Elizeu/sandbox/citocromo c

From Proteopedia

Revision as of 11:59, 3 May 2018

Introduction

-- Structural Description

The function of a protein is determined by its shape. The shape of a protein is determined by its primary structure (sequence of amino acids). Based on the analysis of the primary structure, this protein is water soluble secretory, which suggests that it is periplasmic. The periplasm is a concentrated gel-like matrix in the space between the inner cytoplasmic membrane and the bacterial outer membrane called the periplasmic space in gram-negative bacteria. The N-terminal sequence of AlgQ1 is REATW (Arginine, Glutamic acid, Alanine, Threonine, Tryptophan). The first 24 amino acid residues play the role of a signal peptide. A signal peptide is a short peptide including between 16 to 30 amino acids, which is found at the N-terminus of proteins that are destined toward the secretory pathway. The bulk of this part includes 5 to 16 hydrophobic amino acids. These hydrophobic residues tend to create a single α-helix and are also referred to as “h-region”. there is typically a number of amino acids at the end of the signal peptide that is recognized and cleaved by signal peptidase and therefore named cleavage site. AlgQ1 and AlgQ2 are two periplasmic proteins with the almost very similar function which is mediating the transport of the substrate. The crystal structure of AlgQ2 consist of two domains separated by a cleft and binds and releases alginate tetrasaccharide by creating conformational change in these two domains. To mention some of the different forms of this protein we can take a look into 5H6U, 5H71, 1KWH, 1J1N in PDB. As an alginate binding protein, the dissociation constants (Kd) are estimated. This constant is 6 μg/mL for AlgQ1 and 4 μg/mL for AlgQ2. Results from UV absorption spectroscopy indicate that both of these proteins are alginate specific. X-ray crystallography shows interactions between proteins and oligosaccharides. Keiko Momma et al. provides what they have found by X-ray, in a table, which is shown here.

AlgQ1 in its two forms (Apo and Holo) comprises 490 amino acid residues, indicating that proteins are truncated. The C-terminal amino acid is determined to be Tyrosine. In addition, the amino acid analysis suggests that AlgQ1 is truncated between Tyr490 and Gly491. Ramachandran plot analysis shows that most non-glycine residues are located in the most favorable regions. There is only one exception to this, which is Lys251, (apo-AlgQ1, φ=65° and ψ=-141°; holo-AlgQ1-TE, φ=62° and ψ=-133°; and holo-AlgQ1-DI (1Y3N), φ=65° and ψ=-139°), and it is present in an allowed region. Lys251 is located next to the terminus of a helix (H12/C). We can see the apo-AlgQ1 as a cartoon presentation, made up of two globular domains N domain and c domain, consisting of residues 1-133, 310-400 and 134-309, 401-490 respectively. As mentioned in CATH classification, these two domain both are in a class of alpha/beta proteins, showing 3-Layer(aba) Sandwich architecture, having the topology of D-Maltodextrin-Binding Proteins; domain 2 and the homology of both of these domains as can be predicted is Periplasmic binding protein-like II. If we want to assess how SCOP classify this protein, we can see that SCOP sees this protein as a one domain totally, but the same as in CATH, from the alpha and beta proteins. In addition, this protein belongs to Periplasmic binding protein-like superfamily and comes from Phosphate binding protein-like family.

The two domains that we introduced are connected to each other through 3 loop segments consisting of residues 133-136, 292-347, and 399-401. The disaccharide is bound to the deep cleft between N and C domains. When N-domains of apo and holo forms of the protein were superimposed, then a rotation angle of 0.6 degrees was needed for the C domain to be superimposed. Structures of a holo-AlgQ with tetrasaccharide and disaccharide (AlgQ1) are almost the same. Here we can see the binding sites holo-algQ1-DI. This bound consists of ΔM1-M2 with α-anomeric M2 at S1 and S2. ΔM, M, and G denote unsaturated D-mannuronate, saturated D-mannuronate, and saturated L-guluronate, respectively. The bound oligosaccharides interact with surrounding amino acids. Keiko momma et al. summarized hydrogen bond interactions between the bound alginate oligosaccharides and alginate binding proteins. The number of direct hydrogen bonds between AlgQ1 and the disaccharide in holo-AlgQ1 DI is 11 and the number of associated water molecules is 10. Five water molecules are located at S3 and S4 subsites in holo-AlgQ1-DI. The number of C-C contacts that AlgQ1 and disaccharide holo-AlgQ1-DI have is 30, which indicates that the nonreducing end of sugar is in a significant involvement with AlgQ1.