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Browsing Theses & Dissertations by Author "Acevedo Morantes, Claudia Y."
Acevedo Morantes, Claudia Y.; Ramírez-Vick, Jaime E.; College of Arts and Sciences - Sciences; Martínez-Cruzado, Juan Carlos; Ríos-Velázquez, Carlos; Department of Biology; Pérez-Muñoz, Carlos A.
Rhodobacter sphaeroides is a facultative photoheterotroph organism, belonging to the
α-3 subdivision of the Proteobacteria. It has many modes of growth conferring advantage
when the environmental conditions change. These different metabolic pathways involve a
diversity of hemoproteins like cytochrome c2 (cyt c2). Within the cyt c2 maturation pathway a
diversity of proteins is involved. CcmE is a chaperone protein involved in the covalent
binding of a heme group through a histidine (H) residue, and delivering it to the CX2CH
motif of the apo-cytochrome c2.. This study involves an in silico analysis of a hypothetical
CcmE protein from Rhodobacter sphaeroides 2.4.1. Primers were designed based on the
predicted ccmE gene sequence at GenBank and the translation was made using the ExPASy
server. One hundred twenty-five CcmE sequences obtained from diverse organisms and
related to CcmE from R. sphaeroides were used to generate a Multiple Sequence Alignment
(MSA) using the ProbCons and T-Coffee applications. Two well conserved motifs
Y*TGILPDLF*REG and LAKH*DE are found to be present in all sequences analyzed. A
selection of conserved blocks from the MSA was used to generate a phylogenetic tree
resulting in seven groups. The GEnt application found that tyrosine (Y*) and phenylalanine
(F*) at the first motif and histidine (H*) at the second motif have the highest entropy score,
implying a key functional role in the CcmE protein family. Finally, using the VMD
application, the structure of the CcmE protein is compared: one from CcmE sequence
obtained from in silico analysis against the CcmE obtained from the database of E. coli. All
of these sequences have the six stranded β-sheet and histidine (H) and tyrosine (Y) residues
involved in interactions between CcmE and the heme group. Our results for motifs of
CCME_Rhodo are also in agreement with preliminary studies from CcmE obtained from
database of E. coli. Our analysis suggest the presence of two well conserved motifs with
internal gaps of variable length, consistent with previously published predictions. Using the
predicted consensus sequences obtained from MEME analysis, we were able to predict the
structure of CCME_Rhodo (obtained in silico) and compare it with the CcmE protein from E.
coli (PDB ID 1SR3). These newly identified sequences are now more amenable for study
using classic protein expression that may experimentally elucidate its structure and function.