title: Statistical correlation of nonconservative substitutions of HIV gp41 variable amino acid residues with the R5X4 HIV-1 phenotype.
abstract: BACKGROUND
  The interaction of the envelope glycoprotein of HIV-1 (gp120/gp41) with coreceptor molecules has important implications for specific cellular targeting and pathogenesis. Experimental and theoretical evidences have shown a role for gp41 in coreceptor tropism, although there is no consensus about the positions involved. Here we analyze the association of physicochemical properties of gp41 amino acid residues with viral tropism (X4, R5, and R5X4) using a large set of HIV-1 sequences. Under the assumption that conserved regions define the complex structural features essential for protein function, we focused our search only on amino acids in the gp41 variable regions.
  
  
  METHODS
  Gp41 amino acid sequences of 2823 HIV-1 strains from all clades with known coreceptor tropism were retrieved from Los Alamos HIV Database. Consensus sequences were constructed for homologous sequences (those obtained from the same patient and having the same tropism) in order to avoid bias due to sequence overrepresentation, and the variability (entropy) per site was determined. Comparisons of hydropathy index (HI) and charge (Q) of amino acid residues at highly variable positions between coreceptor groups were performed using two non-parametrical tests and Benjamini-Hochberg correction. Pearson's correlation analysis was performed to determine covariance of HI and Q values.
  
  
  RESULTS
  Calculation of variability per site rendered 58 highly variable amino acid positions. Of these, statistical analysis rendered significantly different HI or Q only for the R5 vs. R5X4 comparison at twelve positions: 535, 602, 619, 636, 640, 641, 658, 662, 667, 723, 756 and 841. The largest differences in particular amino acid frequencies between coreceptor groups were found at 619, 636, 640, 641, 662, 723 and 756. A hydrophobic tendency of residues 619, 640, 641, 723 and 756, along with a hydrophilic/charged tendency at residues 636 and 662 was observed in R5X4 with respect to R5 sequences. HI of position 640 covariated with that of 602, 619, 636, 662, and 756.
  
  
  CONCLUSIONS
  Variability and significant correlations of physicochemical properties with viral phenotype suggest that substitutions at residues in the loop (602 and 619), the HR2 (636, 640, 641, 662), and the C-terminal tail (723, 756) of gp41 may contribute to phenotype of R5X4 strains.
authors.affiliation: Programa de Maestría y Doctorado en Ciencias Bioquímicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Distrito Federal, 04510, México.
authors.forename: Elena
authors.initials: E
authors.lastname: Pacheco-Martínez
authors.affiliation: Unidad de Radio Oncología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Secretaría de Salud, Avenida Vasco de Quiroga No.15, ᅟDistrito Federal, 14080, México.
authors.forename: Evangelina
authors.initials: E
authors.lastname: Figueroa-Medina
authors.affiliation: Departmento de Física Teórica, Instituto de Física, Universidad Nacional Autónoma de México, Ciudad Universitaria, ᅟDistrito Federal, 04510, México.|Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Ciudad Univesitaria, ᅟDistrito Federal, 04510, México.
authors.forename: Carlos
authors.initials: C
authors.lastname: Villarreal
authors.affiliation: Departmento de Sistemas Complejos, Instituto de Física, Universidad Nacional Autónoma de México, Ciudad Universitaria, ᅟDistrito Federal, 04510, México.|Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Ciudad Univesitaria, ᅟDistrito Federal, 04510, México.
authors.forename: Germinal
authors.initials: G
authors.lastname: Cocho
authors.affiliation: Departmento de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, ᅟDistrito Federal, 04510, México.
authors.forename: José L
authors.initials: JL
authors.lastname: Medina-Franco
authors.affiliation: Departmento de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, ᅟDistrito Federal, 04510, México.
authors.forename: Oscar
authors.initials: O
authors.lastname: Méndez-Lucio
authors.affiliation: Departmento de Immunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Distrito Federal, México. leonorhh@biomedicas.unam.mx.
authors.forename: Leonor
authors.initials: L
authors.lastname: Huerta
mesh_terms: D000595:Amino Acid Sequence; D019943:Amino Acid Substitution; D000596:Amino Acids; D014644:Genetic Variation; D015699:HIV Envelope Protein gp120 / Q000235:genetics / Q000378:metabolism; D015700:HIV Envelope Protein gp41 / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D015658:HIV Infections / Q000378:metabolism / Q000821:virology*; D015497:HIV-1 / Q000145:classification* / Q000502:physiology*; D006801:Humans; D010641:Phenotype; D019718:Receptors, CXCR4 / Q000235:genetics* / Q000378:metabolism; D054380:Receptors, CXCR5 / Q000235:genetics* / Q000378:metabolism; D056189:Viral Tropism
chemical_list: D000596:Amino Acids; D015699:HIV Envelope Protein gp120; D015700:HIV Envelope Protein gp41; D019718:Receptors, CXCR4; D054380:Receptors, CXCR5