| 1. |
- Cohen, Serge X., et al.
(författare)
-
Towards complete validated models in the next generation of ARP/wARP
- 2004
-
Ingår i: Acta Crystallographica Section D. - 0907-4449 .- 1399-0047. ; 60:Pt 12 Pt 1, s. 2222-9
-
Tidskriftsartikel (refereegranskat)abstract
- The design of a new versatile control system that will underlie future releases of the automated model-building package ARP/wARP is presented. A sophisticated expert system is under development that will transform ARP/wARP from a very useful model-building aid to a truly automated package capable of delivering complete, well refined and validated models comparable in quality to the result of intensive manual checking, rebuilding, hypothesis testing, refinement and validation cycles of an experienced crystallographer. In addition to the presentation of this control system, recent advances, ideas and future plans for improving the current model-building algorithms, especially for completing partially built models, are presented. Furthermore, a concept for integrating validation routines into the iterative model-building process is also presented.
|
|
| 2. |
- Davis, Andrew M, et al.
(författare)
-
Application and limitations of X-ray crystallographic data in structure-based ligand and drug design.
- 2003
-
Ingår i: Angew Chem Int Ed Engl. - 0570-0833. ; 42:24, s. 2718-36
-
Forskningsöversikt (populärvet., debatt m.m.)abstract
- Structure-based design usually focuses upon the optimization of ligand affinity. However, successful drug design also requires the optimization of many other properties. The primary source of structural information for protein-ligand complexes is X-ray crystallography. The uncertainties introduced during the derivation of an atomic model from the experimentally observed electron density data are not always appreciated. Uncertainties in the atomic model can have significant consequences when this model is subsequently used as the basis of manual design, docking, scoring, and virtual screening efforts. Docking and scoring algorithms are currently imperfect. A good correlation between observed and calculated binding affinities is usually only observed only when very large ranges of affinity are considered. Errors in the correlation often exceed the range of affinities commonly encountered during lead optimization. Some structure-based design approaches now involve screening libraries by using technologies based on NMR spectroscopy and X-ray crystallography to discover small polar templates, which are used for further optimization. Such compounds are defined as leadlike and are also sought by more traditional high-throughput screening technologies. Structure-based design and HTS technologies show important complementarity and a degree of convergence.
|
|
| 3. |
- Davis, Andrew M., et al.
(författare)
-
Limitations and lessons in the use of X-ray structural information in drug design
- 2008
-
Ingår i: Drug Discovery Today. - : Elsevier BV. - 1359-6446 .- 1878-5832. ; 13:19-20, s. 831-841
-
Forskningsöversikt (refereegranskat)abstract
- The use of X-ray crystal structure models continues to provide a strong stimulus to drug discovery, through the direct visualisation of ligand-receptor interactions. There is sometimes a limited appreciation of the uncertainties introduced during the process of deriving an atomic model from the experimentally observed electron density. Here, some of these uncertainties are highlighted with recent examples from the literature, together with snippets of advice for the medicinal chemist embarking on using X-ray crystal structure information in a drug discovery programme.
|
|
| 4. |
- Gorbalenya, Alexander E., et al.
(författare)
-
Practical application of bioinformatics by the multidisciplinary VIZIER consortium
- 2010
-
Ingår i: Antiviral Research. - : Elsevier. - 0166-3542 .- 1872-9096. ; 87:2, s. 95-110
-
Forskningsöversikt (refereegranskat)abstract
- This review focuses on bioinformatics technologies employed by the EU-sponsored multidisciplinary VIZIER consortium (Comparative Structural Genomics of Viral Enzymes Involved in Replication, FP6 Project: 2004-511960, active from 1 November 2004 to 30 April 2009), to achieve its goals. From the management of the information flow of the project, to bioinformatics-mediated selection of RNA viruses and prediction of protein targets, to the analysis of 3D protein structures and antiviral compounds, these technologies provided a communication framework and integrated solutions for steady and timely advancement of the project. RNA viruses form a large class of major pathogens that affect humans and domestic animals. Such RNA viruses as HIV, Influenza virus and Hepatitis C virus are of prime medical concern today, but the identities of viruses that will threaten human population tomorrow are far from certain. To contain outbreaks of common or newly emerging infections, prototype drugs against viruses representing the Virus Universe must be developed. This concept was championed by the VIZIER project which brought together experts in diverse fields to produce a concerted and sustained effort for identifying and validating targets for antivirus therapy in dozens of RNA virus lineages.
|
|
| 5. |
- Grahn, Elin, et al.
(författare)
-
New crystal structures of human glutathione transferase A1-1 shed light on glutathione binding and the conformation of the C-terminal helix.
- 2006
-
Ingår i: Acta Crystallogr D Biol Crystallogr. - 0907-4449. ; 62:Pt 2, s. 197-207
-
Tidskriftsartikel (refereegranskat)abstract
- Human glutathione transferase A1-1 is a well studied enzyme, but despite a wealth of structural and biochemical data a number of aspects of its catalytic function are still poorly understood. Here, five new crystal structures of this enzyme are described that provide several insights. Firstly, the structure of a complex of the wild-type human enzyme with glutathione was determined for the first time at 2.0 angstroms resolution. This reveals that glutathione binds in the G site in a very similar fashion as the glutathione portion of substrate analogues in other structures and also that glutathione binding alone is sufficient to stabilize the C-terminal helix of the protein. Secondly, we have studied the complex with a decarboxylated glutathione conjugate that is known to dramatically decrease the activity of the enzyme. The T68E mutant of human glutathione transferase A1-1 recovers some of the activity that is lost with the decarboxylated glutathione, but our structures of this mutant show that none of the earlier explanations of this phenomenon are likely to be correct. Thirdly, and serendipitously, the apo structures also reveal the conformation of the crucial C-terminal region that is disordered in all previous apo structures. The C-terminal region can adopt an ordered helix-like structure even in the apo state, but shows a strong tendency to unwind. Different conformations of the C-terminal regions were observed in the apo states of the two monomers, which suggests that cooperativity could play a role in the activity of the enzyme.
|
|
| 6. |
|
|
| 7. |
- Hederos, Sofia, et al.
(författare)
-
A new enzyme by rational design - the incorporation of a single His residue enables efficient thioester hydrolysis by human glutathione transferase A1-1
- 2004
-
Ingår i: Proc. Nat. Acad. Sci.. ; 101, s. 13163-13167
-
Tidskriftsartikel (refereegranskat)abstract
- A strategy for rational enzyme design is reported and illustrated by the engineering of a protein catalyst for thiol-ester hydrolysis. Five mutants of human glutathione (GSH; gamma-Glu-Cys-Gly) transferase A1-1 were designed in the search for a catalyst and to provide a set of proteins from which the reaction mechanism could be elucidated. The single mutant A216H catalyzed the hydrolysis of the S-benzoyl ester of GSH under turnover conditions with a k(cat)/K(M) of 156 M(-1) x min(-1), and a catalytic proficiency of >10(7) M(-1) when compared with the first-order rate constant of the uncatalyzed reaction. The wild-type enzyme did not hydrolyze the substrate, and thus, the introduction of a single histidine residue transformed the wild-type enzyme into a turnover system for thiol-ester hydrolysis. By kinetic analysis of single, double, and triple mutants, as well as from studies of reaction products, it was established that the enzyme A216H catalyzes the hydrolysis of the thiol-ester substrate by a mechanism that includes an acyl intermediate at the side chain of Y9. Kinetic measurements and the crystal structure of the A216H GSH complex provided compelling evidence that H216 acts as a general-base catalyst. The introduction of a single His residue into human GSH transferase A1-1 created an unprecedented enzymatic function, suggesting a strategy that may be of broad applicability in the design of new enzymes. The protein catalyst has the hallmarks of a native enzyme and is expected to catalyze various hydrolytic, as well as transesterification, reactions.
|
|
| 8. |
- Hederos, Sofia, et al.
(författare)
-
Incorporation of a single His residue by rational design enables thiol-ester hydrolysis by human glutathione transferase A1-1.
- 2004
-
Ingår i: Proc Natl Acad Sci U S A. - 0027-8424. ; 101:36, s. 13163-7
-
Tidskriftsartikel (refereegranskat)abstract
- A strategy for rational enzyme design is reported and illustrated by the engineering of a protein catalyst for thiol-ester hydrolysis. Five mutants of human glutathione (GSH; gamma-Glu-Cys-Gly) transferase A1-1 were designed in the search for a catalyst and to provide a set of proteins from which the reaction mechanism could be elucidated. The single mutant A216H catalyzed the hydrolysis of the S-benzoyl ester of GSH under turnover conditions with a k(cat)/K(M) of 156 M(-1) x min(-1), and a catalytic proficiency of >10(7) M(-1) when compared with the first-order rate constant of the uncatalyzed reaction. The wild-type enzyme did not hydrolyze the substrate, and thus, the introduction of a single histidine residue transformed the wild-type enzyme into a turnover system for thiol-ester hydrolysis. By kinetic analysis of single, double, and triple mutants, as well as from studies of reaction products, it was established that the enzyme A216H catalyzes the hydrolysis of the thiol-ester substrate by a mechanism that includes an acyl intermediate at the side chain of Y9. Kinetic measurements and the crystal structure of the A216H GSH complex provided compelling evidence that H216 acts as a general-base catalyst. The introduction of a single His residue into human GSH transferase A1-1 created an unprecedented enzymatic function, suggesting a strategy that may be of broad applicability in the design of new enzymes. The protein catalyst has the hallmarks of a native enzyme and is expected to catalyze various hydrolytic, as well as transesterification, reactions.
|
|
| 9. |
|
|
| 10. |
- Jakobsson, Emma, et al.
(författare)
-
Crystallization of a truncated soluble human semicarbazide-sensitive amine oxidase.
- 2005
-
Ingår i: Acta Crystallograph Sect F Struct Biol Cryst Commun. - 1744-3091. ; 61:Pt 3, s. 274-8
-
Tidskriftsartikel (refereegranskat)abstract
- Human semicarbazide-sensitive amine oxidase (SSAO) is a homodimeric copper-containing monoamine oxidase that occurs in both a membrane-bound and a soluble form. SSAO is also known as vascular adhesion protein-1 (VAP-1). A truncated soluble form of human SSAO (comprising residues 29-763) was expressed in human embryonic kidney 293 cells and purified to homogeneity. Tetragonal crystals were obtained and a data set extending to 2.5 A was collected. The crystals are merohedrally twinned and the estimation of the twinning fraction was complicated by pseudo-symmetry and the anisotropic character of the crystals. Using a recently developed method for twinning detection that is insensitive to phenomena such as anisotropy or pseudo-symmetry [Padilla & Yeates (2003), Acta Cryst. D59, 1124-1130], the twinning fraction was estimated to be 0.3. The structure was eventually solved by molecular replacement in space group P4(3).
|
|
| 11. |
- Jakobsson, Emma, 1974-
(författare)
-
Structural Studies of Echinococcus granulosus Fatty-acid-binding Protein 1 and Human Semicarbazide-sensitive Amine Oxidase
- 2005
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The parasite Echinococcus granulosus causes hydatid disease, a major zoonosis. A fatty-acid-binding protein, EgFABP1, is important for the parasite, as it must acquire almost all its lipids from its environment or the host. The structure of EgFABP1 has been solved and refined to 1.6 Å resolution. The structure reveals that EgFABP1 has the 10-stranded β-barrel fold typical of the family of intracellular lipid-binding proteins. Human semicarbazide-sensitive amine oxidase (SSAO; EC 1.4.3.6), also known as vascular adhesion protein-1, is a copper-containing monoamine oxidase that occurs both as a membrane-bound protein and in a soluble form in plasma. SSAO has been implicated in glucose transport in adipocytes, the differentiation of adipose cells and the leukocyte extravasation process. Toxic reaction products have been suggested to cause some of the vascular complications associated with diabetes and SSAO is therefore of pharmaceutical interest.The structure of a truncated, soluble form of human SSAO has been determined to 2.5 Å resolution. The structure reveals that a leucine residue located adjacent to the active site could function as a gate controlling its accessibility. An RGD motif is displayed on the surface where it could be involved in integrin binding and possibly play a role in the shedding of SSAO from the membrane. Carbohydrate moieties are observed at five out of six potential N-glycosylation sites. Carbohydrates attached to Asn 232 flank the active site entrance and might influence substrate specificity. The structure also reveals a vicinal disulfide bridge, which we hypothesise could act as a redox switch involved in the protein’s mechanism of action. The structure of a complex of SSAO and the irreversible inhibitor 2-hydrazinopyridine has been solved and refined to 2.9 Å resolution. Both structures together will aid efforts to identify natural substrates, provide valuable information for the design of specific inhibitors and direct further studies.
|
|
| 12. |
- Jakobsson, Emma, et al.
(författare)
-
Structure of human semicarbazide-sensitive amine oxidase/vascular adhesion protein-1.
- 2005
-
Ingår i: Acta Crystallogr D Biol Crystallogr. - 0907-4449. ; 61:Pt 11, s. 1550-62
-
Tidskriftsartikel (refereegranskat)abstract
- Semicarbazide-sensitive amine oxidase (SSAO) belongs to a ubiquitous family of copper-containing amine oxidases (CuAOs). SSAO is also known as vascular adhesion protein-1 (VAP-1) and has been identified as one of the adhesion molecules involved in the leukocyte-extravasation process. The structure of a truncated soluble form of human SSAO has been solved and refined to 2.5 A. As expected, SSAO is a homodimer with a fold typical of the CuAO family. The topaquinone (TPQ) cofactor and a copper ion characteristic of CuAOs are present in the active site, with the TPQ in the active ;off-copper' conformation. The structure reveals that a leucine residue (Leu469) located adjacent to the active site could function as a gate controlling its accessibility. An RGD motif is displayed on the surface, where it could be involved in integrin binding and possibly play a role in the shedding of SSAO from the membrane. Carbohydrate moieties are observed at five of six potential N-glycosylation sites. Carbohydrates attached to Asn232 flank the active-site entrance and might influence substrate specificity. The structure of an adduct of SSAO and the irreversible inhibitor 2-hydrazinopyridine has been solved and refined to 2.9 A resolution. Together, these structures will aid efforts to identify natural substrates, provide valuable information for the design of specific inhibitors and direct further studies.
|
|
| 13. |
|
|
| 14. |
- Jakobsson, Emma, et al.
(författare)
-
The crystal structure of Echinococcus granulosus fatty-acid-binding protein 1.
- 2003
-
Ingår i: Biochim Biophys Acta. - 0006-3002. ; 1649:1, s. 40-50
-
Tidskriftsartikel (refereegranskat)abstract
- We describe the 1.6 A crystal structure of the fatty-acid-binding protein EgFABP1 from the parasitic platyhelminth Echinococcus granulosus. E. granulosus causes hydatid disease, which is a major zoonosis. EgFABP1 has been implicated in the acquisition, storage, and transport of lipids, and may be important to the organism since it is incapable of synthesising most of its lipids de novo. Moreover, EgFABP1 is a promising candidate for a vaccine against hydatid disease.The crystal structure reveals that EgFABP1 has the expected 10-stranded beta-barrel fold typical of the family of intracellular lipid-binding proteins, and that it is structurally most similar to P2 myelin protein. We describe the comparison of the crystal structure of EgFABP1 with these proteins and with an older homology model for EgFABP1.The electron density reveals the presence of a bound ligand inside the cavity, which we have interpreted as palmitic acid. The carboxylate group of the fatty acid interacts with the protein's P2 motif, consisting of a conserved triad R em leader R-x-Y. The hydrophobic tail of the ligand assumes a fairly flat, U-shaped conformation and has relatively few interactions with the protein.We discuss some of the structural implications of the crystal structure of EgFABP1 for related platyhelminthic FABPs.
|
|
| 15. |
|
|
| 16. |
- Jones, T Alwyn, et al.
(författare)
-
Experimental data for structure papers.
- 2007
-
Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 317:5835, s. 194-195
-
Tidskriftsartikel (refereegranskat)
|
|
| 17. |
- Kleywegt, Gerard J.
(författare)
-
Crystallographic refinement of ligand complexes
- 2007
-
Ingår i: Acta Crystallographica Section D. - 0907-4449 .- 1399-0047. ; 63:1, s. 94-100
-
Tidskriftsartikel (refereegranskat)abstract
- Model building and refinement of complexes between biomacromolecules and small molecules requires sensible starting coordinates as well as the specification of restraint sets for all but the most common non-macromolecular entities. Here, it is described why this is necessary, how it can be accomplished and what pitfalls need to be avoided in order to produce chemically plausible models of the low-molecular-weight entities. A number of programs, servers, databases and other resources that can be of assistance in the process are also discussed.
|
|
| 18. |
- Kleywegt, Gerard J.
(författare)
-
On vital aid : the why, what and how of validation
- 2009
-
Ingår i: Acta Crystallographica Section D. - 0907-4449 .- 1399-0047. ; 65:Pt 2, s. 134-139
-
Tidskriftsartikel (refereegranskat)abstract
- Limitations to the data and subjectivity in the structure-determination process may cause errors in macromolecular crystal structures. Appropriate validation techniques may be used to reveal problems in structures, ideally before they are analysed, published or deposited. Additionally, such techniques may be used a posteriori to assess the (relative) merits of a model by potential users. Weak validation methods and statistics assess how well a model reproduces the information that was used in its construction (i.e. experimental data and prior knowledge). Strong methods and statistics, on the other hand, test how well a model predicts data or information that were not used in the structure-determination process. These may be data that were excluded from the process on purpose, general knowledge about macromolecular structure, information about the biological role and biochemical activity of the molecule under study or its mutants or complexes and predictions that are based on the model and that can be tested experimentally.
|
|
| 19. |
- Kleywegt, Gerard J
(författare)
-
Quality control and validation.
- 2006
-
Ingår i: Methods Mol Biol. - 1064-3745. ; 364, s. 255-72
-
Forskningsöversikt (populärvet., debatt m.m.)abstract
- This chapter discusses two important aspects of the structure determination process that are related to the accuracy and reliability of the crystallographic model under investigation. Quality control is defined as the analysis of an intermediate model to identify aspects of it that are unusual in some sense and that could, therefore, be a result of errors in the model building or refinement process. Any such errors need to be fixed, if at all possible, prior to analysis and publication of the model. Validation is the process of assessing the reliability of the final model (or certain aspects of it, e.g., the active site residues) that is about to be analyzed, published, deposited, and possibly used in follow-up studies.
|
|
| 20. |
- Kleywegt, Gerard J
(författare)
-
Separating model optimization and model validation in statistical cross-validation as applied to crystallography.
- 2007
-
Ingår i: Acta Crystallographica Section D. - 0907-4449 .- 1399-0047. ; 63:9, s. 939-940
-
Tidskriftsartikel (refereegranskat)abstract
- Statistical cross-validation has become an integral part of the model-refinement process in macromolecular crystallography. However, the test set of reflections, for which the free R value is calculated, is used both to optimize the parameterization of the structure model and to validate the model itself. This practice could introduce bias and diminish the value of R(free) as an independent check of model quality. It is proposed here that by introducing a dormant hold-out set of reflections, any problems with such bias can be avoided. This procedure requires only a small modification of the standard cross-validation protocol.
|
|
| 21. |
- Kleywegt, Gerard J, et al.
(författare)
-
The Uppsala Electron-Density Server
- 2004
-
Ingår i: Acta Crystallographica Section D. - 0907-4449 .- 1399-0047. ; 60:Pt 12 Pt 1, s. 2240-2249
-
Tidskriftsartikel (refereegranskat)abstract
- The Uppsala Electron Density Server (EDS; http://eds.bmc.uu.se/) is a web-based facility that provides access to electron-density maps and statistics concerning the fit of crystal structures and their maps. Maps are available for approximately 87% of the crystallographic Protein Data Bank (PDB) entries for which structure factors have been deposited and for which straightforward map calculations succeed in reproducing the published R value to within five percentage points. Here, an account is provided of the methods that are used to generate the information contained in the server. Some of the problems that are encountered in the map-generation process as well as some spin-offs of the project are also discussed.
|
|
| 22. |
- Kleywegt, Gerard J., et al.
(författare)
-
ValLigURL : a server for ligand-structure comparison and validation
- 2007
-
Ingår i: Acta Crystallographica Section D. - 0907-4449 .- 1399-0047. ; 63, s. 935-938
-
Tidskriftsartikel (refereegranskat)abstract
- A new web-based tool called ValLigURL is described. It can be used by practising crystallographers to validate the geometry of a ligand and to compare the conformation of a ligand with all instances of that ligand in the structural database (wwPDB). In addition, it can be used by structural bioinformaticians to survey the quality or conformational diversity of any ligand across the entire structural database. The server is freely accessible at the URL http://eds.bmc.uu.se/eds/valligurl.php.
|
|
| 23. |
- Koivula, Anu, et al.
(författare)
-
The active site of cellobiohydrolase Cel6A from Trichoderma reesei: the roles of aspartic acids D221 and D175.
- 2002
-
Ingår i: J Am Chem Soc. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 124:34, s. 10015-24
-
Tidskriftsartikel (refereegranskat)abstract
- Trichoderma reesei cellobiohydrolase Cel6A is an inverting glycosidase. Structural studies have established that the tunnel-shaped active site of Cel6A contains two aspartic acids, D221 and D175, that are close to the glycosidic oxygen of the scissile bond and at hydrogen-bonding distance from each other. Here, site-directed mutagenesis, X-ray crystallography, and enzyme kinetic studies have been used to confirm the role of residue D221 as the catalytic acid. D175 is shown to affect protonation of D221 and to contribute to the electrostatic stabilization of the partial positive charge in the transition state. Structural and modeling studies suggest that the single-displacement mechanism of Cel6A may not directly involve a catalytic base. The value of (D2O)(V) of 1.16 +/- 0.14 for hydrolysis of cellotriose suggests that the large direct effect expected for proton transfer from the nucleophilic water through a water chain (Grotthus mechanism) is offset by an inverse effect arising from reversibly breaking the short, tight hydrogen bond between D221 and D175 before catalysis.
|
|
| 24. |
- Novotny, Marian, et al.
(författare)
-
A survey of left-handed helices in protein structures.
- 2005
-
Ingår i: J Mol Biol. - 0022-2836. ; 347:2, s. 231-41
-
Tidskriftsartikel (refereegranskat)abstract
- All naturally occurring amino acids with the exception of glycine contain one or more chiral carbon atoms and can therefore occur in two different configurations, L (levo, left-handed) and D (dextro, right-handed). Proteins are almost exclusively built from L-amino acids. The stereochemical bias of nature is further reflected at the secondary structure level where right-handed helices are strongly preferred over left-handed helices. The handedness of helices has not received much attention in the past and is often overlooked during the analysis, description and deposition of experimentally solved protein structures. Therefore, an extensive survey of left-handed helices in the Protein Data Bank (PDB) was undertaken to analyse their frequency of occurrence, length, amino acid composition, conservation and possible structural or functional role. All left-handed helices (of four or more residues) in a non-redundant subset of the PDB, were identified using hydrogen-bonding analysis, comparison of related structures, and experimental electron density assessment to filter out likely spurious and artefactual hits. This analysis yielded 31 verified left-handed helices in a set of 7284 proteins. The phi angles of the residues in the left-handed helices lie between 30 degrees and 130 degrees and the psi angles lie between -50 degrees and 100 degrees . Most of the helices are short (four residues) and for 87% of them, it was possible to determine that they are important for the stability of the protein, for ligand binding, or as part of the active site. This suggests that, even though left-handed helices are rare, when they do occur, they are structurally or functionally significant. Four secondary structure assignment programs were tested for their ability to identify the handedness of the helices. Of these programs, only DSSP correctly assigns the handedness.
|
|
| 25. |
|
|
| 26. |
|
|
| 27. |
- Novotny, Marian, 1979-
(författare)
-
Applications of Structural Bioinformatics for the Structural Genomics Era
- 2007
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Structural bioinformatics deals with the analysis, classification and prediction of three-dimensional structures of biomacromolecules. It is becoming increasingly important as the number of structures is growing rapidly. This thesis describes three studies concerned with protein-function prediction and two studies about protein structure validation.New protein structures are often compared to known structures to find out if they have a known fold, which may provide hints about their function. The functionality and performance of eleven fold-comparison servers were evaluated. None of the tested servers achieved perfect recall, so in practise a combination of servers should be used.If fold comparison does not provide any hints about the function of a protein, structural motif searches can be employed. A survey of left-handed helices in known protein structures was carried out. The results show that left-handed helices are rare motifs, but most of them occur in active or ligand-binding sites. Their identification can therefore help to pinpoint potentially important residues.Sometimes all available methods fail to provide hints about the function of a protein. Therefore, the potential of using docking techniques to predict which ligands are likely to bind to a particular protein has been investigated. Initial results show that it will be difficult to build a reliable automated docking protocol that will suit all proteins.The effect of various phenomena on the precision of accessible surface area calculations was also investigated. The results suggest that it is prudent to report such values with a precision of 50 to 100 Å2.Finally, a survey of register shifts in known protein structures was carried out. The identified potential register shifts were analysed and classified. A machine-learning approach ("rough sets") was used in an attempt to diagnose register errors in structures.
|
|
| 28. |
|
|
| 29. |
- Novotny, Marian, et al.
(författare)
-
Evaluation of protein fold comparison servers.
- 2004
-
Ingår i: Proteins. - 1097-0134. ; 54:2, s. 260-70
-
Tidskriftsartikel (refereegranskat)abstract
- When a new protein structure has been determined, comparison with the database of known structures enables classification of its fold as new or belonging to a known class of proteins. This in turn may provide clues about the function of the protein. A large number of fold comparison programs have been developed, but they have never been subjected to a comprehensive and critical comparative analysis. Here we describe an evaluation of 11 publicly available, Web-based servers for automatic fold comparison. Both their functionality (e.g., user interface, presentation, and annotation of results) and their performance (i.e., how well established structural similarities are recognized) were assessed. The servers were subjected to a battery of performance tests covering a broad spectrum of folds as well as special cases, such as multidomain proteins, Calpha-only models, new folds, and NMR-based models. The CATH structural classification system was used as a reference. These tests revealed the strong and weak sides of each server. On the whole, CE, DALI, MATRAS, and VAST showed the best performance, but none of the servers achieved a 100% success rate. Where no structurally similar proteins are found by any individual server, it is recommended to try one or two other servers before any conclusions concerning the novelty of a fold are put on paper.
|
|
| 30. |
- Novotny, Marian, et al.
(författare)
-
On the precision of calculated solvent-accessible surface areas
- 2007
-
Ingår i: Acta Crystallographica Section D. - 0907-4449 .- 1399-0047. ; 63:2, s. 270-274
-
Tidskriftsartikel (refereegranskat)abstract
- The fact that protein structures are dynamic by nature and that structure models determined by X-ray crystallography, electron microscopy (EM) and nuclear magnetic resonance (NMR) spectroscopy have limited accuracy limits the precision with which derived properties can be reported. Here, the issue of the precision of calculated solvent-accessible surface areas (ASAs) is addressed. A number of protein structures of different sizes were selected and the effect of random shifts applied to the atomic coordinates on ASA values was investigated. Standard deviations of the ASA calculations were found to range from ∼10 to ∼80 Å2. Similar values are obtained for a handful of cases in the Protein Data Bank (PDB) where `ensembles' of crystal structures were refined against the same data set. The ASA values for 69 hen egg-white lysozyme structures were calculated and a standard deviation of the ASA of 81 Å2 was obtained (the average ASA value was 6571 Å2). The calculated ASA values do not show any correlation with factors such as resolution or overall temperature factors. A molecular-dynamics (MD) trajectory of lysozyme was also analysed. The ASA values during the simulation covered a range of more than 800 Å2. If different programs are used, the ASA values obtained for one small protein show a spread of almost 600 Å2. These results suggest that in most cases reporting ASA values with a precision better than 10 Å2 is probably not realistic and a precision of 50–100 Å2 would seem prudent. The precision of buried surface-area calculations for complexes is also discussed.
|
|
| 31. |
- Okmane, Laura, et al.
(författare)
-
Glucomannan and beta-glucan degradation by Mytilus edulis Cel45A : Crystal structure and activity comparison with GH45 subfamily A, B and C
- 2022
-
Ingår i: Carbohydrate Polymers. - : Elsevier. - 0144-8617 .- 1879-1344. ; 277
-
Tidskriftsartikel (refereegranskat)abstract
- The enzymatic hydrolysis of barley beta-glucan, konjac glucomannan and carboxymethyl cellulose by a beta-1,4-D-endoglucanase MeCel45A from blue mussel, Mytilus edulis, which belongs to subfamily B of glycoside hydrolase family 45 (GH45), was compared with GH45 members of subfamilies A (Humicola insolens HiCel45A), B (Trichoderma reesei TrCel45A) and C (Phanerochaete chrysosporium PcCel45A). Furthermore, the crystal structure of MeCel45A is reported.Initial rates and hydrolysis yields were determined by reducing sugar assays and product formation was characterized using NMR spectroscopy. The subfamily B and C enzymes exhibited mannanase activity, whereas the subfamily A member was uniquely able to produce monomeric glucose. All enzymes were confirmed to be inverting glycoside hydrolases. MeCel45A appears to be cold adapted by evolution, as it maintained 70% activity on cellohexaose at 4 degrees C relative to 30 degrees C, compared to 35% for TrCel45A. Both enzymes produced cellobiose and cellotetraose from cellohexaose, but TrCel45A additionally produced cellotriose.
|
|
| 32. |
- Read, Randy J., et al.
(författare)
-
A New Generation of Crystallographic Validation Tools for the Protein Data Bank
- 2011
-
Ingår i: Structure. - : Elsevier BV. - 0969-2126 .- 1878-4186. ; 19:10, s. 1395-1412
-
Tidskriftsartikel (refereegranskat)abstract
- This report presents the conclusions of the X-ray Validation Task Force of the worldwide Protein Data Bank (PDB). The PDB has expanded massively since current criteria for validation of deposited structures were adopted, allowing a much more sophisticated understanding of all the components of macromolecular crystals. The size of the PDB creates new opportunities to validate structures by comparison with the existing database, and the now-mandatory deposition of structure factors creates new opportunities to validate the underlying diffraction data. These developments highlighted the need for a now assessment of validation criteria. The Task Force recommends that a small set of validation data be presented in an easily understood format, relative to both the full PDB and the applicable resolution class, with greater detail available to interested users. Most importantly, we recommend that referees and editors judging the quality of structural experiments have access to a concise summary of well-established quality indicators.
|
|
| 33. |
- Read, Randy J, et al.
(författare)
-
Case-controlled structure validation
- 2009
-
Ingår i: Acta Crystallographica Section D. - 0907-4449 .- 1399-0047. ; 65:Pt 2, s. 140-147
-
Tidskriftsartikel (refereegranskat)abstract
- Although many factors influence the quality of a macromolecular crystal structure, validation criteria are usually only calibrated using one of these factors, the resolution. For many purposes this is sufficient, but there are times when one wishes to compare one set of structures with another and the comparison may be invalidated by systematic differences between the sets in factors other than resolution. This problem can be circumvented by borrowing from medicine the idea of the case-matched control: each structure of interest is matched with a control structure that has similar values for all relevant factors considered in this study. In addition to resolution, these include the size of the structure (as measured by the volume of the asymmetric unit) and the year of deposition. This approach has been applied to address two questions: whether structures from structural genomics efforts reach the same level of quality as structures from traditional sources and whether the impact factor of the journal in which a structure is published correlates with structure quality. In both cases, once factors influencing quality have been controlled in the comparison, there is little evidence for a systematic difference in quality.
|
|
| 34. |
- Strömbergsson, Helena, et al.
(författare)
-
A chemogenomics view on protein-ligand spaces
- 2009
-
Ingår i: BMC Bioinformatics. - 1471-2105. ; 10:Suppl.6, s. S13-
-
Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Chemogenomics is an emerging inter-disciplinary approach to drug discovery that combines traditional ligand-based approaches with biological information on drug targets and lies at the interface of chemistry, biology and informatics. The ultimate goal in chemogenomics is to understand molecular recognition between all possible ligands and all possible drug targets. Protein and ligand space have previously been studied as separate entities, but chemogenomics studies deal with large datasets that cover parts of the joint protein-ligand space. Since drug discovery has traditionally focused on ligand optimization, the chemical space has been studied extensively. The protein space has been studied to some extent, typically for the purpose of classification of proteins into functional and structural classes. Since chemogenomics deals not only with ligands but also with the macromolecules the ligands interact with, it is of interest to find means to explore, compare and visualize protein-ligand subspaces. RESULTS: Two chemogenomics protein-ligand interaction datasets were prepared for this study. The first dataset covers the known structural protein-ligand space, and includes all non-redundant protein-ligand interactions found in the worldwide Protein Data Bank (PDB). The second dataset contains all approved drugs and drug targets stored in the DrugBank database, and represents the approved drug-drug target space. To capture biological and physicochemical features of the chemogenomics datasets, sequence-based descriptors were computed for the proteins, and 0, 1 and 2 dimensional descriptors for the ligands. Principal component analysis (PCA) was used to analyze the multidimensional data and to create global models of protein-ligand space. The nearest neighbour method, computed using the principal components, was used to obtain a measure of overlap between the datasets. CONCLUSION: In this study, we present an approach to visualize protein-ligand spaces from a chemogenomics perspective, where both ligand and protein features are taken into account. The method can be applied to any protein-ligand interaction dataset. Here, the approach is applied to analyze the structural protein-ligand space and the protein-ligand space of all approved drugs and their targets. We show that this approach can be used to visualize and compare chemogenomics datasets, and possibly to identify cross-interaction complexes in protein-ligand space.
|
|
| 35. |
- Strömbergsson, Helena, 1975-
(författare)
-
Chemogenomics: Models of Protein-Ligand Interaction Space
- 2009
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The large majority of the currently used drugs are small molecules that interact with proteins. Understanding protein-ligand recognition is thus central to drug discovery and design. Improved experimental techniques have resulted in an immense growth of drug target information. This has stimulated the development of chemogenomics and proteochemometrics (PCM) that take target information as well as ligand information into account to study the genomic effect of potential drugs. This thesis is concerned with modeling protein-ligand recognition, and the aim is to develop models that generalize to the entire protein-ligand space. To this end, protein-ligand interaction data has been extracted and manually curated from public databases, protein and ligand descriptors have been computed, and predictive models have been induced with machine-learning methods. An introduction to chemogenomics, machine learning, and PCM modeling is given in the thesis summary, which is followed by five research papers. Paper I shows that it is possible to induce interpretable models with a non-linear rule-based method, and paper II demonstrates that local descriptors of protein structure may be used to induce PCM models that cover proteins differing in sequence and fold. In paper III, such local descriptors are used to induce a PCM model on a large dataset that includes all major enzyme classes. This demonstrates that the local descriptors may be used to induce generalized models that span the entire known structural enzyme-ligand space. Paper IV describes a step towards proteome-wide PCM models, and shows that it is possible to predict high- and low-affinity complexes using a set of protein and ligand descriptors that do not require knowledge of 3D structure. Finally, paper V presents a method to visualize and compare protein-ligand chemogenomic subspaces, which may be used to predict unwanted cross-interactions of drugs with other proteins in the proteome.
|
|
| 36. |
- Strömbergsson, Helena, 1975-, et al.
(författare)
-
Interaction Model Based on Local Protein Substructures Generalizes to the Entire Structural Enzyme-Ligand Space
- 2008
-
Ingår i: Journal of chemical information and modelling. - : American Chemical Society (ACS). - 1549-960X .- 1549-9596. ; 48:11, s. 2278-2288
-
Tidskriftsartikel (refereegranskat)abstract
- Chemogenomics is a new strategy in in silico drug discovery, where the ultimate goal is to understand molecular recognition for all molecules interacting with all proteins in the proteome. To study such cross interactions, methods that can generalize over proteins that vary greatly in sequence, structure, and function are needed. We present a general quantitative approach to protein−ligand binding affinity prediction that spans the entire structural enzyme-ligand space. The model was trained on a data set composed of all available enzymes cocrystallized with druglike ligands, taken from four publicly available interaction databases, for which a crystal structure is available. Each enzyme was characterized by a set of local descriptors of protein structure that describe the binding site of the cocrystallized ligand. The ligands in the training set were described by traditional QSAR descriptors. To evaluate the model, a comprehensive test set consisting of enzyme structures and ligands was manually curated. The test set contained enzyme-ligand complexes for which no crystal structures were available, and thus the binding modes were unknown. The test set enzymes were therefore characterized by matching their entire structures to the local descriptor library constructed from the training set. Both the training and the test set contained enzyme-ligand complexes from all major enzyme classes, and the enzymes spanned a large range of sequences and folds. The experimental binding affinities (pKi) ranged from 0.5 to 11.9 (0.7−11.0 in the test set). The induced model predicted the binding affinities of the external test set enzyme-ligand complexes with an r2 of 0.53 and an RMSEP of 1.5. This demonstrates that the use of local descriptors makes it possible to create rough predictive models that can generalize over a wide range of protein targets.
|
|
| 37. |
- Strömbergsson, Helena, et al.
(författare)
-
Towards proteome-wide interaction models using the proteochemometrics approach
- 2010
-
Ingår i: Molecular Informatics. - : Wiley. - 1868-1743 .- 1868-1751. ; 29:6-7, s. 499-508
-
Tidskriftsartikel (refereegranskat)abstract
- A proteochemometrics model was induced from all interaction data in the BindingDB database, comprizing in all 7078 protein-ligand complexes with representatives from all major drug target categories. Proteins were represented by alignment-independent sequence descriptors holding information on properties such as hydrophobicity, charge, and secondary structure. Ligands were represented by commonly used QSAR descriptors. The inhibition constant (pK(i)) values of protein-ligand complexes were discretized into "high" and "low" interaction activity. Different machine-learning techniques were used to induce models relating protein and ligand properties to the interaction activity. The best was decision trees, which gave an accuracy of 80% and an area under the ROC curve of 0.81. The tree pointed to the protein and ligand properties, which are relevant for the interaction. As the approach does neither require alignments nor knowledge of protein 3D structures virtually all available protein-ligand interaction data could be utilized, thus opening a way to completely general interaction models that may span entire proteomes.
|
|
| 38. |
- Tars, Kaspars, et al.
(författare)
-
Structural basis of the suppressed catalytic activity of wild-type human glutathione transferase T1-1 compared to its W234R mutant
- 2006
-
Ingår i: Journal of Molecular Biology. - : Elsevier BV. - 0022-2836 .- 1089-8638. ; 355:1, s. 96-105
-
Tidskriftsartikel (refereegranskat)abstract
- The crystal structures of wild-type human theta class glutathione-S-transferase (GST) T1-1 and its W234R mutant, where Trp234 was replaced by Arg, were solved both in the presence and absence of S-hexyl-glutathione. The W234R mutant was of interest due to its previously observed enhanced catalytic activity compared to the wild-type enzyme. GST T1-1 from rat and mouse naturally contain Arg in position 234, with correspondingly high catalytic efficiency. The overall structure of GST T1-1 is similar to that of GST T2-2, as expected from their 53% sequence identity at the protein level. Wild-type GST T1-1 has the side-chain of Trp234 occupying a significant portion of the active site. This bulky residue prevents efficient binding of both glutathione and hydrophobic substrates through steric hindrance. The wild-type GST T1-1 crystal structure, obtained from co-crystallization experiments with glutathione and its derivatives, showed no electron density for the glutathione ligand. However, the structure of GST T1-1 mutant W234R showed clear electron density for S-hexyl-glutathione after co-crystallization. In contrast to Trp234 in the wild-type structure, the side-chain of Arg234 in the mutant does not occupy any part of the substrate-binding site. Instead, Arg234 is pointing in a different direction and, in addition, interacts with the carboxylate group of glutathione. These findings explain our earlier observation that the W234R mutant has a markedly improved catalytic activity with most substrates tested to date compared to the wild-type enzyme. GST T1-1 catalyzes detoxication reactions as well as reactions that result in toxic products, and our findings therefore suggest that humans have gained an evolutionary advantage by a partially disabled active site.
|
|
| 39. |
- Yusuf, Dilmurat, et al.
(författare)
-
An alternative method for the evaluation of docking performance : RSR vs RMSD.
- 2008
-
Ingår i: Journal of chemical information and modeling. - : American Chemical Society (ACS). - 1549-9596 .- 1549-960X. ; 48:7, s. 1411-1422
-
Tidskriftsartikel (refereegranskat)abstract
- A new assessment criterion for docking poses is proposed in which experimental electron density is taken into account when evaluating the ability of docking programs to reproduce experimentally observed binding modes. Three docking programs (Gold, Glide, and Fred) were used to generate poses for a set of 88 protein-ligand complexes for which the crystal structure is known. The new criterion is based on the real space R-factor (RSR), which measures how well a group of atoms-in our case the ligand-fits the experimental electron density by comparing that density to the expected density, calculated from the model (i.e., the predicted ligand pose). The RSR-based measure is compared to the traditional criterion, the root-mean-square distance (RMSD) between the docking pose and the binding configuration in the crystallographic model. The results highlight several shortcomings of the RMSD criterion that do not affect the RSR-based measure. Examples illustrate that the RSR-derived approach allows a more meaningful a posteriori assessment of docking methods and results. Practical implications for docking evaluations and for methodological development work in this field are discussed.
|
|
