Homology modeling



In amino acid sequence (the "query sequence" or "target"). Almost all homology modeling techniques rely on the identification of one or more known protein structures (known as "templates" or "parent structures") likely to resemble the structure of the query sequence, and on the production of an alignment that maps residues in the query sequence to residues in the template sequence. The sequence alignment and template structure are then used to produce a structural model of the target. Because protein structures are more conserved than protein sequences, detectable levels of sequence similarity usually imply significant structural similarity.[1]

The quality of the homology model is dependent on the quality of the sequence alignment and template structure. The approach can be complicated by the presence of alignment gaps (commonly called indels) that indicate a structural region present in the target but not in the template, and by structure gaps in the template that arise from poor resolution in the experimental procedure (usually quaternary structure of a protein may be difficult to predict from homology models of its subunit(s). Nevertheless, homology models can be useful in reaching qualitative conclusions about the biochemistry of the query sequence, especially in formulating hypotheses about why certain residues are conserved, which may in turn lead to experiments to test those hypotheses. For example, the spatial arrangement of conserved residues may suggest whether a particular residue is conserved to stabilize the folding, to participate in binding some small molecule, or to foster association with another protein or nucleic acid.

Homology modeling can produce high-quality structural models when the target and template are closely related, which has inspired the formation of a structural genomics consortium dedicated to the production of representative experimental structures for all classes of protein folds.[3] The chief inaccuracies in homology modeling, which worsen with lower sequence identity, derive from errors in the initial sequence alignment and from improper template selection.[4] Like other methods of structure prediction, current practice in homology modeling is assessed in a biannual large-scale experiment known as the Critical Assessment of Techniques for Protein Structure Prediction, or CASP.

Motivation

The method of homology modeling is based on the observation that protein protein NMR for every protein of interest, homology modeling can provide useful structural models for generating hypotheses about a protein's function and directing further experimental work.

There are exceptions to the general rule that proteins sharing significant sequence identity will share a fold. For example, a judiciously chosen set of mutations of less than 50% of a protein can cause the protein to adopt a completely different fold.[5][6] However, such a massive structural rearrangement is unlikely to occur in evolution, especially since the protein is usually under the constraint that it must fold properly and carry out its function in the cell. Consequently, the roughly folded structure of a protein (its "topology") is conserved longer than its amino-acid sequence and much longer than the corresponding DNA sequence; in other words, two proteins may share a similar fold even if their evolutionary relationship is so distant that it cannot be discerned reliably. For comparison, the function of a protein is conserved much less than the protein sequence, since relatively few changes in amino-acid sequence are required to take on a related function.

Steps in model production

The homology modeling procedure can be broken down into four sequential steps: template selection, target-template alignment, model construction, and model assessment.[1] The first two steps are often essentially performed together, as the most common methods of identifying templates rely on the production of sequence alignments; however, these alignments may not be of sufficient quality because database search techniques prioritize speed over alignment quality. These processes can be performed iteratively to improve the quality of the final model, although quality assessments that are not dependent on the true target structure are still under development.

Optimizing the speed and accuracy of these steps for use in large-scale automated structure prediction is a key component of structural genomics initiatives, partly because the resulting volume of data will be too large to process manually and partly because the goal of structural genomics requires providing models of reasonable quality to researchers who are not themselves structure prediction experts.[1] Fully automated predictions with no human intervention are studied in a CASP parallel project known as CAFASP.

Template selection and sequence alignment

The critical first step in homology modeling is the identification of the best template structure, if indeed any are available. The simplest method of template identification relies on serial pairwise sequence alignments aided by database search techniques such as FASTA and BLAST. More sensitive methods based on multiple sequence alignment - of which PSI-BLAST is the most common example - iteratively update their position-specific scoring matrix to successively idenfity more distantly related homologs. This family of methods has been shown to produce a larger number of potential templates and to identify better templates for sequences that have only distant relationships to any solved structure. operon. However, a template with a poor E-value should generally not be chosen, even if it is the only one available, since it may well have a wrong structure, leading to the production of a misguided model. A better approach is to submit the primary sequence to fold-recognition servers or, better still, consensus meta-servers which improve upon individual fold-recognition servers by identifying similarities (consensus) among independent predictions.

Often several candidate template structures are identified by these approaches. Although some methods can generate hybrid models from multiple templates, most methods rely on a single template. Therefore, choosing the best template from among the candidates is a key step, and can affect the final accuracy of the structure significantly. This choice is guided by several factors, such as the similarity of the query and template sequences, of their functions, and of the predicted query and observed template secondary structures. Perhaps most importantly, the coverage of the aligned regions: the fraction of the query sequence structure that can be predicted from the template, and the plausibility of the resulting model. Thus, sometimes several homology models are produced for a single query sequence, with the most likely candidate chosen only in the final step.

It is possible to use the sequence alignment generated by the database search technique as the basis for the subsequent model production; however, more sophisticated approaches have also been explored. One proposal generates an ensemble of stochastically defined pairwise alignments between the target sequence and a single identified template as a means of exploring "alignment space" in regions of sequence with low local similarity.[7] "Profile-profile" alignments that first generate a sequence profile of the target and systematically compare it to the sequence profiles of solved structures; the coarse-graining inherent in the profile construction is thought to reduce noise introduced by sequence drift in nonessential regions of the sequence.[8]

Model generation

Given a template and an alignment, the information contained therein must be used to generate a three-dimensional structural model of the target, represented as a set of Cartesian coordinates for each atom in the protein. Three major classes of model generation methods have been proposed.[9]

Fragment assembly

The original method of homology modeling relied on the assembly of a complete model from conserved structural fragments identified in closely related solved structures. For example, a modeling study of loops where the majority of the sequence differences were localized. Thus unsolved proteins could be modeled by first constructing the conserved core and then substituting variable regions from other proteins in the set of solved structures.[10] Current implementations of this method differ mainly in the way they deal with regions that are not conserved or that lack a template.[11]

Segment matching

The segment-matching method divides the target into a series of short segments, each of which is matched to its own template fitted from the Protein Data Bank. Thus, sequence alignment is done over segments rather than over the entire protein. Selection of the template for each segment is based on sequence similarity, comparisons of van der Waals radii of the divergent atoms between target and template. [12]

Satisfaction of spatial restraints

The most common current homology modeling method takes its inspiration from calculations required to construct a three-dimensional structure from data generated by dihedral angles - serve as the basis for a global optimization procedure that originally used conjugate gradient energy minimization to iteratively refine the positions of all heavy atoms in the protein.[13]

This method had been dramatically expanded to apply specifically to loop modeling, which can be extremely difficult due to the high flexibility of loops in proteins in aqueous solution.[14] A more recent expansion applies the spatial-restraint model to cryoelectron microscopy studies, which provide low-resolution information that is not usually itself sufficient to generate atomic-resolution structural models.[15] To address the problem of inaccuracies in initial target-template sequence alignment, an iterative procedure has also been introduced to refine the alignment on the basis of the initial structural fit.[16] The most commonly user software in spatial restraint-based modeling is MODELLER and a database called ModBase has been established for reliable models generated with it.[17]

Loop modeling

Regions of the target sequence that are not aligned to a template are modeled by arginine are notoriously difficult to predict. Moreover, small errors in χ1 (and, to a lesser extent, in χ2) can cause relatively large errors in the positions of the atoms at the terminus of side chain; such atoms often have a functional importance, particularly when located near the active site.

Model assessment

Assessment of homology models without reference to the true target structure is usually performed with two methods: membrane proteins.

Statistical potentials are empirical methods based on observed residue-residue contact frequencies among proteins of known structure in the PDB. They assign a probability or energy score to each possible pairwise interaction between DOPE. Statistical potentials are more computationally efficient than energy calculations.[18]

Physics-based energy calculations aim to capture the interatomic interactions that are physically responsible for protein stability in solution, especially CHARMM.[19]

A very extensive model validation report can be obtained using the [WHAT_CHECK] software. WHAT_CHECK is one option of the [WHAT IF] software package; it produces a many page document with extensive analyses of nearly 200 scientific and administrative aspects of the model. WHAT_CHECK is available as a [free server]; it can also be used to validate experimentally determined structures of macromolecules.

One newer method for model assessment relies on machine learning techniques such as neural nets, which may be trained to assess the structure directly or to form a consensus among multiple statistical and energy-based methods. Very recent results using support vector machine regression on a jury of more traditional assessment methods outperformed common statistical, energy-based, and machine learning methods.[20]

Structural comparison methods

The assessment of homology models' accuracy is straightforward when the experimental structure is known. The most common method of comparing two protein structures uses the root-mean-square deviation (RMSD) metric to measure the mean distance between the corresponding atoms in the two structures after they have been superimposed. However, RMSD does underestimate the accuracy of models in which the core is essentially correctly modeled, but some flexible protein backbone atoms to minimize the noise created by poorly modeled side chain rotameric states, which most modeling methods are not optimized to predict.[22]

Benchmarking

Several large-scale benchmarking efforts have been made to assess the relative quality of various current homology modeling methods. LiveBench and EVA run continuously to assess participating servers' performance in prediction of imminently released structures from the PDB. CASP and CAFASP serve mainly as evaluations of the state of the art in modeling, while the continuous assessments seek to evaluate the model quality that would be obtained by a non-expert user employing publicly available tools.

Accuracy

The accuracy of the structures generated by homology modeling is highly dependent on the sequence identity between target and template. Above 50% sequence identity, models tend to be reliable, with only minor errors in side chain packing and rotameric state, and an overall RMSD between the modeled and the experimental structure falling around 1 Â. This error is comparable to the typical resolution of a structure solved by NMR. In the 30-50% identity range, errors can be more severe and are often located in loops. Below 30% identity, serious errors occur, sometimes resulting in the basic fold being mis-predicted.[9] This low-identity region is often referred to as the "twilight zone" within which homology modeling is extremely difficult, and to which it is possibly less suited than fold recognition methods.[23]

At high sequence identities, the primary source of error in homology modeling derives from the choice of the template or templates on which the model is based, while lower identities exhibit serious errors in sequence alignment that inhibit the production of high-quality models.[4] It has been suggested that the major impediment to quality model production is inadequacies in sequence alignment, since "optimal" structural alignments between two proteins of known structure can be used as input to current modeling methods to produce quite accurate reproductions of the original experimental structure.[24]

Attempts have been made to improve the accuracy of homology models built with existing methods by subjecting them to force field parameterizations may not be sufficiently accurate for this task, since homology models used as starting structures for molecular dynamics tend to produce slightly worse structures.[25] Slight improvements have been observed in cases where significant restraints were used during the simulation.[26]

Sources of error

The two most common and large-scale sources of error in homology modeling are poor template selection and inaccuracies in target-template sequence alignment.[4][27] Controlling for these two factors by using a structural alignment, or a sequence alignment produced on the basis of comparing two solved structures, dramatically reduces the errors in final models; these "gold standard" alignments can be used as input to current modeling methods to produce quite accurate reproductions of the original experimental structure.[24] Results from the most recent CASP experiment suggest that "consensus" methods collecting the results of multiple fold recognition and multiple alignment searches increase the likelihood of identifying the correct template; similarly, the use of multiple templates in the model-building step may be less optimal than the use of the single correct template but more optimal than the use of a single suboptimal one.[27] Alignment errors may be minimized by the use of a multiple alignment even if only one template is used, and by the iterative refinement of local regions of low similarity.[1][7] A lesser source of model errors are errors in the template structure. The [PDBREPORT] database lists several million, mostly very small but occasionally dramatic, errors in experimental (template) structures that have been deposited in the PDB.

Serious local errors can arise in homology models where an insertion or deletion mutation or a gap in a solved structure result in a region of target sequence for which there is no corresponding template. This problem can be minimized by the use of multiple templates, but the method is complicated by the templates' differing local structures around the gap and by the likelihood that a missing region in one experimental structure is also missing in other structures of the same protein family. Missing regions are most common in loops where high local flexibility increases the difficulty of resolving the region by structure-determination methods. Although some guidance is provided even with a single template by the positioning of the ends of the missing region, the longer the gap, the more difficult it is to model. Loops of up to about 9 residues can be modeled with moderate accuracy in some cases if the local alignment is correct.[1] Larger regions are often modeled individually using ab initio structure prediction techniques, although this approach has met with only isolated success.[28]

The rotameric states of side chains and their internal packing arrangement also present difficulties in homology modeling, even in targets for which the backbone structure is relatively easy to predict. This is partly due to the fact that many side chains in crystal structures are not in their "optimal" rotameric state as a result of energetic factors in the hydrophobic core and in the packing of the individual molecules in a protein crystal.[29] One method of addressing this problem requires searching a rotameric library to identify locally low-energy combinations of packing states.[30] It has been suggested that a major reason that homology modeling so difficult when target-template sequence identity lies below 30% is that such proteins have broadly similar folds but widely divergent side chain packing arrangements.[2]

Utility

Uses of the structural models include molecular docking, and functional annotation of genes identified in an organism's genome.[31] Even low-accuracy homology models can be useful for these purposes, because their inaccuracies tend to be located in the loops on the protein surface, which are normally more variable even between closely related proteins. The functional regions of the protein, especially its active site, tend to be more highly conserved and thus more accurately modeled.[9]

Homology models can also be used to identify subtle differences between related proteins that have not all been solved structurally. For example, the method was used to identify cation binding sites on the Na2+/K+ yeast Saccharomyces cerevisiae, resulting in nearly 1000 quality models for proteins whose structures had not yet been determined at the time of the study, and identifying novel relationships between 236 yeast proteins and other previously solved structures.[34]

See also

References

  1. ^ a b c d e f g Marti-Renom MA, Stuart AC, Fiser A, Sanchez R, Melo F, Sali A. (2000). Comparative protein structure modeling of genes and genomes. Annu Rev Biophys Biomol Struct 29: 291-325.
  2. ^ a b Chung SY, Subbiah S. (1996.) A structural explanation for the twilight zone of protein sequence homology. Structure 4: 1123–27.
  3. ^ Williamson AR. (2000). Creating a structural genomics consortium. Nat Struct Biol 7 S1(11s):953.
  4. ^ a b c Venclovas C, Margeleviĉius M. (2005). Comparative modeling in CASP6 using consensus approach to template selection, sequence-structure alignment, and structure assessment. Proteins 61(S7):99-105.
  5. ^ Dalal S, Balasubramanian S, Regan L. (1997). Transmuting alpha helices and beta sheets. Fold Des 2(5):R71-9.
  6. ^ Dalal S, Balasubramanian S, Regan L. (1997). Protein alchemy: changing beta-sheet into alpha-helix. Nat Struct Biol 4(7):548-52.
  7. ^ a b Muckstein U, Hofacker IL, Stadler PF. (2002). Stochastic pairwise alignments. Bioinformatics 18 Suppl 2:S153-60.
  8. ^ Rychlewski L, Zhang B, Godzik A. (1998). Fold and function predictions for Mycoplasma genitalium proteins. Fold Des 3(4):229-38.
  9. ^ a b c Baker D, Sali A. (2001). Protein structure prediction and structural genomics. Science 294(5540):93-96.
  10. ^ Greer J. (1981). Comparative model-building of the mammalian serine proteases 153(4):1027-42.
  11. ^ Wallner B, Elofsson A. (2005). All are not equal: A benchmark of different homology modeling programs. Protein Science 14:1315-1327.
  12. ^ Levitt M. (1992). Accurate modeling of protein conformation by automatic segment matching. J Mol Biol 226(2): 507-33.
  13. ^ Sali A, Blundell TL. (1993). Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 234(3):779-815.
  14. ^ Fiser A, Sali A. (2003). ModLoop: automated modeling of loops in protein structures. Bioinformatics 19(18):2500-1.
  15. ^ Topf M, Baker ML, Marti-Renom MA, Chiu W, Sali A. (2006). Refinement of protein structures by iterative comparative modeling and CryoEM density fitting. J Mol Biol 357(5):1655-68.
  16. ^ John B, Sali A. Comparative protein structure modeling by iterative alignment, model building and model assessment. Nucleic Acids Res 31(14):3982-92.
  17. ^ Ursula Pieper, Narayanan Eswar, Hannes Braberg, M.S. Madhusudhan, Fred Davis, Ashley C. Stuart, Nebojsa Mirkovic, Andrea Rossi, Marc A. Marti-Renom, Andras Fiser, Ben Webb, Daniel Greenblatt, Conrad Huang, Tom Ferrin, Andrej Sali. MODBASE, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res 32, D217-D222, 2004.
  18. ^ a b Sippl MJ. (1993). Recognition of Errors in Three-Dimensional Structures of Proteins. Proteins 17:355-62.
  19. ^ Lazaridis T. and Karplus M. 1999a. Discrimination of the native from misfolded protein models with an energy function including implicit solvation. J. Mol. Biol. 288: 477–487
  20. ^ Eramian D, Shen M, Devos D, Melo F, Sali A, Marti-Renom MA. (2006). A composite score for predicting errors in protein structure models. Protein Science 15:1653-1666.
  21. ^ a b Zemla A. (2003). LGA - A Method for Finding 3-D Similarities in Protein Structures. Nucleic Acids Research, 31(13):3370-3374.
  22. ^ Mount DM. (2004). Bioinformatics: Sequence and Genome Analysis 2nd ed. Cold Spring Harbor Laboratory Press: Cold Spring Harbor, NY.
  23. ^ Blake JD, Cohen FE. (2001). Pairwise sequence alignment below the twilight zone. J Mol Biol 307(2):721-35.
  24. ^ a b Zhang Y and Skolnick J. (2005). The protein structure prediction problem could be solved using the current PDB library. Proc. Natl. Acad. Sci. USA 102(4):1029-34.
  25. ^ Koehl P, Levitt M. (1999). A brighter future for protein structure prediction. Nat Struct Biol 6(2):108-11.
  26. ^ Flohil JA, Vriend G, Berendsen HJ. (2002). Completion and refinement of 3-D homology models with restricted molecular dynamics: application to targets 47, 58, and 111 in the CASP modeling competition and posterior analysis. Proteins 48(4):593-604.
  27. ^ a b Ginalski K. (2006). Comparative modeling for protein structure prediction. Curr Opin Struct Biol 16(2):172-7.
  28. ^ Kryshtafovych A, Venclovas C, Fidelis K, Moult J. (2005). Progress over the first decade of CASP experiments. Proteins 61(S7):225-36.
  29. ^ Vasquez M. (1996). Modeling side-chain conformation. Curr Opin Struct Biol 6(2):217-21.
  30. ^ Wilson C, Gregoret LM, Agard DA. (1993). Modeling side-chain conformation for homologous proteins using an energy-based rotamer search. J Mol Biol 229(4):996-1006.
  31. ^ Gopal S, Schroeder M, Pieper U, Sczyrba A, Aytekin-Kurban G, Bekiranov S, Fajardo JE, Eswar N, Sanchez R, Sali A, Gaasterland T. (2001). Homology-based annotation yields 1,042 new candidate genes in the Drosophila melanogaster genome. Nat Genet 27(3):337-40.
  32. ^ Ogawa H, Toyoshima C. (2002). Homology modeling of the cation binding sites of Na+K+-ATPase. Proc Natl Acad Sci USA 99(25):15977-15982
  33. ^ Capener CE, Shrivastava IH, Ranatunga KM, Forrest LR, Smith GR, Sansom MSP. (2000). Homology Modeling and Molecular Dynamics Simulation Studies of an Inward Rectifier Potassium Channel. Biophys J 78(6):2929-2942
  34. ^ Sánchez R, Sali A. (1998). Large-scale protein structure modeling of the Saccharomyces cerevisiae genome. Proc Natl Acad Sci USA 95(23):13597-13602.
 
This article is licensed under the GNU Free Documentation License. It uses material from the Wikipedia article "Homology_modeling". A list of authors is available in Wikipedia.