I.  Open Reading Frames (ORF) Located on the Human Cyclin Dependent Kinase 2 Gene (cdk2). 
 
 
 
 
 
 
 
 Figure 1:  Largest open reading frame (ORF) on human cyclin dependent kinase 2.  MacDNAsis generates a series of three ORF searches in a stack (frame 1 on the top and frame 3 on the bottom).  The red triangles indicate start codons, the green lines are stop codons, and the black box indicates the largest ORF.  The largest ORF is situated between the 59th and the 1102th base pairs.  This protein encodes a protein of 348 base pairs, and the predicted molecular weight of this protein is 39.71501 kda.  To view the human cdk2 cDNA sequence from which this analysis was generated, please click here.
 
 
 
 

II.  Kyte & Doolittle Hydropathy Plot

Figure 2:  Kyte and Doolittle hydropathy plot of human cyclin dependent kinase 2.  The Kyte and Doolittle hydropathy plot generated by MacDNAsis predicts potential transmembrane domains, as well as hydrophobic and hydrophilic regions of a protein molecule.  The X-axis represents the number of the amino acid within the protein sequence, and the Y-axis represents the hydrophobicity of the amino acid being analyzed.  Positive Y-axis values indicate hydrophobic regions of the protein molecule, and negative Y-axis values indicate hydrophilic regions of the protein molecule.  Peaks on the plot rising to or above 1.8 suggest probable transmembrane domains within the protein molecule.  According to this plot, six areas of potential hydrophobicity can be seen approximately at positions 40, 100, 150, 210, 260 and 305.  This evidence suggests that human cyclin dependent kinase 2 is an integral membrane protein.
 
 
 
 
 

III.  Hopps & Woods Antigenicity Plot

 
 Figure 3:  Hopps & Wood antigenicity plot of human cyclin dependent kinase 2.  The Hopps & Wood antigenicity plot generated by MacDNAsis predicts the hydrophobicity of a protein molecule.  The X-axis represents the number of the amino acid within the protein sequence, and the Y-axis represents the hydrophobicity of the amino acid being analyzed.  Positive Y-axis values indicate hydrophilic regions of the protein molecule, and negative Y-values indicate hydrophobic regions of the protein molecule.  Hydrophilic regions of a protein molecule indicate cytoplasmic or extracellular exposure.  A highly exposed epitope increases binding between the corresponding antibody and itself.  Based on the plot, hydrophilic regions in human cyclin dependent kinase 2 appear to be almost equally distributed within the protein. The highest peak occurs around amino acid 100.  This segment of the protein would be a good potential epitope region.
 
 
 
 
 

IV.  Predicted Secondary Structure of Human Cyclin Dependent Kinase 2

 
Figure 4:  Computer generated prediction of the secondary protein structure of human cyclin Dependent Kinase 2.  The Chou, Fasman, and Rose analysis generated by MacDNAsis predicts the secondary structure of a protein molecule based on the primary structure of the protein molecule.  As indicated in the legend, blue bars represent alpha-helices, red-striped bars represent beta strands, green bars represent turns in the structure, and black checkered bars represent coiled domains.  There are 348 amino acids in human cdk2, and according to the predicted to the model, there is one major turn in the secondary structure as well as multiple alpha-helices, beta-pleated sheets, and coils. When compared to the Ras Mol image of human cdk2, the predicted structure seems relatively consistent (best viewed in Display:ribbons). 
 
 
 
 
 

V.  Multiple Amino Acid Sequence Alignment for Five Organisms

 
Figure 5:  Representative portion of a multiple sequence alignment of the amino acids of five genbank organisms (arab-arabindopsis thaliana, fly-drosophila melanogaster, human-homo sapiens, mouse-mus musculus, and yeast-saccharomyces cerevisiae.) Numbers to the left and right of the sequences and above each group indicate amino acid number.  Letters represent amino acids, with dashes (-) inserted to maximize sequence alignment.  Black boxes indicate amino acid conservation. Based on this figure, there are certain areas within the alignment that show a degree a homology, however, the majority of the human cdk2 protein shows a relatively low degree of homology with the four other organisms.  This may be due to the fact that there are numerous types of protein kinases within a species, as well as across various species.  To view the complete cDNA and amino acid sequences of the five studied organisms, please click on the following: arab, fly, human, mouse, or yeast.
 
 
 
 

VI.  Phylogenetic Tree of Human Cyclin Dependent Kinase 2 Derived from Five Organisms
Ma

 
 
 
 Figure 6:  Phylogenetic Tree illustrating the percentage of homology between the amino acid sequences of five Genbank organisms (arab-arabindopsis thaliana, fly-drosophila melanogaster, human-homo sapiens, mouse-mus musculus, and yeast-saccharomyces cerevisiae.)   MacDNAsis generated a phylogenetic tree depicting the determined amino acid sequence conservation among the five organisms.  Based on the figure, human cyclin dependent kinase 2 shows little homology as compared to the four other organisms.  The highest percent homology was between human and mouse (11.8%), and the lowest percent homology was between fly and yeast (5.5%).  To view the complete cDNA and amino acid sequences of the five studied organisms, please click on the following: arab, fly, human, mouse, or yeast.
 

To return to my homepage, please click here.
To return to the Davidson College Biology Department Homepage, please click here.

Please send comments and suggestions to: krrusso@davidson.edu.