Prediction of the amount of secondary structure of proteins using unassigned NMR spectra: a tool for target selection in structural proteomics

Abstract

With the advent of structural genomics, the need for fast structural information about unknown proteins has increased. We describe a new methodology, based on 13C, 15N and ¹H chemical shift dispersion to predict the amount of secondary structure of unassigned proteins from their 15N- and/or 13C-edited heteronuclear single quantum coherence (HSQC) spectra. This methodology has been coded into a software called PASSNMR (Prediction of the Amount of Secondary Structure by Nuclear Magnetic Resonance), which can be accessed directly from the Internet. PASSNMR program is a powerful tool for screening proteins for proteomic or structural genomic investigations when used with recent methodologies that take advantage of the use of the antibiotic rifampicin to selectively label the heterologous proteins expressed in E. coli. PASSNMR analysis can be useful as a first approach to predict the amount of secondary structure in proteins to structural genomics. Information about the secondary structure of proteins can be obtained even before protein purification, with small quantities of protein, just by performing two simple nuclear magnetic resonance (NMR) experiments and using PASSNMR program.

chemical shift dispersion; PASSNMR; prediction of secondary structure; structural proteomics; target selection

GENOMICS AND BIOINFORMATICS

RESEARCH ARTICLE

Prediction of the amount of secondary structure of proteins using unassigned NMR spectra: a tool for target selection in structural proteomics

Vitor Hugo Moreau^{I, II}; Ana Paula Valente^II; Fábio C.L. Almeida^II

^INúcleo de Biotecnologia, Faculdade de Tecnologia e Ciências, Salvador, BA, Brazil

^IICentro Nacional de Ressonância Magnética Nuclear de Macromoléculas, Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil

^{Send correspondence to}

ABSTRACT

With the advent of structural genomics, the need for fast structural information about unknown proteins has increased. We describe a new methodology, based on ¹³C, ¹⁵N and ¹H chemical shift dispersion to predict the amount of secondary structure of unassigned proteins from their ¹⁵N- and/or ¹³C-edited heteronuclear single quantum coherence (HSQC) spectra. This methodology has been coded into a software called PASSNMR (Prediction of the Amount of Secondary Structure by Nuclear Magnetic Resonance), which can be accessed directly from the Internet. PASSNMR program is a powerful tool for screening proteins for proteomic or structural genomic investigations when used with recent methodologies that take advantage of the use of the antibiotic rifampicin to selectively label the heterologous proteins expressed in E. coli. PASSNMR analysis can be useful as a first approach to predict the amount of secondary structure in proteins to structural genomics. Information about the secondary structure of proteins can be obtained even before protein purification, with small quantities of protein, just by performing two simple nuclear magnetic resonance (NMR) experiments and using PASSNMR program.

Key words: chemical shift dispersion, PASSNMR, prediction of secondary structure, structural proteomics, target selection.

Introduction

The genome of a variety of organisms has been sequenced and the scientific community is now investigating the large amount of information available. Understanding the functioning of the newly discovered genes will have a great impact on almost all fields of research and may lead to novel treatments for cancers and other diseases (Onyango et al., 2004; Smith and Sacchettini, 2003; Chambers et al., 2000; Christendat, 2000). The scientific community is discussing strategies for quickly analyzing this deluge of new information. In this sense, computational methods are important for mining the genome to look for primary, secondary and tertiary structure homologies between proteins.

One problem in structural proteomics is that only a small group of protein folds are determined because the selection of proteins for experimental analysis is often based on their solubility and flexibility. In this way, this leads to the same classes of "well-behaved" proteins being selected for study and, consequently, only known folding motifs being resolved. The major challenge in this field is to develop methods for pre-screening potential structural targets for possible novel folding structures patterns. The process of pre-screening is principally accomplished by computational processes which restrict protein candidates (Linding et al., 2003; Christendat et al., 2000; Brenner, 2000). Target proteins have to be prioritized according to interest and accessibility and improved target-screening methods can be very important because the selection of appropriate candidates relies on arbitrary boundaries and is thus largely imprecise (Brenner, 2000). Prestegard et al. (2001) proposed the use of NMR spectroscopy as a tool for the selection of structured proteins as targets for structural determination.

The dependence of ¹Ha, ¹H^N, ¹³C chemical shifts on the secondary structure of proteins has been extensively studied (Tjandra and Bax, 1997; Ösapay and Case, 1994; Spera and Bax, 1991; Wishart et al., 1991; Wishart et al., 1991b; Pastore and Saudek, 1990; Williamson, 1990; Saito, 1986; Ando et al., 1984; Pardi et al., 1984). Heteronuclear correlation spectra (¹³C/¹⁵N) can be obtained without protein purification and at low cost by using the rifampicin protocol recently proposed by our group (Galvão-Botton et al., 2003; Almeida et al., 2001). This methodology enables the selective ¹³C/¹⁵N labeling of the heterologous protein expressed in bacteria. The present paper describes a new methodology to extract quantitative information from heteronuclear correlation spectra edited by ¹⁵N and/or ¹³C without requiring resonance assignments. It is possible to predict the amount of secondary structure only based on cross peak dispersion. This methodology was coded into a computer program for the prediction of the amount of secondary structure by NMR (PASSNMR) which was designed in our laboratory to be used in combination with the rifampicin protocol (Galvão-Botton et al., 2003; Almeida et al., 2001), thus creating a system for rapidly screening the structure of protein candidates for possible structure determination in structural proteomics.

Material and Methods

The PASSNMR program was written in the Practical Extraction and Report Language (Perl) version 5.0 using an IBM-PC workstations running Linux version 2.2, and should be fully compatible with all Unix variants and Windows systems. Starfiles of 72 proteins were obtained from BioMagRes Bank (Seavy et al., 1991) and their resonance assignments were used to reconstruct both ¹³C- and ¹⁵N-HSQC spectra of these proteins. Only Starfiles of proteins that had complete ¹³C and ¹⁵N assignments and three-dimensional structures determined by NMR were used.

Training procedures

The amount of a-helix and b-sheet, and non-ab structure was determined by analysis of the structure of the 72 proteins as found in the Protein Data Bank. These values are represented as a percentage at the primary sequence involved in these 3 structural motifs, such that the sum of all 3 is 100%. The non-ab structural types includes random coil, loops, turns, etc.

We devided ¹³C-HSQC and ¹⁵N-HSQC spectra into 10x10 areas (Figure 1) and determined the fraction of the total number of peaks within each area for every protein. The number of peaks in some areas was found to be proportional to the amount of secondary structure the protein had. The areas that showed a correlation coefficient greater then 0.3 (i.e. moderately correlated according to Anderson and Finn (1996)) between the fraction of the total peaks within that area (n_i) and the amount of secondary structure (P) were considered as one individual hint (P_i) for the training procedure for the amount of secondary structure in the protein.

The slope and the intercept of the regression line fitting the points of each area was substituted into Equation 1a to calculate the individual hints for each area. The hints were taken into account using the square of the correlation coefficient of the correlation curve for each area as a weighing factor. For the first prediction, the weighted average on the correlation coefficient for all individual hints was calculated for both ¹³C-HSQC and ¹⁵N-HSQC spectra as shown in Equation 1b.

where P_i is the individual hint of the area i; n_i is the fraction of peaks that lie on the area i; a_i and b_i are, respectively, the slope and intercept of the curve in area i; P is the unrefined prediction of the amount of the secondary structure and r_i is the correlation coefficient for the area i.

External refinement: as the sum of all types of secondary structure in protein should be equal to 100%, the predicted values of the amount of a-helix, b-sheet and non-ab structure for each protein were summed and the values corrected such that to the sum reached 100%. We corrected the predicted values according to the inverse of their correlation coefficient using the equation:

where P_ext is the externally refined value of the prediction; P is the unrefined value of the prediction; r_t is the sum of the correlation coefficients of the areas for all three types of structure and r_i is the sum of the correlation coefficient of the areas for the secondary structure that is being corrected.

Internal refinement: another refinement was applied to increase the fidelity of the prediction. The slope and the intercept values of the correlation plot (between the externally refined prediction and the real values of secondary structure) are forced to become 1 and 0, respectively. Thus, in all data points for the three kinds of structure, the equation of the straight line formed by the correlation between the real and the predicted values for each kind of structure was applied as:

where P_int is the amount of secondary structure after internal refinement, and a_p and b_p are, respectively, the slope and the intercept of the linear regression from P_ext predictions.

Many other conditions and refinement methods were tested (e.g. a different number of areas, etc.) but none of them gave results as good as those used.

The input for PASSNMR prediction must be a text peak list files of ¹³C-HSQC and ¹⁵N-HSQC spectra but peak assignment in unnecessary.

Results

To correlate chemical shift dispersion with the amount of secondary structure, ¹³C-HSQC and ¹⁵N-HSQC spectra were constructed based on the assignments obtained from Star files of 72 proteins taken from the BioMagRes Bank. The spectra were divided into areas (Figure 1) and the number of peaks in each area counted. The ratio of the number of peaks in each area divided by the total number of cross-peaks in each spectrum was calculated and found to be proportional to the amount of secondary structure in each protein obtained from the protein data bank (q.v. Materials and Methods).

The ¹³C-HSQC (A) and ¹⁵N-HSQC (B) spectra of Rous Sarcoma Virus capsid protein (Campos-Oliva et al., 2000) (Figure 1, filled circles) and Periplasmic Chaperone FinC (Pellecchia et al., 1998) (Figure 1, open circles) were divided into areas as described in the Material and Methods.

Anderson and Finn (1996) considered that correlation coefficients of between 0.3 and 0.6 are moderate, so the areas with correlation coefficients within this range were used as an individual hint for secondary structure prediction. No area showed a correlation coefficient higher that 0.6 and areas with a correlation coefficient lower than 0.3 were discarded. Areas that displayed moderate correlation coefficients between the percentage of total peaks and the amount of secondary structure in the proteins for both in ¹³C-HSQC and ¹⁵N-HSQC are shown in Table 1.

Some areas showed opposite correlation with the amount of a-helix and b-sheet in proteins, i.e., the greater the number of peaks for an a-helical protein, the smaller the number of peaks for a b-sheeted protein in the same area, and vice versa. For instance, area B8 of ¹³C-HSQC showed negative correlation with a-helix and positive with b-sheet (Table 1 and Figure 2).

The areas that showed moderate correlation (Table 1) were selected for coding the software. The slope and intercept obtained for the curve of each area were used to build an empirical equation (Equations 1a and 1b, Materials and Methods). With individual hints weighted with the square of the correlation coefficient. The square of the correlation coefficient indicates the probability of the event predicted in the correlation (Anderson and Finn, 1996), with the correlation coefficient of 1 indicating a 100% chance of the event occuring. Area B7 was not used because it gave positive correlation both for b-sheet and non-ab structure (Table 1).

The correlations between the predictions made by PASSNMR and the real amount of secondary structure in the 72 proteins, obtained from PDB, for a-helix, b-sheet and non-ab are shown in Figure 3. We named this first prediction as 'unrefined', because it was based only on the individual hints given by each area (Equation 1a and 1b). The unrefined prediction had good correlation with the real values for most proteins, with correlation coefficients of 0.84 for the a-helix, 0.86 for the b-sheet and 0.48 for the non-ab structure.

Since the sum of all types of secondary structure in proteins must reach 100%, we summed the amount of the three types of secondary structure for all proteins and the values for the unrefined prediction of total structure rounded 100% (Figure 4). This means that, although the primary prediction of the three types of secondary structure was based on three independent parameters, the total amount of secondary structure of the proteins was very close to the actual value. This can be used as a first argument for the reliability of the prediction. The prediction was refined by correcting the previous unrefined prediction assuming that the sum of the predicted percentage for the three kinds of structure (a-helix, b-sheet and non-ab structure) reached 100% in every protein studied. In cases where that sum was not equal to 100%, the external refinement was applied as in Equation 2. The external refinement (q.v. Material and Methods) raised the correlation coefficient between real and predicted values to 0.85 for a-helix, 0.86 for b-sheet and 0.65 for the non-ab structure. Although the areas correlation coefficients are considered moderated (0.3 to 0.6), the result correlation is strong (>0.6) (Anderson and Finn, 1996). This was due to the large number of individual hints for each kind of secondary structure and resulted in a more reliable prediction.

Internal refinement was then applied to the three kinds of structure as in Equation 3. Because the correlation coefficient of a curve is not affected by multiplying it values by a constant, internal refinement did not improve the correlation coefficients of predicted data but did improve the reliability of the prediction. The final correlation after external and internal refinements between real and predicted amounts of structure for a-helix, b-sheet and non-ab strucutre is shown in Figure 5. The same correlation done exclusively with areas from the ¹⁵N-HSQC spectra (data not shown) produced correlation coefficients of 0.70 for a-helix and 0.71 for b-sheet, but non-ab structure cannot be estimated using only ¹⁵N-HSQC data, so the non-ab structure values are more reliable if calculed by subtracting the sum of the values for the a and b structures from 100%.

As a test case, we used BioMagRes Bank proteins with complete assignment and their three-dimensional structure solved by X-ray crystallography. These proteins were not used to build PASSNMR because their NMR structures were not available. The efficiency of the method is illustrated by the top set data in Table 2. Most of the predictions are in good agreement with the X-ray structure. Note that the PASSNMR program was able to identify the absence of a-helix in domain 1 of CD2. The predictions using only the ¹⁵N-edited spectrum were also efficient.

We also used the PASSNMR program to investigate some proteins that are being studied in our laboratory. The results were compared with homologous proteins that have their three-dimensional structure deposited in Protein Data Bank (PDB). The values for the amount of a-helix, b-sheet and non-ab structure for these proteins are given in the middle and bottom data sets of Table 2. The prediction for P. sativum plant defensin was compared both with homologous proteins and with real values from the NMR structure determined in our laboratory (Almeida et al., 2002). As can be seen (Table 2), the predicted values are in good agreement with the PDB data, taking in account the possible structural differences between the proteins used and their homologues. Here again the prediction using only ¹⁵N-HSQC data were in good agreement with the actual amount of secondary structure in the tested proteins. It is worth mentioning that the PASSNMR program could detect the absence of a b-sheet in the Opaque2 protein. Although the structure of this protein is not solved it is known to be fully helical since it is a coiled coil leucine zipper (Moreau et al., 2004).

Discussion

The chemical shift index is a reliable parameter for determining the secondary structure in proteins (Wishart and Sykes, 1994; Wishart, et al., 1992; Wishart et al., 1991a,b). Although 2D heteronuclear correlation spectrum by itself provides no information regarding chemical shift assignments, some data on the secondary structure of proteins can be extracted from spectral chemical shift dispersion. In principle, such data contains information relating to the amount of a-helix and b-sheet present in the protein (Wishart and Sykes, 1994; Wishart, et al., 1992; Wishart et al., 1991a,b).

Many methods have been developed to speeding up structural characterization of unknown proteins, mainly after the advent of genome sequencing projects. Most methodologies have the objective of finding structural similarities with known proteins. Primary structure homology has been used for this purpose and is undoubtedly one of the most useful methods (Altschul et al., 1990). Without primary sequence homology, function can be annotated from secondary or tertiary homology with known proteins (Bhaduri et al., 2004; Jung and Lee, 2004; Li and Lu, 2001; Meiler et al., 2000; Jones, 1999a,b; Rychlewski et al., 1999; Thompson and Goldstein, 1997; Sander and Schneider, 1991; Kabsch and Sander, 1983). Methods to find secondary and tertiary structure homology are continuing to be developed and become more reliable when based on, or associated to, experimental data. For example, Bujnicki et al. (2001) used NMR secondary structure restrains and Monte Carlo dynamics to make a blind prediction of the tertiary structure of the N-terminal domain of the I-TEVI homing endonuclease and Cornilescu et al. (1999) developed a software to predict the f and y angles in proteins by searching a database for chemical shift and sequence homology, while Ayers et al. (1999) proposed the use of NMR secondary structure assignments to perform similarity searches and fold recognition of unknown proteins.

A technique for predicting the amount of secondary structure based on NMR data without the need of assignments is shown in our paper and resulted in the PASSNMR program. The reliability of the predictions can be estimated from the square of the correlation coefficients as 72% for a-helix, 74% for b-sheet and 42% for non-ab but if only ¹⁵N-HSQC data is used the correctness of the prediction is 49% for a-helix, 50% for b-sheet.

The prediction of the amount of non-ab structure was not as good due to the lower number of areas showing correlation between the number of peaks and the amount of non-ab structure (Table 1), possibly because it is a class with several types of structure (random coil, loops, turns, etc.). However, this behavior does not decrease the reliability of the method since the predicted amount of non-ab structure can be corrected using the values from a-helix and b-sheet. Even so, users of PASSNMR program should note that, in cases where the sum of the three kinds of structures is not equal to 100%, the value for the amount of non-ab structure is the less accurate. In fact, after the external refinement, only the correlation coefficient for non-ab structure changes significantly, indicating that the prediction for this kind of structure is based not only on the areas hints but mainly on the a-helix and b-sheet values.

We recently proposed the use of rifampicin for the selective labeling of heterologous proteins expressed in E. coli (Galvão-Botton et al., 2003; Almeida et al., 2001). This simple methodology permits very rapid preparation of uniformly ¹⁵N/¹³C-labeled NMR samples because purification is not demanded. It is possible to obtain a good quality NMR spectrum in few minutes at low cost, preparing the sample in 20-50 mL of growth media. Serber et al. (2001) reported the in situ HSQC spectrum of a protein in living cells. PASSNMR can still give quantitative information on the secondary structure of the proteins inside the cell.

The PASSNMR program can provide important information, especially on structural proteomics, by providing clues on how structured the protein is and which kind of secondary structure is present. This information can be useful for classifying proteins in structural groups, for testing the optimal sample conditions (e.g. pH and salt concentration) and for choosing more structured proteins to high throughput production for three-dimensional structure determination by NMR spectroscopy or X-ray crystallography. One step in target selection which limits the number of working proteins is the solubilization and formation of well-diffracting crystals and good NMR spectra (Christendat et al., 2000). The main reason for this limitation may be the presence of unstructured regions in the proteins. In fact, the number of deposits in the protein data bank decreases steeply when the amount of unstructured regions in proteins is higher than 10% (Prestegard et al., 2001). The PASSNMR program, used in conjunction with the rifampicin protocol (Galvão-Botton et al., 2003; Almeida et al., 2001), can provide important information on the amount of protein secondary structure within a few days of protein expression, small growth media volumes and easy and rapid NMR methods. This information can be used not only to select more structured targets for three-dimensional structure determination, but also to test better sample preparation conditions to increase the solubility and decrease the flexibility of unstructured regions of the proteins under investigation.

There are several advantages of using the PASSNMR program over other current methodologies. Wishart et al. (1991a,b) analyzed the prediction made from circular dichroism (CD) data for 14 proteins and found about about 32% of precision for a-helix, and a level of precision comparable to that of the PASSNMR program for b-structure. In addition, CD spectroscopy requires pure protein samples while PASSNMR prediction can be obtained without protein purification, making PASSNMR useful in target selection for structural proteomics.

Many algorithms have been developed for the theoretical prediction of the protein secondary structure (Liu et al., 2004; Jones, 1991a,b; Rychlewski et al., 1999; Thompson and Goldstein, 1997; Sander and Schneider, 1991) and although most of these algorithms are very accurate and useful, they provide no information concerning the real state of the sample because this can be modified by changing the conditions of the medium (e.g. pH, concentration of ligands, ionic strength and temperature), so methods such as PASSNMR, based on experimental data, may be more reliable than the use of theoretical algorithms.

The use of chemical shift dispersion to perform secondary structure prediction is not new and has been shown to be very reliable (Ayers et al., 1999; Ösapay and Case, 1994; Spera and Bax, 1991; Wishart et al., 1991a,b; Cornilescu et al., 1991). Indeed, the use of the chemical shift index (CSI) as restrains for structure calculation has been considered and is a powerful tool to this end (Cornilescu et al., 1991). However, chemical shift assignments are requested by all methods based on CSI. Although PASSNMR is less precise than some CSI methods, it has a great advantage that if it is used together with rifampicin protocol (Galvão-Botton et al., 2003; Almeida et al., 2001) both chemical shift assignment and protein purification are unnecessary. Prestegard et al. (2001) proposed the use of NMR as a tool for target selection for structural proteomics and, as mentioned above, the PASSNMR program can be used for structure proteomics without the need for protein purification because PASSNMR predictions can be made with the same samples used to test the expression of the proteins. This is very useful when a fast screening is required for choosing more structured proteins, such as in the selection of targets for structural proteomics.

Abbreviations

HSQC: Heteronuclear Single Quantum Coherence; PASSNMR: Prediction of the Amount of Secondary Structure by NMR; PERL: Practical Extraction and Report Language; PDB: Protein Data Bank.

Acknowledgments

This work was supported by International Center of Genetic Engineering and Biotechnology (ICGEB, Trieste, It) and the Brazilian agencies Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ), Centro de Apoio à Pesquisa (CAPES), Conselho Nacional de Pesquisa (CNPq) and Projeto Nacional de Excelência (PRONEX). We thank Professor Jerson Silva for discussion and support and also Dr. Jon Lapham and Dr. Alvicler Magalhães for discussion on Perl programming.

Internet Resources

The PASSNMR program is available for academic use at the homepage of the Centro Nacional de Ressonância Magnética Nuclear de Macromoléculas - CNRMN (http://cnrmn. bioqmed.ufrj.br).

Received: September 20, 2005; Accepted: March 15, 2006.

Associate Editor: Carlos F.M. Menck

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Publication Dates

• Publication in this collection
  21 Nov 2006
• Date of issue
  2006

History

• Accepted
  15 Mar 2006
• Received
  20 Sept 2005