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             MacDNAsis Analysis of Histone H1
                                                       by David Lamar

MacDNAsis was used to analyze the structure of human histone H1.  Human cDNA for the histone H1 gene was used.  To see the results of a GenBank search for histone H1 click here.

Figure 1 is the result of analysis of the human histone H1 cDNA to determine the largest open reading frame (ORF) for the gene.  The blue-highlighted row is the largest ORF.  To view the cDNA and amino acid sequence for the human histone H1 gene click here.

                    Figure 1:  Representation of the Largest Open Reading Frame for Human Histone H1:
                    The red triangles indicate start codons and the green lines represent stop codons.  The
                    blue row indicates the open reading frame from histone H1.  The gene appears to ext-
                    end from base pair 1 to base pair 585.

The ORF determined from Figure 1 was translated to predict the molecular weight of Histone H1.  The protein was predicted to consist of 195 amino acids and to weigh 20,861.81 daltons (Data not shown).

The predicted amino acid sequence for histone H1 was used to create a hydropathy plot, an antigenicity plot, and to predict the protein's secondary structure.  Figure 2 is a hydropathy plot.  It can be used to predict whether or not protein is an integral membrane protein.  According to Kyte and Doolittle, a reading above 2.00 on the plot suggests that that domain of the protein is a transmembrane domain.

                  Figure 2:  Kyte and Doolittle Hydropathy Plot for Histone H1:  It appears that histone H1 could be
                       loosely associated to the membrane due to the peak near amino acid 30.  But because this is the
                       only peak that reaches the threshold and histone H1 is known to be bound to DNA, it is unlikely
                       to be an integral membrane protein.

Figure 3 is a Hopp and Woods antigenicity plot.  This plot is used to determine what domains of the protein would be good candidates against which one could make an effective monoclonal antibody.  The highest peaks indicate the most hydrophilic domains which would not be likely to be transmembrane domains or tucked in the interior of the protein.  One would assume that domains such as these would accessible to an antibody in vivo.

                         Figure 3:  Hopp and Woods Antigenicity Plot for Histone H1:  This plot suggests many
                         possibilities for an antibody binding domain.  The peak near amino acid 110 and amino
                         acid 150 are potentially successful domains.

Figure 4 is a Chou, Fasman, and Rose analysis to predict the secondary structure of histone H1.
                            Figure 4:  Chou, Fasman, and Rose Prediction of Histone H1 Secondary Structure.

Figure 5 are the results from a comparison of the amino acid sequences of histone H1 from five different species: the human (Homo sapiens), the sea urchin (Echinolampas crassa), the house mouse (Mus musculus), the fruit fly (Drosophila melanogaster), the mussel (Mytilus edulis).  Click on the genus-species name for each animal to view their histone H1 amino acid sequence.

                        Figure 5: Comparison of Histone H1 Amino Acid Sequences for Five Different Species:
                        The common names of the animals used for the comparison are given to the right.  The
                        black-outlined, yellow-lettered single letter amino acid symbols indicate an amino acid
                        whose place in the sequence is identical with at least one other species.

Figure 6 is a phylogeny of the five species (Homo sapiens, Echinolampas crassa, Mus musculus, Drosophila melanogaster, Mytilus edulis) used in the comparison based on amino acid sequence similarity for histone H1.  Click on the genus-species names above to view the histone H1 amino acid sequence for each species.
                              Figure 6:  Phylogenetic Tree of Histone H1 similarity Among Five Species:  As
                              one would expect, human and mouse histone H1 are very similar.  All animals
                              seems to have high similarity.  This could mean that the shape of histone H1 can
                              not very greatly and still function correctly.

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