Question

1. Align human cardiac and skeletal isoforms of human myosin-binding protein C. Show alignment. Where these isoforms differ most of all from each other?

2. Predict secondary structure of the region where isoforms are most different. Do you think if it is disordered region or if it has compact tertiary structure?

Answer 1

Human cardiac myosin binding protein c is aligned with skeletal isoforms:

The sequence of cardiac myosin choosen is: 

1. >AAC04620.1 cardiac myosin binding protein-C [Homo sapiens]

The sequence of skeletal isoform choosen is: 

1. >NP_996555.1 myosin-binding protein C, slow-type isoform 2 [Homo sapiens]
2. >NP_996556.1 myosin-binding protein C, slow-type isoform 3 [Homo sapiens]
3. >NP_001241652.1 myosin-binding protein C, slow-type isoform 10 [Homo sapiens]

Multiple Sequence alignment:

Aligning more than 3 sequences to compare the conserved regions multiple sequence alignment is done.

Cardiac myosin binding protein-C is compared with skeletal isoforms 2,3 and 10

Results:

The multiple sequence alignment between the sequences is found to be highly conserved. Slight differences can be found in the alignment. These slight differences found to be the one that is responsible for the different skeletal isoforms.

Secondary structure prediction:

Secondary structure of these sequences is predicted using GOR tool in Expasy.

1. >AAC04620.1 cardiac myosin binding protein-C [Homo sapiens]

2. >NP_996555.1 myosin-binding protein C, slow-type isoform 2 [Homo sapiens]

3. >NP_996556.1 myosin-binding protein C, slow-type isoform 3 [Homo sapiens]

4. >NP_001241652.1 myosin-binding protein C, slow-type isoform 10 [Homo sapiens]

Results:

protein sequence secondary structure prediction has shown that these sequences has 3 main protein secondary structures

• Alpha helix
• Extented strand
• Random coil

They differ slightly in there percentage of these structures present. These sequences found to have highly similar secondary structures.

Conserved domain comparison:

When comparing the conserved domains between the sequences, human cardiac myosin binding protein-C found to have a domain Ig-titin-like domain which is not present in the skeletal isomers.

The skeletal isoforms have ig-super family domain which is not present in the human cardiac myosin binding protein C.

Interpretation:

These sequences compared are highly similar. Cardiac myosin binding protein C has a domain difference when compared with the skeletal isoforms. The secondary structures are also in the similar percentage present in between the proteins. These proteins do not have any disordered regions; they have compact tertiary structure formation and well conserved domain for the proper protein functioning.