Subtle evolutionary changes in the distribution of N-glycosylation sequons in the HIV-1 envelope glycoprotein 120

Rao, R. Shyama Prasad; Wollenweber, Bernd

doi:10.7150/ijbs.6.407

Cited by 7 publications

(13 citation statements)

References 42 publications

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“…Here, the expected proportion of sequon types is equal to the proportion of different amino acids in a protein according to zero order Markov chain. That is, given 20 types of amino acids, a maximum of 20 sequon types (NXS and NXT separately) may be expected in a protein [ 19 , 20 ]. Table 1 also shows the observed proportion of sequon types for experimentally confirmed N- glycosylated sites in eukaryotic proteins.…”

Section: Discussionmentioning

confidence: 99%

“…The influenza A H3N2 hemagglutinin (HA) sequences (1319) were downloaded from the Influenza Virus Resource at National Centre for Biotechnology Information [ 17 ] and the HIV-1 glycoprotein-120 (gp120) sequences (11333) were downloaded from HIV database at Los Alamos National Laboratory [ 18 , 20 ].…”

Section: Methodsmentioning

confidence: 99%

“…The amino acid proportions were calculated from the pooled amino acid frequencies for each group. The expected probabilities of sequon types are equal to the proportions of individual types of amino acids according to zero order Markov chain [ 19 , 20 ].…”

Section: Methodsmentioning

confidence: 99%

“…For HA and gp120 sequences, the actual sequon density was considered the number of sequons per 100 amino acid residues. The expected sequon density was calculated from the second order Markov chain [ 19 , 20 ].…”

Section: Methodsmentioning

confidence: 99%

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Do N-glycoproteins have preference for specific sequons?

Rs¹,

Bernd²

2010

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Protein N-glycosylation requires the presence of asparagine (N) in the consensus tri-peptide NXS/T (where X is any amino acid, S is serine and T is threonine). Several factors affect the glycosylation potential of NXS/T sequons and one such factor is the type of amino acid at position X. While proline was shown to negatively affect N-glycosylation, the nature of other amino acids at this position is not clear. Using Markov chain analysis of tri-peptide NXS/T from viral, archaeal and eukaryotic proteins as well as experimentally confirmed N-glycosylated sequons from eukaryotic proteins, we show here that the occurrence of most sequon types differ significantly from the expected probability. Sequon types with F, G, I, S, T and V amino acids are consistently preferred while those with P and charged amino acids are under-represented in all four groups. Further, proteins contained far fewer number of possible sequon types (maximum 20 types for NXS or NXT taken separately) for any given number of sequons, which may be explained based on random sampling. Consistent with the present finding, majority of the over-represented sequons found in two important viral envelope glycoproteins (hemagglutinin of influenza A H3N2 and glycoprotein120 of HIV-1) are indeed preferred sequon types, which may provide a selective advantage. Accordingly, although there seems to be some preference for sequons, this preference may not be unique to N-glycosylation.

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Do N-glycoproteins have preference for specific sequons?

Rs¹,

Bernd²

2010

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“…of N-linked glycosylation is indispensable. The glycosylation site of covalent attachment is the asparagine residue (N) within the canonical amino acid sequence, asparagine-Xserine/threonine, where X could be any amino acid except proline, which is avoided due to conformational hindrance (Rao and Wollenweber, 2010 (Fig. 3).…”

Section: N-linked Glycosylation Of the Envelope Glycoproteins Of Fvsmentioning

confidence: 99%

Comparative analysis of the envelope glycoproteins of foamy viruses

Sun¹,

Wen²,

Liu³

et al. 2012

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Summary. -One of the most fascinating findings in retrovirology is the construction of viral vectors based on foamy viruses (FVs) for gene therapy. The envelope glycoprotein (Env), one of the structural proteins of FV, is an important antigen in the immunoassays, as it is highly specific. To compare the characteristics of all 15 available FV Envs, the phylogenesis, hydrophobicity, modifications, and conserved motifs were analyzed based on the Env sequences. Meanwhile, the secondary structures of transmembrane (TM) domains of FV Envs were predicted. The results of phylogenetic analyses based on Envs indicated that the foamy viruses from different hosts could form three groups. The hydrophobicity analysis revealed that FV Envs had two prominent hydrophobic regions, which was similar to other retroviruses. Though the glycosylation, ubiquitination, and the secondary structures of TM domains of FV Envs were in line with other retroviruses, the roles were distinctly different. Interestingly, the analyses of conserved motifs suggested that FV Envs possessed several specific functional motifs.

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N-glycoprotein macroheterogeneity: biological implications and proteomic characterization

Zacchi

Schulz

2015

Glycoconj J

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Glycosylation is a co- and post-translational modification that is critical for the regulation of the biophysical properties and biological activities of diverse proteins. Biosynthetic pathways for protein glycosylation are inherently inefficient, resulting in high structural diversity in mature glycoproteins. Macroheterogeneity is the structural diversity due to the presence or absence of glycans at specific glycosylation sites, and is caused by inefficiency in the initial transfer of glycans to proteins. Here, we review the enzymatic and evolutionary mechanisms controlling macroheterogeneity, its biological consequences in physiological and disease states, its relevance to heterologous production and glycoengineering of glycoproteins, and mass spectrometry based methods for its analysis. We highlight the importance of the analysis of macroheterogeneity for a complete understanding of glycoprotein biosynthesis and function, and emphasize how advances in mass spectrometry glycoproteomics will enable analysis of this critical facet of glycoprotein structural diversity.

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Subtle evolutionary changes in the distribution of N-glycosylation sequons in the HIV-1 envelope glycoprotein 120

Cited by 7 publications

References 42 publications

Do N-glycoproteins have preference for specific sequons?

Do N-glycoproteins have preference for specific sequons?

Comparative analysis of the envelope glycoproteins of foamy viruses

N-glycoprotein macroheterogeneity: biological implications and proteomic characterization

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