ABSTRACT
Application of endoscopy in spinal neurosurgery is one of modern trends of minimally invasive neurosurgery. The aim of this study was to perform comparative analysis of effectiveness in 3 surgical groups with different approaches to lumbar diskectomy applied: microsurgical, endoscopic and endoscopic-assisted. Patients' quality of life concerning ODI, severity of postoperative pain, length of incision, duration of surgery and hospital stay were assessed. We observed no significant differences in three groups according to postoperative ODI index and Macnub and Nurick outcome scales. Endoscopic diskectomy allowed to decrease postoperative pain by discharge, to minimize approach and improve cosmetic effect of surgery. Advantages and disadvantages of different methods are discussed in the paper.
Subject(s)
Endoscopy/methods , Intervertebral Disc Displacement/surgery , Lumbar Vertebrae/surgery , Microsurgery/methods , Adult , Humans , Length of Stay , Male , Middle Aged , Pain, Postoperative/etiologyABSTRACT
gamma-Hexachlorocyclohexane dehydrochlorinase (LinA) is a unique dehydrochlorinase that has no homologous sequence at the amino acid-sequence level and for which the evolutionary origin is unknown. We here propose that LinA is a member of a novel structural superfamily of proteins containing scytalone dehydratase, 3-oxo-Delta(5)-steroid isomerase, nuclear transport factor 2, and the beta-subunit of naphthalene dioxygenase-all known structures with different functions. The catalytic and the active site residues of LinA are predicted on the basis of its homology model. Nine mutants that carry substitutions of the proposed catalytic residues were constructed by site-directed mutagenesis. In addition to these, eight mutants that have a potential to make contact with the substrate were prepared by site-directed mutagenesis. These mutants were expressed in Escherichia coli, and their activities in crude extract were evaluated. Most of the features of the LinA mutants could be explained on the basis of the present LinA model, indicating its validity. We conclude that LinA catalyzes the proton abstraction via the catalytic dyad H73-D25 by a similar mechanism as described for scytalone dehydratase. The results suggest that LinA and scytalone dehydratase evolved from a common ancestor. LinA may have evolved from an enzyme showing a dehydratase activity.
Subject(s)
Bacterial Proteins/chemistry , Catalytic Domain/genetics , Lyases , Amino Acid Sequence , Bacterial Proteins/genetics , Biodegradation, Environmental , Dioxygenases , Evolution, Molecular , Hydro-Lyases , Molecular Sequence Data , Multienzyme Complexes , Multigene Family , Mutagenesis, Site-Directed , Nucleocytoplasmic Transport Proteins , Oxygenases , Protein Folding , Sequence Alignment , Sphingomonas/enzymology , Steroid IsomerasesABSTRACT
The genome sequencing projects and knowledge of the entire protein repertoires of many organisms have prompted new procedures and techniques for the large-scale determination of protein structure, function and interactions. Recently, new work has been carried out on the determination of the function and evolutionary relationships of proteins by experimental structural genomics, and the discovery of protein-protein interactions by computational structural genomics.
Subject(s)
Evolution, Molecular , Genomics/methods , Proteins/physiology , Gene Order , Phylogeny , Protein Structure, Tertiary , Proteins/chemistryABSTRACT
gamma-Hexachlorocyclohexane dehydrochlorinase (LinA) catalyzes the initial steps in the biotransformation of the important insecticide gamma-hexachlorocyclohexane (gamma-HCH) by the soil bacterium Sphingomonas paucimobilis UT26. Stereochemical analysis of the reaction products formed during conversion of gamma-HCH by LinA was investigated by GC-MS, NMR, CD, and molecular modeling. The NMR spectra of 1,3,4,5,6-pentachlorocyclohexene (PCCH) produced from gamma-HCH using either enzymatic dehydrochlorination or alkaline dehydrochlorination were compared and found to be identical. Both enantiomers present in the racemate of synthetic gamma-PCCH were converted by LinA, each at a different rate. 1,2,4-trichlorobenzene (1,2,4-TCB) was detected as the only product of the biotransformation of biosynthetic gamma-PCCH. 1,2,4-TCB and 1,2,3-TCB were identified as the dehydrochlorination products of racemic gamma-PCCH. delta-PCCH was detected as the only product of dehydrochlorination of delta-HCH. LinA requires the presence of a 1,2-biaxial HCl pair on a substrate molecule. LinA enantiotopologically differentiates two 1,2-biaxial HCl pairs present on gamma-HCH and gives rise to a single PCCH enantiomer 1,3(R),4(S),5(S),6(R)-PCCH. Furthermore, LinA enantiomerically differentiates 1,3(S),4(R),5(R),6(S)-PCCH and 1,3(R),4(S),5(S),6(R)-PCCH. The proposed mechanism of enzymatic biotransformation of gamma-HCH to 1,2,4-TCB by LinA consists of two 1,2-anti conformationally dependent dehydrochlorinations followed by 1,4-anti dehydrochlorination.
Subject(s)
Bacterial Proteins/chemistry , Hexachlorocyclohexane/analogs & derivatives , Lyases , Bacterial Proteins/physiology , Gas Chromatography-Mass Spectrometry , Hexachlorocyclohexane/metabolism , Magnetic Resonance Spectroscopy , Molecular ConformationABSTRACT
In 1996, in CASP2, we presented a semimanual approach to the prediction of protein structure that was aimed at the recognition of probable distant homology, where it existed, between a given target protein and a protein of known structure (Murzin and Bateman, Proteins 1997; Suppl 1:105-112). Central to our method was the knowledge of all known structural and probable evolutionary relationships among proteins of known structure classified in the SCOP database (Murzin et al., J Mol Biol 1995;247:536-540). It was demonstrated that a knowledge-based approach could compete successfully with the best computational methods of the time in the correct recognition of the target protein fold. Four years later, in CASP4, we have applied essentially the same knowledge-based approach to distant homology recognition, concentrating our effort on the improvement of the completeness and alignment accuracy of our models. The manifold increase of available sequence and structure data was to our advantage, as well as was the experience and expertise obtained through the classification of these data. In particular, we were able to model most of our predictions from several distantly related structures rather than from a single parent structure, and we could use more superfamily characteristic features for the refinement of our alignments. Our predictions for each of the attempted distant homology recognition targets ranked among the few top predictions for each of these targets, with the predictions for the hypothetical protein HI0065 (T0104) and the C-terminal domain of the ABC transporter MalK (T0121C) being particularly successful. We also have attempted the prediction of protein folds of some of the targets tentatively assigned to new superfamilies. The average quality of our fold predictions was far less than the quality of our distant homology recognition models, but for the two targets, chorismate lyase (T0086) and Appr>p cyclic phosphodiesterase (T0094), our predictions achieved the top ranking.
Subject(s)
Artificial Intelligence , Models, Molecular , Protein Conformation , Protein Folding , Sequence Homology , ATP-Binding Cassette Transporters/chemistry , Archaeal Proteins , Bacteriocins/chemistry , Bacteriophage T7/chemistry , Endodeoxyribonucleases/chemistry , Enterococcus faecalis , Escherichia coli , Oxo-Acid-Lyases/chemistry , Protein Structure, Tertiary , Sequence Analysis, ProteinABSTRACT
The Structural Classification of Proteins (SCOP) database provides a detailed and comprehensive description of the relationships of known protein structures. The classification is on hierarchical levels: the first two levels, family and superfamily, describe near and distant evolutionary relationships; the third, fold, describes geometrical relationships. The distinction between evolutionary relationships and those that arise from the physics and chemistry of proteins is a feature that is unique to this database so far. The sequences of proteins in SCOP provide the basis of the ASTRAL sequence libraries that can be used as a source of data to calibrate sequence search algorithms and for the generation of statistics on, or selections of, protein structures. Links can be made from SCOP to PDB-ISL: a library containing sequences homologous to proteins of known structure. Sequences of proteins of unknown structure can be matched to distantly related proteins of known structure by using pairwise sequence comparison methods to find homologues in PDB-ISL. The database and its associated files are freely accessible from a number of WWW sites mirrored from URL http://scop.mrc-lmb.cam.ac.uk/scop/
Subject(s)
Databases, Factual , Protein Conformation , Evolution, Molecular , Information Storage and Retrieval , Internet , Proteins/chemistry , Proteins/geneticsSubject(s)
Carrier Proteins/chemistry , Cell Cycle Proteins/chemistry , Formate Dehydrogenases/chemistry , Glutamate Decarboxylase/chemistry , Vesicular Transport Proteins , Adenosine Triphosphatases , Models, Molecular , N-Ethylmaleimide-Sensitive Proteins , Protein Conformation , Valosin Containing ProteinABSTRACT
The sequences of at least 23 of the 43 CASP3 targets showed no significant similarity to the sequences of known structures. The experimental structures of all but three of these 23 targets revealed substantial similarities to known structures, with at least eleven of the target structures likely being distantly homologous to known structures. Nineteen of the 23 target structures were available at the time of the final CASP3 meeting in Asilomar in December 1998, whereas the experimental data on the protein folds of the remaining four targets were obtained afterwards. The predicted three-dimensional structures for each of the 23 targets were analyzed to select those predictions sharing with the experimental structures a similar overall fold and/or having correctly folded a substantial fraction of the target sequence. Initially, predicted models were numerically evaluated and the evaluation results aided the selection process. Each target structure was then classified to identify a minimal set of structural features characteristic to its protein fold and evolutionary superfamily. The predictions containing this set were assessed comparatively to find the best predictions for each target. The predictions of new folds were assessed separately. The total number of the selected 'correct' predictions and the quality of these predictions were used to compare the performance of different predictor teams and different prediction methods in the fold prediction/recognition category.
Subject(s)
Protein Conformation , Proteins/chemistry , Bacterial Proteins/chemistry , Escherichia coli/chemistry , Flavodoxin/chemistry , Fungal Proteins , Humans , Models, Molecular , Sequence Homology, Amino AcidABSTRACT
BACKGROUND: Six-stranded beta barrels with a pseudo-twofold axis are found in several proteins. One group comprises a Greek-key structure with all strands antiparallel; an example is the N-terminal domain of ferredoxin reductase. Others involve parallel strands forming two psi structures (the double-psi beta barrel). A recently discovered example of the latter class is aspartate-alpha-decarboxylase (ADC) from Escherichia coli, a pyruvoyl-dependent tetrameric enzyme involved in the synthesis of pantothenate. RESULTS: Visual inspection and automated database searches identified the six-stranded double-psi beta barrel in ADC, Rhodobacter sphaeroides dimethylsulfoxide (DMSO) reductase, E. coli formate dehydrogenase H (FDHH), the plant defense protein barwin, Humicola insolens endoglucanase V (EGV) and, with a circular permutation, in the aspartic proteinases. Structure-based sequence alignments revealed several interactions including hydrophobic contacts or sidechain-mainchain hydrogen bonds that position the middle beta strand under a psi loop, which may significantly contribute to stabilizing the fold. The identification of key interactions allowed the filtering of weak sequence similarities to some of these proteins, which had been detected by sequence database searches. This led to the prediction of the double-psi beta-barrel domain in several families of proteins in eukaryotes and archaea. CONCLUSIONS: The structure comparison and clustering study of double-psi beta barrels suggests that there could be a common homodimeric ancestor to ADC, FDHH and DMSO reductase, and also to barwin and EGV. There are other protein families with unknown structure that are likely to adopt the same fold. In the known structures, the protein active sites cluster around the psi loop, indicating that its rigidity, protrusion and free mainchain functional groups may be well suited to providing a framework for catalysis.
Subject(s)
Iron-Sulfur Proteins , Protein Structure, Secondary , Amino Acid Sequence , Cellulase/chemistry , Formate Dehydrogenases/chemistry , Glutamate Decarboxylase/chemistry , Hydrogenase/chemistry , Models, Molecular , Molecular Sequence Data , Multienzyme Complexes/chemistry , Oxidoreductases/chemistry , Plant Proteins/chemistry , Sequence AlignmentABSTRACT
The Structural Classification of Proteins (SCOP) database provides a detailed and comprehensive description of the relationships of all known proteins structures. The classification is on hierarchical levels: the first two levels, family and superfamily, describe near and far evolutionary relationships; the third, fold, describes geometrical relationships. The distinction between evolutionary relationships and those that arise from the physics and chemistry of proteins is a feature that is unique to this database, so far. The database can be used as a source of data to calibrate sequence search algorithms and for the generation of population statistics on protein structures. The database and its associated files are freely accessible from a number of WWW sites mirrored from URL http://scop. mrc-lmb.cam.ac.uk/scop/
Subject(s)
Databases, Factual , Protein Conformation , Proteins/chemistry , Proteins/classification , Algorithms , Evolution, Molecular , Information Storage and Retrieval , Internet , Protein Folding , Proteins/genetics , Sequence Alignment , Sequence Homology, Amino Acid , Statistics as TopicABSTRACT
In theory, mutations of protein sequences may eventually generate different functions as well as different structures. The observation of such records of protein evolution have been obscured by the dissipation of memory about the ancestors. In the past year, new advances in our understanding of divergent evolution were allowed by new protein structure determinations, including the ClpP proteases, steroid delta-isomerase, carboxypeptidase G2, the thrombin inhibitor triabin and the chloroplast Rieske protein. There is strong evidence for their distant homology with proteins of known structure despite significant functional or structural differences.
Subject(s)
Adenosine Triphosphatases , Electron Transport Complex III , Evolution, Molecular , Genetic Variation , Protein Folding , Protein Structure, Secondary , Proteins/chemistry , Proteins/genetics , Endopeptidase Clp , Insect Proteins , Iron-Sulfur Proteins/chemistry , Models, Molecular , Salivary Proteins and Peptides/chemistry , Serine Endopeptidases/chemistry , Steroid Isomerases/chemistry , gamma-Glutamyl Hydrolase/chemistryABSTRACT
We report the discovery of a novel family of proteins, each member contains tandem pentapeptide (five residue) repeats, described by the motif A(D/N)LXX. Members of this family are both membrane bound and cytoplasmic. The function of these repeats is uncertain, but they may have a targeting or structural function rather than enzymatic activity. This family is most common in cyanobacteria, suggesting a function related to cyanobacterial-specific metabolism. Although no experimental information is available for the structure of this family, it is predicted that the tandem pentapeptide repeats will form a right-handed beta-helical structure. A structural model of the pentapeptide repeats is presented.
Subject(s)
Bacterial Proteins/chemistry , Cyanobacteria/chemistry , Oligopeptides/chemistry , Repetitive Sequences, Nucleic Acid , Amino Acid Sequence , HSP70 Heat-Shock Proteins/chemistry , Models, Molecular , Molecular Sequence Data , Protein Kinases/chemistry , Protein Structure, SecondaryABSTRACT
The Structural Classification of Proteins (SCOP) database provides a detailed and comprehensive description of the relationships of all known protein structures. The classification is on hierarchical levels: the first two levels, family and superfamily, describe near and far evolutionary relationships; the third, fold, describes geometrical relationships. The distinction between evolutionary relationships and those that arise from the physics and chemistry of proteins is a feature that is unique to this database, so far. The database can be used as a source of data to calibrate sequence search algorithms and for the generation of population statistics on protein structures. The database and its associated files are freely accessible from a number of WWW sites mirrored from URL http://scop. mrc-lmb.cam.ac.uk/scop/.
Subject(s)
Databases, Factual , Protein Conformation , Sequence Alignment/standards , Algorithms , Amino Acid Sequence , Database Management Systems , Evaluation Studies as Topic , Molecular Sequence Data , Protein Folding , Sequence Alignment/methodsABSTRACT
The 2.0-A resolution x-ray crystal structure of a novel trimeric antibody fragment, a "triabody," has been determined. The trimer is made up of polypeptides constructed in a manner identical to that previously described for some "diabodies": a VL domain directly fused to the C terminus of a VH domain-i.e., without any linker sequence. The trimer has three Fv heads with the polypeptides arranged in a cyclic, head-to-tail fashion. For the particular structure reported here, the polypeptide was constructed with a VH domain from one antibody fused to the VL domain from an unrelated antibody giving rise to "combinatorial" Fvs upon formation of the trimer. The structure shows that the exchange of the VL domain from antibody B1-8, a Vlambda domain, with the VL domain from antibody NQ11, a Vkappa domain, leads to a dramatic conformational change in the VH CDR3 loop of antibody B1-8. The magnitude of this change is similar to the largest of the conformational changes observed in antibody fragments in response to antigen binding. Combinatorial pairing of VH and VL domains constitutes a major component of antibody diversity. Conformationally flexible antigen-binding sites capable of adapting to the specific CDR3 loop context created upon VH-VL pairing may be employed by the immune system to maximize the structural diversity of the immune response.
Subject(s)
Antibodies/chemistry , Immunoglobulin Fragments/chemistry , Immunoglobulin Variable Region/chemistry , Protein Conformation , Amino Acid Sequence , Animals , Binding Sites , Crystallography, X-Ray , Escherichia coli , Immunoglobulin Heavy Chains/chemistry , Immunoglobulin Light Chains/chemistry , Mice , Molecular Sequence DataABSTRACT
We have discovered that the bacterial toxins aerolysin and pertussis toxin share a common domain. This is surprising because the two toxins affect cells in very different ways. The common domain, which we call the APT domain, consists of two three-stranded antiparallel beta-sheets that come together and wrap around a central pair of helices. The APT domain shares a common fold with the C-type lectins and Link modules, and there appears to be a divergent relationship among the three families. One surface region of the APT domain is highly conserved, raising the possibility that the domains have a common function in both proteins. Mutation of one of the conserved surface residues in aerolysin, Tyr61, results in reduced receptor binding and activity, thus providing evidence that the APT domain may be involved in interaction with the toxin's receptor. Structural and biochemical evidence suggests that the APT domain contains a carbohydrate-binding site that can direct the toxins to their target cells.
Subject(s)
Bacterial Toxins/chemistry , Bacterial Toxins/metabolism , Pertussis Toxin , Virulence Factors, Bordetella/chemistry , Virulence Factors, Bordetella/metabolism , Amino Acid Sequence , Bacterial Toxins/genetics , Binding Sites , Conserved Sequence , Databases, Factual , Humans , Lectins/chemistry , Molecular Sequence Data , Mutagenesis, Site-Directed , Pore Forming Cytotoxic Proteins , Protein Conformation , Protein Folding , Receptors, Cell Surface/metabolism , Sequence Homology, Amino Acid , Structure-Activity Relationship , Tyrosine , Variant Surface Glycoproteins, Trypanosoma/metabolismABSTRACT
The structure of a chromatin binding domain from mouse chromatin modifier protein 1 (MoMOD1) was determined using nuclear magnetic resonance (NMR) spectroscopy. The protein consists of an N-terminal three-stranded anti-parallel beta-sheet which folds against a C-terminal alpha-helix. The structure reveals an unexpected homology to two archaebacterial DNA binding proteins which are also involved in chromatin structure. Structural comparisons suggest that chromo domains, of which more than 40 are now known, act as protein interaction motifs and that the MoMOD1 protein acts as an adaptor mediating interactions between different proteins.
Subject(s)
Archaeal Proteins , Carrier Proteins/chemistry , Chromatin/chemistry , Amino Acid Sequence , Animals , Bacterial Proteins/chemistry , Bacterial Proteins/metabolism , Binding Sites , Carrier Proteins/genetics , Carrier Proteins/metabolism , Chromatin/metabolism , Chromatography, High Pressure Liquid , Chromobox Protein Homolog 5 , Chromosomal Proteins, Non-Histone/chemistry , Chromosomal Proteins, Non-Histone/metabolism , Cloning, Molecular , DNA-Binding Proteins/chemistry , DNA-Binding Proteins/metabolism , Magnetic Resonance Spectroscopy , Mice , Models, Molecular , Molecular Sequence Data , Protein Structure, Secondary , Protein Structure, Tertiary , SolutionsABSTRACT
The Structural Classification of Proteins (SCOP) database provides a detailed and comprehensive description of the relationships of all known proteins structures. The classification is on hierarchical levels: the first two levels, family and superfamily, describe near and far evolutionary relationships; the third, fold, describes geometrical relationships. The distinction between evolutionary relationships and those that arise from the physics and chemistry of proteins is a feature that is unique to this database, so far. SCOP also provides for each structure links to atomic co-ordinates, images of the structures, interactive viewers, sequence data, data on any conformational changes related to function and literature references. The database is freely accessible on the World Wide Web (WWW) with an entry point at URL http://scop.mrc-lmb.cam.ac.uk/scop/