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Logo of nihpaAbout Author manuscriptsSubmit a manuscriptNIH Public Access; Author Manuscript; Accepted for publication in peer reviewed journal;
Int J Bioinform Res Appl. Author manuscript; available in PMC Jan 1, 2011.
Published in final edited form as:
Int J Bioinform Res Appl. 2010; 6(2): 134–146.
PMCID: PMC2849288
NIHMSID: NIHMS100487

Flavitrack analysis of the structure and function of West Nile non-structural proteins

Petr Danecek* and C. H. Schein*§

Abstract

The Flavitrack database groups Flaviviruses, evolutionarily related organisms with high subtype variability, according to their phenotypes. Here, PCPMer tools were used to calculate consensus sequences based on conservation of physicochemical properties (PCP) for 919 sequences of NS2a, a non-structural protein involved in preventing host interferon response to infection. Conserved PCP-motifs were detected, primarily in the N-terminal half of NS2a. One model structure, based on a nuclear receptor, groups residues essential for West Nile infectivity (I59, V61, and M103) in a pocket on the protein surface. These methods will aid in the design of vaccines and specific therapies against Flaviviruses.

Keywords: Consensus sequence, Flavitrack, NS2a, PCPMer, West Nile virus

1 Introduction

Flaviviruses (FV) are important human and animal pathogens. They are transmitted mainly by mosquitoes and ticks and can cause various diseases, including encephalitis and hemorrhagic fever [15, 8]. Flaviviruses are single-stranded positive-sense RNA viruses with three structural proteins (C, prM, and E) and several nonstructural proteins (NS1, NS2a, NS2b, NS3, NS4a, 2K, NS4b, and NS5) (Figure 1) [27]. Many, including Yellow Fever (YF), Japanese encephalitis (JBE), and Dengue (DV1 to DV4) are endemic throughout the tropics and subtropical region of the world. In addition, West Nile virus (WN) has recently become disseminated across the continental United States [11, 9]. Although most cases of WN and other FV are relatively mild, the disease can progress to a fatal encephalitis, which, according to statistics from the Center for Disease Control, has taken the lives of more than 1000 individuals in the US since the first infections were detected in 1999 [1]. The rapid spread of the disease, and the high mortality rates for severe infections (ranging from 3-14%), has brought into focus the need to better understand the mechanisms of pathogenesis. The Flavitrack database [2] was constructed to allow statistically valid comparisons and particularly to define sequence features that correlate with disease severity [23]. Better understanding of these features can aid in the design of multivalent vaccines against FV [6, 18, 10].

Figure 1
Flaviviruses are enveloped viruses with a single-stranded, positive-sense RNA genome. The 10.3kb genome is translated as a single polyprotein, which is cleaved into three structural proteins (capsid, membrane and evelope) and several non-structural proteins, ...

Here, we illustrate some of the methods we have developed to use the data in Flavitrack to determine consensus sequences, and generate information that can aid in understanding the effects of known mutants and sequence variants on pathogenesis. The example we chose is the NS2a protein, a small (231 amino acids in Kunjin, a strain of West Nile that is prevalent in Australia) protein that is cleaved from the middle of the virus polyprotein. Although the structure and function is not known, there is evidence that NS2a plays a role in the formation of virus-induced membranes and in preventing the production of interferon after virus infection [21, 17]. Interferons (IFN) are proteins produced soon after virus infection that play a major role in the humoral defense against viral replication. Although several FV non-structural proteins have been implicated in preventing IFN induction, a single point mutation in NS2a restores the IFN response [20]. Several other sequence variants in this protein also attenuate the virus by affecting encapsidation, as well as host cell responses [28, 17]. This protein is thus a candidate to use in design of antiviral drugs. No experimental structure has been determined for NS2a, nor is its function within the virus life cycle known.

NS2a is the most variable of all FV proteins, according to our analysis, and its sequence identity ranges for mosquito-borne flaviviruses from 20 to 65% (Figure 2). In this work we attempted to identify physicochemical motifs in NS2a common to the mosquito-borne viruses. We first calculated consensus sequences based on conserved physicochemical properties for each of the virus groups separately using the methodology outlined in Section 2.3. The consensus sequences were then analyzed for regions with conserved physicochemical properties, as described in Section 2.2. We also prepared models for this protein. The fold recognition servers [14] returned no significant match, but some of the results suggested that the known mutants may function together in preventing the IFN response. The models and physicochemical motifs are a starting point for structural and mutagenesis studies to explore the function of this protein.

Figure 2
Analysis of the interspecies conservation of the NS2a protein, in terms of sequence identity between FV sequences. The protein is much more conserved in the tick borne flaviviruses (KFD-RF in the above table) and the mosquito borne encephalitic viruses ...

2 Methods

2.1 The Flavitrack Database

The Flavitrack database [2] was established to aid vaccine development efforts against Flaviviruses by providing easy-to-use tools for data retrieval and sequence analysis. Currently, the database contains more than 1400 complete genomic sequences. The data are continually downloaded from the NCBI website and then manually annotated with a “license plate” that encodes information about the disease type, fatality, host, etc. This enables easy interpretation of large multiple sequence alignments. The polyprotein annotations (with respect to the beginning and end of the proteins shown in Figure 1) are added, and, where necessary, the annotations from the NCBI are corrected. Genomic sequences with a desired phenotype can be rapidly selected using the search page of Flavitrack. Here, we used it to filter 919 wild-type NS2a protein sequences of 8 mosquito-borne flavivirus groups: DV1 to DV4, YF, WN, JBE and SLE (St. Louis encephalitis virus). Multiple sequence alignments were then generated with the Clustalw 2.0.3 program with default parameters [16].

2.2 Relative Entropy: a Measure of Sequence Conservation

The aligned sequences of the virus groups were analyzed for conserved/variable regions by calculating the relative entropy (also known as the Kullback-Leibler divergence) according to the five quantitative descriptors E1 to E5 [30]. In this approach, each of the 20 naturally occuring amino acids is represented as a point in a five dimensional space, where the five dimensions roughly correspond to hydrophobicity/hydrophylicity (E1); size (E2); alpha-helix propensity (E3). The property E4 is partially related to the partial specific volume, number of codons and relative abundance of the amino acids; and E5 correlates weakly with β-strand propensity.

The variability of a given column of the multiple alignment (K) was determined by a weighted sum of Kullback-Leibler divergences (Kp) calculated for each property E1 to E5:

K=p=E1E5spKp=p=E1E5spi=1nQp(i)log2Qp(i)Pp(i),
(1)

where Qp are the discrete probability distributions of the five property values observed in the alignment and Pp are the probability distributions of a random sample based on the amino acid distribution in the Flavitrack database. In this equation, the index p iterates over the five properties E1 to E5 and the index i over the discrete probability distribution bins (the 20 amino acids were grouped into 5 bins for each vector, so n = 5). Thus Qp(i) is the fraction of the component p observed in the bin i and Pp(i) is the corresponding background frequency. In other words, Qp(i) gives the frequency at which a group of amino acids that are most closely matched in properties (according to p) occurs in a given column, and Pp(i) is the corresponding expected random frequency calculated over the whole database.

We introduced a modification to the original approach implemented in the PCPMer software suite [29, 4] and used a scaled sum of the relative entropies Kp for the total entropy of a given column rather than their maximum. We scale the individual dimensions of the property space with scale factors sp to yield a “uniform” space, in which all five properties have equal significance. That is, we scaled the five dimensions to obtain the maximum possible entropy of 1 for each of the five properties. This scaling does not affect the results for positions with high entropies (such as conserved Cysteines and Tryptophans), but improves results for lower entropy positions with more common amino acids such as Leucine or Isoleucine.

2.3 Consensus Sequences

The Flavitrack database does not contain the same number of sequences for each group of FV. For example, the multiple sequence alignment which was analysed in this study has 135 WN sequences but only 45 for JBE (Figure 6). Simply aligning all the sequences and calculating relative entropies for this alignment would bias the selection of motifs and conserved residues toward viral groups with the largest number of representatives. One method to overcome this problem is to select individual sequences for each FV group that are to a large extent identical to one another. However, this also masks single residue variability. Here, consensus sequences that reflect the conserved physicochemical properties of each viral group were constructed, and these were then used to evaluate the total relative entropy of the whole alignment.

Figure 6
The consensus sequences of NS2a protein for different groupings of FV are depicted in terms of relative entropies, calculated as described in Methods. Each of the columns corresponds to a whole multiple sequence alignment, where the degree of conservation ...

One problem that may arise is that the same amino acid could be randomly selected at some highly variable position for all groups and the total relative entropy would be then mistakenly considered as that of an absolutely conserved position. For example, in three distinct alignments where a given position was quite random, an Ala residue may be designated. If only the consensus sequences were read into PCPMer, then the latter program would assume that the Ala at this position was quite conserved, as it occurred in three sequences. To prevent this happening, the relative entropies determined when the groups' consensus sequences were calculated are read into PCPMer as well. If the average of these subtype entropies was lower than the entropy at that position calculated for the alignment of the consensus sequences, the lower value was taken instead.

To determine a physicochemical property consensus sequence for each group or alignment of sequences, each position (column of the original alignment) was represented by an amino acid that best approximated the average value of the properties summed over all the amino acids that occur in the column. More specifically, for every position of the multiple sequence alignment we calculated the average property values as

E¯p=j=1mEjpm,
(2)

where m is the number of amino acids in the given column of the alignment; p = E1,…, E5; and Ejp are the five property values of the amino acid at that column of the j-th sequence. The consensus amino acid was that with the least Euclidean distance from the average. Because this geometrical minimization approach might select amino acids which do not appear in the corresponding column of the alignment, we restricted the consensus to the set of amino acids occurring naturally at that position. This restriction is to prevent losing information that may not be captured by the quantitative descriptors.

The five-dimensional property space was biased individually for each column of the alignment to make more significant properties that are most conserved in that column. Except for the bias, the Euclidean distance of an amino acid Aa from Ēp representing average properties was defined in the usual way

|Aa,E¯|=p=E1E5bp|EapE¯p|2.
(3)

The scale factors were calculated as bp = spKp/K, see Equation 1.

2.4 Protein Modeling

We used the basic local alignment search tool (BLAST) [5] and the fold recognition server 3D-PSSM [14] to search for homologues of known function and structure. The NS2a protein sequence was aligned with proteins suggested by the fold recognition server results. Homology modeling was carried out with the MPACK program suite with default parameters [12, 7, 26, 3].

3 Results

3.1 Deriving Conserved Motifs for NS2a

Of all the FV proteins, the NS2a protein is the most variable across the family. As shown in Figure 2, NS2a has very low sequence identity between flavivirus groups. The protein is much more conserved in the tick borne viruses and in the subgroup of mosquito borne viruses causing encephalitic diseases (WN, JBE and SLE), than in mosquito borne overall. Despite the high variability, there are areas of overall physicochemical property conservation, such as for example the positively charged amino acids essential for cleavage by the NS3 protease [24], or the repeated segments of hydrophobic amino acids, which are rich in Leu and Val residues (Figure 3).

Figure 3
Alignment of the Kunjin virus NS2a sequence (accession D00246) to the template (1QKM) as suggested by the fold-recognition server 3D-PSSM. Representative sequences ...

The PCPMer statistical analysis revealed several regions of conserved physicochemical properties common to the group of mosquito borne viruses, as depicted by the thick black and grey lines in Figure 6. The residues D73 and M108, which when mutated resulted in reduction in genome replication and virus attenuation [28], were found to lie within conserved motifs. Another residue, I59, which is critical for NS2a function and its substitution blocked production of virus particles [19, 17], fell outside conserved motifs. Other potentially important residues which are not contained in conserved motifs but are significantly conserved throughout FV in terms of physicochemical properties throughout the alignment are L18, K31, L44, V61, I129, R175, V181, K196-K198, and P215.

3.2 Possible Models for NS2a

The structure of the NS2a protein is not known and BLAST search revealed no close homologue of known function or structure. To find an appropriate template, the sequences of the NS2a protein from representatives of three groups of flaviviruses (YF, DV2 and WN, see Figure 3) were individually submitted to the 3D-PSSM fold recognition server. As the three proteins are only about 20-40% identical to one another, we reasoned that any templates that were returned for all three proteins were likely to represent a starting point for modeling the proteins. While no significant match was found, the server returned the same PDB entries as potential templates for all three proteins, although not in the same order of significance. Several templates were selected based on the coverage and percent identity to the template. All models suggested that the protein is composed of multiple helices, but the models differed in their spatial relationship to one another. In our models, the conserved hydrophobic repeats (11-18, 33-44, 51-61, 74-81, 89-95, 105-114, 136-143, 176-184, as indicated in Figure 6) are predominantly in helical regions. Most of these regions are also sufficiently conserved that they are detected as physicochemical motifs (Figure 6).

One possible model, illustrated here, was based on an alignment from 3D-PSSM with the PDB file 1QKM, a structure for a nuclear receptor protein (Figure 3), which placed three important residues close to each other (Figure 3.2). The average E-value was 4.86 with 18% identity and the template covered 230 residues. The backbone RMSD to the template for the aligned regions was 4Å (due to the flexible loop regions). Another possible model, shown in Figure 3.2, was based on an alignment with the PDB file 1A5T. The average E-value was 5.14 with 20% identity and the template covered 158 residues. The backbone RMSD to the template for the aligned regions was 1Å. This model did not cover the residues A30, I59 and V61. It is likely that other models for this template will be selected in the future when we have more experimental biophysical data.

4 Discussion

A methodology is described here for comparing genomes of the Flaviviruses, closely related organisms which exhibit high subtype variability. We modified existing methods for physicochemical properties conservation analysis [29] and formulated a new method for determining significantly conserved residues by means of the E1-E5 property vectors (Equations 1-3). We then applied these methods to the NS2a protein, the most variable of the FV proteins (Figures 2--6).6). Based on analysis of the sequence, known natural mutations (Table 1) and fold recognition results, we prepared models using the MPACK modeling suite (Figures 3.2, 3.2).

Table 1
Mutations in NS2a interfere with WN virus growth and restore IFN response.

One of the goals of our work is to include all available sequence data, so as best to relate sequence changes to phenotype. Typically, only a few reference sequences, usually chosen at random from all the virus sequences in a group, are compared to one another to determine relationships between the FV groups. However, this can give misleading results. We chose instead to analyze each group separately and then compare the consensus sequences, designed based on the statistical analysis of conserved physicochemical properties, to one another.

While the NS2a protein is variable throughout both the mosquito-borne and hemorrhagic groups, it is quite conserved within the group of mosquito-borne viruses causing encephalitic diseases (WN, JBE, SLE; Figures 2--6).6). A few highly conserved positions in the protein correlate with its ability to interfere with interferon production by the host cell. For example, most of the mutations that are known to affect NS2a's function map to the relatively more conserved N-terminus. Further, even though there is considerable diversity at the amino acid level, comparison by either amino acid polarity (Figure 3) or according to the E1-E5 property vectors (Figure 6) shows that the overall physicochemical parameters are conserved across the sequence to some degree, and it is likely that these properties account for the protein's functions.

The models shown were based on the structures 1QKM and 1A5T as templates. Although the functional significance of these models cannot at the present time be determined without experimental evidence, the overall structure of the model based on 1QKM (Figure 3.2) is consistent with what is know about the NS2a protein from sequence analysis, and data from mutations and viral adaptation revertants [17]. Although the sequence is rich in conserved hydrophobic residues, the structure based on the model 1QKM suggests that the protein could fold so as to expose conserved positively charged residues, especially those that are cleavage sites for polyprotein processing, in loop regions. The model also brings together three important residues, at different areas of the primary sequence. However, two other important residues, A30 and T149, fall outside this area. The models can be further tested by mutations of other residues in the vicinity of these functional point mutations.

In conclusion, we have established tools to determine consensus sequences according to physicochemical properties of FV proteins. As many of the essential NS proteins do not closely resemble any known protein, bioinformatic analysis of their conserved residues and structural modeling are starting points to define their functions in virus replication.

Figure 4
One possible model of the NS2a protein of Kunjin (WN) virus, based on PDB structure 1QKM, showing the position of residues known to affect the function of the protein. Three of the residues (I59, V61, M108) group together in a negatively charged pocket. ...
Figure 5
Another possible model of the NS2a protein of Kunjin (WN) virus, based on PDB structure 1A5T.

Acknowledgments

This work was supported by the NIH grant AI064913. Breanne Yingling, UTMB summer undergraduate researcher, did mutation analysis for this paper.

Biographical notes

Petr Danecek received his Ph.D. degree in biophysics in 2008 from the Charles University in Prague, Czech Republic. He is currently working as a postdoctoral researcher at the University of Texas Medical Branch, USA.

• 

Catherine H. Schein, PhD, Associate Professor, is a computational biologist with training in biochemistry, chemical engineering and microbiology. Her current work is in databases for analyzing epitopes of allergens (Structural database of allergenic proteins, SDAP) and viral proteins (Flavitrack), sequence analysis and decomposition (PCPmer), drug design (inhibitors of bacterial toxins and protein aggregation), protein modeling, NMR structure analysis and production of recombinant proteins for structural, functional and clinical studies. She has published over 80 papers and reviews, holds several patents and edited the book Nuclease Methods and Protocols (Humana Press, 2001).

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