Bch2Ibm Biochemistry & Molecular Biology Assessment Answers

 ‘Protein-ligand interactions’

One of the major tasks of any scientist is to present and explain their work to others. Scientific research and the related fields of medicine, nutrition, agriculture and many others rely absolutely on sharing new discoveries and insights. Scientific research is reported in specialist journals and at scientific meetings where other scientists gather to hear the latest developments. New ideas and new explanations grow out of the work of many individual scientists who discuss their work together.

Background

Proteins are the most prevalent macromolecule in biological systems, and they participate in the majority of cellular functions. They are immensely diverse, varying significantly in size, structure and function. Proteins are involved in a multiplicity of processes including cell signaling (hormones, antibodies and receptors), cellular transport (haemoglobin, neurotransmitter and ion transporters), cell structure (actin, tubulin, and keratin), motor function (myosin, dynein and kinesin) and metabolism. The function of proteins usually requires some form of interaction with another molecule. The molecule or substance which is bound to the protein to form a functional complex is referred to as a ‘ligand’. Many proteins interact with multiple ligands which can range from ions or other small molecules to other macromolecules, sometimes including other copies of the protein itself.

Task

For this assignment you are asked to investigate, at the molecular level, the interplay between a protein and a ligand with which it interacts. You are free to investigate a protein-ligand interaction of your own choosing and that you find interesting (many examples are provided below to help you make a choice). You will plan your literature research, gather information about the protein, its ligand and the function induced by this interaction, and then use this information to write a report on the major features of the protein-ligand complex.

1.Histone is the key protein component of a chromatin that acts in the form of spools around which a double helical strand of DNA is wound. The H1 proteins have a central and globular domain along with a short-N (70-80 amino acid) and a long-C (100 amino acid) terminal tail. The protein H1 is involved in packaging of the beads on a ring structures into higher order in a nucleosome. These H1 histones are 200 amino acids long (Zhou et al., 2013). On the other hand, the DNA has three chemical components namely, a sugar deoxyribose, four nitrogenous bases and a phosphate group. The nitrogenous bases are adenine, cytosine, guanine and thymine, each of which can be characterized into either purine or pyrimidine. All of these components of the DNA are arranged in the form of groups named nucleotides, each of which contains the sugar, a phosphate and any one of these bases.

2.Unlike the function of other histone molecules like H2, H3 and H4, H1 molecule does not form the nucleosome bead but attaches to the top of the nucleosome structure and helps in keeping the wrapped DNA in its place (Hergeth & Schneider, 2015). H1 is also found in half the volume of the rest four histones that add two molecules to nucleosome beads. Besides binding to the nucleosome, H1 protein also attaches to the linker DNA that is an estimated 20-80 nucleotides in its length and located in a region between the nucleosomes, thereby facilitating the stabilisation of the 30 nm long, zigzagged chromatin fibre (Harshman, Young, Parthun & Freitas, 2013). Ionic extraction of the linker histones from reconstituted or native chromatin fibres have been found to play a role in promoting the unfolding of the structure of 30 nm fibres to beads-on-a-string, under conditions that are predominantly hypotonic.

3.H1 histone plays an important role in mediating gene activity. One of the primary features of the interaction between the H1 histone and a DNA strand is associated with the preference of the histone for the presence of a supercoiled DNA double helix. The interaction of H1 with DNA helps in the process of ribosome formation. Upon modification of the H1 histones due to the accumulation of phosphate groups, commonly referred to as the process of phosphorylation, an array of changes occur in gene activity near vicinity of the H1 that has been phosphorylated. Acetylation of the tail of histone on a nucleosome is found allied to chromatin unfolding and an increase in the activity of regional transcriptional (Venkatesh & Workman, 2015). Furthermore, the interaction between H1 and the DNA is essential for every basic cellular processes that need access of DNA such as, transcription, repair and replication. H1 acts as either a positive or a negative regulator of the transcription process. Furthermore, poly-ubiquitylated H1 acts as an essential intermediate in the signalling process associated with double stranded break response in a DNA. The interaction between H1 and DNA also acts as an important target for ubiquitylation, following a UV-induced damage (Thorslund et al., 2015).

4.Linker H1 have been identified to attach close near the sites of entry and exit of the linker DNA, present on the core of the nucleosome, thereby facilitating the aggregation of two segments of linker DNA. The globular domain has a diameter of an estimated 2.9 nm and gets folded in solution, thereby unveiling three α-helices. Presence of two DNA binding sites on reverse sides of the molecule is a characteristic feature that makes H1 highly dynamic, with assistance of its C-terminal domain. This binding of H1 to linker DNA enables shift of chromatin towards extra condensed forms. Although chromatin fibres that lack H1 are able to fold till a certain limit, evidences emphasise on the fact that more compact chromatin fibre is achieved in presence of H1 histone (Rothbart & Strahl, 2014). Nonspecific binding of H1 to DNA results in primary assembly formation with other structures that are directed by electrostatic interaction. 

5.The interaction between H1 and DNA occurs in the subcellular organelle called the nucleus. Most of the H1 proteins inside the nucleus remain bound to the chromatin.

6.Absence of H1 and DNA interaction will prevent formation of the solenoid shaped chromatin fibre. The H1 will also show a failure in protecting 15-30 bases of additional DNA. Knockout of three H1 subtypes have also shown a global lessening in the repeat length of nucleosomes and decompaction of chromatin fibres, which in turn will create an impact on transcription (Izzo & Schneider, 2016). Thus, the nucleosomes will not be linked into higher order structures, and an absence of the interaction will directly affect cell survival.