representation of the analog on the visual display means, whereby changes in three-dimensional structure of the CAP-Gly domain consequent on changes in chemical structure can be visually monitored;
- (g) repeating steps (d) through (f) to produce a multiplicity of analogs;
- (h) selecting an analog structure represented by a three-dimensional representation wherein the three-dimensional configuration and spatial arrangement of regions involved in function of the CAP-Gly domain remain substantially preserved;
- (i) synthesizing the selected analog by means of recombinant DNA technology;
- and
- (j) determining the CAP-Gly domain function of the synthesized CAP-Gly domain analog, whereby an analog having the activity is a mimic of the three-dimensional structure of the CAP-Gly domain.
8 more elements
An analog structure of a CAP-Gly domain produced by;
- (a) determining the three-dimensional coordinates of atoms of a CAP-Gly domain;
- (b) providing a computer having a memory means, a data input means, a visual display means, the memory means containing three-dimensional molecular simulation software operable to retrieve coordinate data from the memory means and to display a three-dimensional representation of a molecule on the visual display means and being operable to produce a three-dimensional representation of an analog of the molecule responsive to operator-selected changes to the chemical structure of the molecule and to display the three-dimensional representation of the analog;
- (c) inputting three-dimensional coordinate data of the atoms of the CAP-Gly domain into the computer and storing the data in the memory means;
- (d) displaying a three-dimensional representation of the CAP-Gly domain on the visual display means;
- (e) inputting into the data input means of the computer at least one operator-selected change in chemical structure of the CAP-Gly domain;
- (f) executing the molecular simulation software to produce a modified three-dimensional molecular representation of the analog structure;
- and
- (g) displaying the three-dimensional representation of the analog on the visual display means, whereby changes in three-dimensional structure of the Cap-Gly domain consequent on changes in chemical structure can be visually determined.
5 more elements
A ligand of CAP-Gly domain containing polypeptide, wherein method of identifying the ligand comprises:
- (a) using a three-dimensional structure of any CAP-Gly domain or portions thereof as defined by atomic coordinates of F53F4.3 according to Table 2;
- (b) employing the three-dimensional structure to design or select the potential ligand;
- (c) synthesizing the potential ligand;
- (d) contacting the potential ligand with the CAP-Gly domain containing protein;
- and
- (e) determining whether the potential ligand binds to the CAP-Gly domain containing protein.
3 more elements
A method for identifying an interacting partner for a protein containing a CAP-Gly domain, comprising:
- (a) providing a CAP-Gly domain or analog thereof;
- (b) contacting the CAP-Gly domain or analog thereof with potential. interacting partners;
- and
- (c) determining the presence of interaction between the CAP-Gly domain or analog thereof and the potential interacting partners, thereby identifying an interacting partner of the protein containing a CAP-Gly domain.
1 more element
An apparatus for determining whether a compound will interact with a protein containing a CAP-Gly domain, comprising:
- (a) a memory that stores
- (i) the three-dimensional coordinates and identities of the atoms of the CAP-Gly domain that together form a solvent-accessible surface;
- and
- (ii) executable instructions;
- and
- (b) a processor that executes instructions to:
- (i) receive three-dimensional structural information for a candidate compound;
- (ii) determine if the three-dimensional structure of the candidate compound is complementary to the structure of the solvent-accessible surface of the CAP-Gly domain;
- and
- (iii) output the results of the determination.
7 more elements
A computer-readable storage medium comprising digitally-encoded structural data, wherein the data comprise the identity and three-dimensional coordinates of at least 6 amino acids of the CAP-Gly domain.
A repository of reference three-dimensional coordinates, and software configured to:
- (a) receive a subject set of coordinates which comprise a subject structure;
- (b) compare each subject set of coordinates to the reference set of coordinates;
- (c) calculate the root mean squared deviation of the subject set of coordinates from the reference set of coordinates;
- and
- (d) compare the root mean squared deviation from step (c) to limit values, whereby if the deviation from step (c) is less than or equal to the limit values, the subject structure is assigned a function based on the subject structure's similarity to CAP-Gly domain structure.
2 more elements
A method of determining relationships between two or more polypeptide structures, comprising:
- (a) obtaining a reference structure, wherein the reference structure is a structure of a polypeptide comprising the CAP-Gly domain or a portion thereof;
- (b) obtaining at least one subject structure;
- (c) determining a topology diagram for each of the reference and subject structures;
- (d) comparing the topology diagram of the reference structure and the topology diagram of the subject structure;
- and
- (e) assigning a relationship between the reference structure and any subject structure, wherein if the topology diagrams of the subject structures correspond to the topology diagram of the reference structure, the proteins have substantially the same protein fold.
3 more elements
A polypeptide that comprises any amino acid sequence that adopts structure substantially similar to that of a polypeptide comprising the CAP-Gly domain or a portion thereof as indicated by a method of comparison, comprising:
- (a) obtaining a reference structure, wherein the reference structure is a structure of a polypeptide comprising the CAP-Gly domain or a portion thereof;
- (b) obtaining at least one subject structure;
- (c) determining a topology diagram for each of the reference and subject structures;
- (d) comparing the topology diagram of the reference structure and the topology diagram of the subject structure;
- and
- (e) assigning a relationship between the reference structure and any subject structure, wherein if the topology diagrams of the subject structures correspond to the topology diagram of the reference structure, the proteins have substantially the same protein fold.
3 more elements
A method of identifying a compound that alters a function of a CAP-Gly domain containing protein comprising:
- (a) providing a model of the structure of the CAP-Gly domain;
- (b) studying the interaction of at least one candidate ligand with the model;
- (c) selecting a compound which is predicted to act as a ligand;
- and
- (d) determining that the selected compound will alter a function of a CAP-Gly domain containing protein.
2 more elements
A method of screening compounds to identify ligands with biological effects, the method comprising:
- (a) contacting a polypeptide comprising a CAP-Gly domain with at least one compound;
- (b) assaying for a selected biological effect;
- (c) assaying for the selected biological effect in the absence of the at least one compound;
- and
- (d) comparing the level of the selected biological effect in (b) to that in (c), whereby compounds are identified as ligands with biological effects when the level of the selected biological effect in (b) differs from the level of the selected biological effect in step (c).
2 more elements
Dependencies are inferred from the claim text.