Protein Motif – an Overview

Published: 2021-08-27 19:10:08
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Identify a named protein within the Ig family (not an antibody) and a named protein that is involved in gene regulation or DNA transcription and evaluate the importance of the structural motifs that are found in these proteins to the structure and function. You may make reference to the hierarchy of protein structure in the discussions. Include images of each of these proteins in your submission (with citations of source) to use when making your evaluation. For the gene regulation or DNA transcription protein motifs. Note there is more than one motif for these proteins, you only need to choose one but there must be a reference to a protein that contains it. L1 Cell adhesion molecules (CAM) are a class of heavy glycosylation transmembrane proteins used to maintain tissue architecture (Chung and Seung, 2012). They are expressed in neural cell types such as postmitotic neurons, Schwann cells and sensory neurons (Itoh et, al 2004, Yip et, al. 1998). They belong to the immunoglobulin (Ig) superfamily as they contain the Ig domain and fibronectin type three repeats.
The Ig fold is known by its two cysteine residues forming antiparallel beta-pleated sheets, stabilized by a disulfide bridge (Aplin et, al). L1 like other adhesion molecules are chain-like in structure, although the Ig domain they possess promotes flexibility. As a result, they fold in on themselves, for example, L1 neurofascin have a horseshoe shape which is essential for homophilic identification and binding across membranes (Liu et, al. 2010). The domain interaction between Ig domains is hydrophobic in nature which promotes homophilic interactions (Chung and Seung, 2012). L1 binds to extracellular matrix molecules or to cell adhesion receptors to affect cell-cell specificity promoting neural growth and synaptic plasticity along with the added function of cell signaling (Chung and Seung, 2012, Romano et, al.). L1 CAMs have a specific amino acid sequence known as the RGD motif. A motif is a conserved amino acid sequence that illustrates the connectivity between secondary structures.
The RGD motif can be found within the sixth Ig domain, a tripeptide, with the sequence Arginine-glycine-Aspartic acid, which is responsible for binding to cell-surface glycoprotein molecules known as integrins. This is achieved by recognizing changes in molecular cellular environments using their extracellular domains. This motif recognizes and binds specifically to the ?v?3, ?5?1, ?v?1, and ?IIb?3 integrins through heterophilic interactions controlled by divalent calcium ions (Fielding-Habermann et, al 1997, Helena et, al. 2012). L1 CAMs spontaneously trimerize as a form of molecular stability, increasing their infinity for both homophilic and heterophilic binding. The horseshoe structure is critical for binding as they collectively bind to adjacent molecules to promote cell architecture (Kiryushko et, al 2007). Although L1 CAMs and integrin beta residues are designed to recognize each other if the conformational environment of the RGD motif changes slightly will determine the integrin it recognizes and binds to. This has been shown to be dependent on cofactors and extracellular matrix molecules. (Felding-Habermann et, al 1997,) Helicases are defined as motor proteins that travel along and unwinds the helical structure of DNA, by breaking stable hydrogen bonds, using energy provided by ATP hydrolysis (Ding et, al. 2015, Narendra and Renu Tuteja 2004). This action allows access to the hereditary information secured within the molecule. Helicases pack a vast array of functions not limited to transcription, telomere maintenance, replication, repair, and recombination (Raney et, al. 2014). Helicase belongs to the SF1 and SF2 families with as nine conserved motifs.
One of the motifs within the SF 1 family is the Q motif, seventeen to twenty-two amino acids upstream (Tanner et, al 2003). Commonly found in dead-box helicase and ATPase molecules, consisting of a nine amino acid sequence (Gly-phe-x-x-pro-x-pro-ile-Gln) with an unchanging glutamine residue earning its name. This motif is conserved in most helicases and the affinity of helicases for nucleotide substrates, because of conformational changes once ATP has been bound. The Q motif has high specificity for adenine recognition and binding, due to the formation of hydrogen bonds at positions N6 and 7 of adenine (Cordin et, al. 2004).
The glutamine residue that is conserved contributes to protein oligomerization and enzymatic activity, where helicases can self-assemble to form complexes. This dimerization assembly promotes catalytic activity. Without the Q motif helicases may operate as monomers in solution (Ding et, al. 2015). Helicases are more catalytically effective as dimer complexes. In the helicase structures the P loop upstream, the Q motif can exist in a closed or open conformation. The open conformation occurs when a ligand molecule is bound. Typically a phosphate-bearing molecule, here the Q motif with the aid of phenylalanine can detect the loop with bound ATP (Tanner et, al. 2003). This regulates the affinity for adenine and acts as an activator switch for ATP hydrolysis, while subtly maintaining stable interactions between the remaining helicase motifs, the basic requirement for catalysis. It has been noted that the glutamine residue once removed from the motif prevents DNA binding and hydrolysis of ATP, as seen where it is not conserved across both SF superfamilies (Fairman-Williams et, al. 2010). The Q motif directly interacts with the adenine residue, changing its coherent orientation in order for effective catalysis (Ding et, al 2015). The removal of glutamine prevents this step and the adenine cannot fit in the active site for hydrolysis.  

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