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1.
Behav Brain Res ; 323: 154-161, 2017 04 14.
Artigo em Inglês | MEDLINE | ID: mdl-28174030

RESUMO

BACKGROUND: The applicability of various neurological scores has not been sufficiently characterized in the anterior injection model of subarachnoid hemorrhage (SAH). Therefore this study was performed to evaluate different behavioral tests for quantifying disease severity. METHODS: Different volumes of autologous blood were injected stereotaxically into the prechiasmatic cistern of mice. Sham controls underwent the same procedure without blood injection. The following seven days after surgery, mice were evaluated for behavioral deficits by the SHIRPA score, beam balance and flex field analyses. Brains were further processed for histological analyses. RESULTS: Flex field analysis of SAH animals showed a significant reduction of locomotor activity compared to controls in the first two days after SAH. This reduction was more intense in animals with a higher amount of injected blood. The SHIRPA score revealed a significant reduction in motor behavior in SAH animals two days after surgery. A significant increase of GFAP expression, Fluoro Jade C and TUNEL positive cells as well as microthrombi was observed in SAH animals compared to sham controls in the early phase of SAH. There was a significant negative correlation between flex field righting and the number of degenerative neurons or microthrombi in the first two days after SAH. CONCLUSION: The results of flex field analysis and SHIRPA single test show behavioral and functional deficits in the first two days after SAH in parallel to histological alterations indicating neuronal damage. In summary these tests can be used as functional outcome parameters in the anterior injection model of SAH.


Assuntos
Comportamento Animal , Modelos Animais de Doenças , Hemorragia Subaracnóidea/psicologia , Animais , Astrócitos/patologia , Encéfalo/patologia , Camundongos Endogâmicos C57BL , Atividade Motora , Neurônios/patologia , Hemorragia Subaracnóidea/patologia
2.
Neurocrit Care ; 22(2): 293-8, 2015 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-25142825

RESUMO

BACKGROUND: Spontaneous intracerebral hemorrhage (ICH) is associated with high morbidity and mortality. Cortical spreading depolarizations (CSDs) increase brain matrix metalloproteinase (MMP)-9 activity leading to perihematomal edema expansion in experimental ICH. METHODS: The purpose of this report is to describe cerebral metabolic changes and brain extracellular MMP-9 levels in a patient with CSDs and perihematomal edema expansion after ICH. RESULTS: We present a 66-year-old male patient with ICH who underwent craniotomy for hematoma evacuation. Multimodal neuromonitoring data of the perihematomal region revealed metabolic distress and increased MMP-9 levels in the brain extracellular fluid during perihematomal edema progression. At the same time, subdural electrocorticography showed clusters of CSDs, which disappeared after ketamine anesthesia on day six. Perihematomal edema regression was associated with decreasing cerebral MMP-9 levels. CONCLUSIONS: This novel association between clusters of CSDs, brain metabolic distress, and increased MMP-9 levels expands our knowledge about secondary brain injury after ICH. The role of ketamine after this devastating disorder needs further studies.


Assuntos
Edema Encefálico/fisiopatologia , Córtex Cerebral/fisiopatologia , Hemorragia Cerebral/fisiopatologia , Metaloproteinase 9 da Matriz/metabolismo , Monitorização Neurofisiológica/métodos , Idoso , Edema Encefálico/etiologia , Edema Encefálico/metabolismo , Córtex Cerebral/metabolismo , Hemorragia Cerebral/complicações , Hemorragia Cerebral/metabolismo , Hemorragia Cerebral/cirurgia , Humanos , Masculino
3.
Allergy ; 69(2): 208-15, 2014 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-24224690

RESUMO

BACKGROUND: Birch pollen allergies are frequently associated with adverse reactions to various fruits, nuts, or vegetables, described as pollen-food syndrome (PFS) and caused by cross-reactive IgE antibodies primarily directed against Bet v 1. Specific immunotherapy (SIT) represents an effective treatment for inhalant allergies; however, successful birch pollen SIT does not correlate well with the amelioration of concomitant food allergies. METHODS: As vaccine candidates, apple Mal d 1 as well as hazelnut Cor a 1 derivatives were designed by in silico backbone analyses of the respective allergens. The proteins were produced by site-directed mutagenesis as fold variants of their parental allergens. Because Mal d 1 and Cor a 1 form cysteine-mediated aggregates, nonaggregative cysteine to serine mutants were also generated. The proteins were characterized physicochemically, immunologically, and in in vivo models with or without adjuvant. RESULTS: The structurally modified proteins showed significantly decreased IgE binding capacity. Notably, both in vivo models revealed reduced immunogenicity of the hypoallergenic fold variants. When formulated with alum, the monomeric cysteine mutants induced a similar immune response as the aggregated parental allergens, which is in contrast with data published on Bet v 1. CONCLUSION: These findings lead to the suggestion that the Bet v 1 structure has unique intrinsic properties, which could account for its high allergenicity. Obviously, these characteristics are not entirely shared with its food homologues from apple and hazelnut. Thus, it is important to tackle pollen-related food allergies from different angles for the generation of effective vaccine candidates to treat birch PFS.


Assuntos
Alérgenos/química , Alérgenos/imunologia , Antígenos de Plantas/imunologia , Hipersensibilidade Alimentar/imunologia , Animais , Antígenos de Plantas/química , Reações Cruzadas/imunologia , Ensaio de Imunoadsorção Enzimática , Feminino , Humanos , Camundongos , Camundongos Endogâmicos BALB C , Mutagênese Sítio-Dirigida , Proteínas de Plantas/química , Proteínas de Plantas/imunologia , Estrutura Secundária de Proteína , Proteínas Recombinantes/química , Proteínas Recombinantes/imunologia
4.
Neurology ; 78(16): 1215-20, 2012 Apr 17.
Artigo em Inglês | MEDLINE | ID: mdl-22442433

RESUMO

OBJECTIVE: Selective amygdalohippocampectomy (AHE) has been associated with postoperative cerebral vasospasm (CVS) in patients with medically intractable temporal lobe epilepsy. The incidence in temporal lobe resection (TLR) is unknown. This retrospective cohort study evaluates the incidence of and risk factors for the development of CVS in patients with TLR and AHE. METHODS: A total of 119 patients were included between 1998 and 2009. All patients were evaluated by standardized preoperative and postoperative transcranial Doppler sonography (TCD) evaluations and neurologic examinations. Postoperative CT scans were evaluated by an independent radiologist and the volume of bleeding within the resection cavity was quantified. RESULTS: Of 107 patients with longitudinal TCD data, 35 (32.7%) developed postoperative CVS. The incidence of CVS did not differ between patients with TLR and AHE. CVS was associated with female gender and a higher bleeding volume in the postoperative CT scan (p = 0.035 and 0.046). Patients with CVS showed a significantly higher incidence of postoperative neurologic signs and symptoms (48.6%) compared to patients without CVS (25%, p = 0.015). The mean length of stay was significantly prolonged in patients with diffuse CVS compared to patients with localized CVS or no CVS (28.8 ± 10.9, 24.2 ± 6.6, and 18.2 ± 6.1 days, p < 0.001). CONCLUSION: CVS is a frequent complication of surgery for temporal lobe epilepsy irrespective of the resection method. Important risk factors for the development of postoperative CVS are female gender and a higher amount of bleeding in the postoperative CT. Patients with CVS more frequently have neurologic signs and symptoms resulting in prolonged hospital stay.


Assuntos
Epilepsia do Lobo Temporal/cirurgia , Complicações Pós-Operatórias/epidemiologia , Vasoespasmo Intracraniano/epidemiologia , Adulto , Tonsila do Cerebelo/cirurgia , Áustria/epidemiologia , Epilepsia do Lobo Temporal/complicações , Feminino , Hipocampo/cirurgia , Humanos , Incidência , Masculino , Estudos Retrospectivos , Fatores de Risco , Lobo Temporal/cirurgia , Vasoespasmo Intracraniano/complicações
6.
Allergy ; 64(4): 647-51, 2009 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-19154550

RESUMO

BACKGROUND: The pollen-food syndrome (PFS) is an association of food allergies to fruits, nuts, and vegetables in patients with pollen allergy. Mal d 1, the major apple allergen, is one of the most commonly associated food allergens for birch pollen-allergic patients suffering from PFS. Although the reactions are due to cross-reactive IgE antibodies originally raised against pollen Bet v 1, not every Bet v 1-allergic patient develops clinical reactions towards apple. AIM OF THE STUDY: We speculate that distinct IgE epitopes are responsible for the clinical manifestation of PFS. To test this hypothesis we grafted five Mal d 1 stretches onto Bet v 1. The grafted regions were 7- or 8-amino acids long encompassing amino acids residues previously shown to be crucial for IgE recognition of Bet v 1. METHODS: A Bet v 1-Mal d 1 chimeric protein designated BMC was expressed in Escherichia coli and purified to homogeneity. IgE reactivity of BMC was tested with patients' sera originating from (i) Bet v 1-allergic patients displaying no clinical symptoms upon ingestion of apples; and (ii) Bet v 1-allergic patients displaying allergic symptoms upon ingestion of apples and other Bet v 1-related foods. RESULTS AND CONCLUSION: Compared to birch pollen-allergic individuals, patients suffering from PFS showed significantly higher IgE reactivity with BMC (chimeric protein). The results suggest that the Mal d 1 regions grafted onto the Bet v 1 sequence comprise important IgE epitopes recognized by Bet v 1-allergic patients suffering from allergy to apples.


Assuntos
Alérgenos/imunologia , Epitopos de Linfócito B/imunologia , Hipersensibilidade Alimentar/imunologia , Proteínas de Plantas/imunologia , Antígenos de Plantas , Betula/imunologia , Western Blotting , Reações Cruzadas , Ensaio de Imunoadsorção Enzimática , Humanos , Malus/efeitos adversos , Malus/imunologia , Pólen/imunologia , Reação em Cadeia da Polimerase , Proteínas Recombinantes/imunologia
7.
Eur J Neurol ; 15(11): e99-100, 2008 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-18803650
8.
J Neurol ; 255(11): 1617-24, 2008 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-19156484

RESUMO

BACKGROUND: External ventricular drainage (EVD) is frequently necessary in neurological and neurosurgical intensive care patients. A major complication of this procedure is an EVD-related venticulitis or meningitis. The purpose of this review is (1) to address the magnitude of the problem in the neurocritical care patient population, (2) to discuss the difficulties in providing an appropriate and timely diagnosis of this disease entity and (3) to propose an algorithm for both rapid diagnosis and appropriate therapy. METHODS: A MEDLINE literature search was carried out for studies from January 1990 through March 2008 reporting on ventriculostomy, EVD-related central nervous system infections, in particular ventriculitis and meningitis. RESULTS: EVD-related ventriculitis is a serious nosocomial complication in the neurocritical care setting where EVD catheters are frequently used for the management of elevated ICP secondary to acute hydrocephalus primarily caused by subarachnoid and intraventricular hemorrhage or traumatic brain injury. Infection rate is high with reported incidences in the range of 5 % up to more than 20 %. Predisposing factors for infection are non-adherence to rigid insertion and maintenance protocols, leakage of cerebrospinal fluid (CSF), catheter irrigation and the frequency of EVD manipulation. Diagnosis is frequently impaired either by the presence of systemic inflammation due to the primary disease or because the hemorrhagic CSF itself may cause an inflammatory reaction. Furthermore, the most common pathogens involved in EVD-related infections, i. e., staphylococci, initially provoke only a mild inflammatory response in the CSF and therefore patients rarely present with clear-cut clinical signs indicating severe central nervous system infection, in particular, ventriculitis. CONCLUSION: Nosocomial EVD-related ventriculitis is a significant cause of morbidity and mortality in critically ill neurological patients. Rapid diagnosis and prompt initiation of appropriate antimicrobial therapy is needed. A stepwise algorithm for the management of EVD-related ventriculitis is proposed.


Assuntos
Infecções do Sistema Nervoso Central , Ventrículos Cerebrais , Cuidados Críticos , Infecção Hospitalar , Encefalite , Meningite , Algoritmos , Cateterismo , Infecções do Sistema Nervoso Central/diagnóstico , Infecções do Sistema Nervoso Central/epidemiologia , Infecções do Sistema Nervoso Central/microbiologia , Infecções do Sistema Nervoso Central/terapia , Líquido Cefalorraquidiano , Infecção Hospitalar/diagnóstico , Infecção Hospitalar/epidemiologia , Infecção Hospitalar/microbiologia , Infecção Hospitalar/terapia , Encefalite/diagnóstico , Encefalite/epidemiologia , Encefalite/microbiologia , Encefalite/terapia , Humanos , Meningite/diagnóstico , Meningite/epidemiologia , Meningite/microbiologia , Meningite/terapia , Fatores de Risco
9.
Neuropathol Appl Neurobiol ; 33(5): 560-71, 2007 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-17442059

RESUMO

Cerebral malaria (CM) is associated with high mortality and morbidity as a certain percentage of survivors suffers from persistent neurological sequelae. The mechanisms leading to death and functional impairments are yet not fully understood. This study investigated biochemical and morphological markers of apoptosis in the brains of mice infected with Plasmodium berghei ANKA. Cleaved caspase-3 was detected in the brains of animals with clinical signs of CM and immunoreactivity directly correlated with the clinical severity of the disease. Caudal parts of the brain showed more intense immunoreactivity for cleaved caspase-3. Double-labelling experiments revealed processing of caspase-3 primarily in neurons and oligodendrocytes. These cells also exhibited apoptotic-like morphological profiles in ultrastructural analysis. Further, cleavage of caspase-3 was found in endothelial cells. In contrast to neurons and oligodendrocytes, apoptosis of endothelial cells already occurred in early stages of the disease. Our results are the first to demonstrate processing of caspase-3 in different central nervous system cells of animals with CM. Apoptosis of endothelial cells may represent a critical issue for the development of the disease in the mouse model. Neurological signs and symptoms might be attributable, at least in part, to apoptotic degeneration of neurons and glia in advanced stages of murine CM.


Assuntos
Apoptose/fisiologia , Encéfalo/enzimologia , Encéfalo/ultraestrutura , Caspase 3/metabolismo , Malária Cerebral/enzimologia , Malária Cerebral/patologia , Animais , Western Blotting , Imunofluorescência , Imuno-Histoquímica , Camundongos , Camundongos Endogâmicos C57BL , Microscopia Eletrônica de Transmissão , Plasmodium berghei
11.
Eur J Neurol ; 14(1): 117-20, 2007 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-17222126

RESUMO

Recurrent bleeding episodes of cavernomas especially in the brainstem can cause progressive neurological deficits. Therefore brainstem cavernomas are still a therapeutic dilemma and a treatment challenge for the neuro critical care community. We report a 39-year-old woman with spontaneous ataxia diplopia and vomiting, who has been treated for multiple intracerebral cavernomas during the last 10 years. A cerebral computed tomography (cCT) revealed a re-bleeding cavernoma in the left cerebral peduncle with consecutive obstructive hydrocephalus. As a result of the difficult anatomical location, no surgical approach was possible. As an off-label treatment, recombinant activated factor VII (rFVIIa) was administered to prevent possible further bleeding and especially further sequelae. The patient recovered well and no adverse events and especially no further bleeding of the cavernoma were observed. To our knowledge, this is the first report of the safe and successful use of rFVIIa to treat re-bleeding episodes in cavernomas. Further clinical studies are needed to specify the future potential of rFVIIa.


Assuntos
Neoplasias do Sistema Nervoso Central/tratamento farmacológico , Fator VII/uso terapêutico , Hemangioma Cavernoso do Sistema Nervoso Central/tratamento farmacológico , Hemorragia/tratamento farmacológico , Doença Aguda , Adulto , Neoplasias do Sistema Nervoso Central/diagnóstico por imagem , Fator VIIa , Feminino , Hemangioma Cavernoso do Sistema Nervoso Central/diagnóstico por imagem , Hemorragia/diagnóstico por imagem , Humanos , Radiografia , Proteínas Recombinantes/uso terapêutico
13.
Neuropathol Appl Neurobiol ; 32(2): 177-88, 2006 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-16599946

RESUMO

Different features of sensorimotor function and behaviour were studied in murine cerebral malaria (CM) and malaria without cerebral involvement (non-CM) applying the primary screen of the SHIRPA protocol. Histopathological analysis of distinct brain regions was performed and the relative size of haemorrhages and plugging of blood cells to brain vasculature was analysed. Animals suffering from CM develop a wide range of behavioural and functional alterations in the progressive course of the disease with a statistically significant impairment in all functional categories assessed 36 h prior to death when compared with control animals. Early functional indicators of cerebral phenotype are impairments in reflex and sensory system and in neuropsychiatric state. Deterioration in function is paralleled by the degree of histopathological changes with a statistically significant correlation between the SHIRPA score of CM animals and the mean size of brain haemorrhage. Furthermore, image analysis yielded that the relative area of the brain lesions was significantly larger in the forebrain and brainstem compared with the other regions of interest. Our results indicate that assessment of sensory and motor tasks by the SHIRPA primary screen is appropriate for the early in vivo discrimination of cerebral involvement in experimental murine malaria. Our findings also suggest a correlation between the degree of functional impairment and the size of the brain lesions as indicated by parenchymal haemorrhage. Applying the SHIRPA protocol in the functional characterization of animals suffering from CM might prove useful in the preclinical assessment of new antimalarial and potential neuroprotective therapies.


Assuntos
Comportamento Animal/fisiologia , Encéfalo/patologia , Malária Cerebral/patologia , Malária Cerebral/fisiopatologia , Testes Neuropsicológicos , Animais , Modelos Animais de Doenças , Processamento de Imagem Assistida por Computador , Camundongos , Camundongos Endogâmicos C57BL
14.
Neuroepidemiology ; 26(1): 37-44, 2006.
Artigo em Inglês | MEDLINE | ID: mdl-16254452

RESUMO

The charts of 114 consecutive patients with chronic meningitis admitted to a general hospital in Bangkok, Thailand, between 1993 and 1999 were retrospectively reviewed. The most common causative agents were Cryptococcus neoformans (54%) and Mycobacterium tuberculosis (37%). HIV and other underlying diseases had a major impact on the presentation of chronic cryptococcal meningitis patients. Compared to HIV-negative cryptococcal meningitis patients (21%), HIV-positives (79%) had a significantly lower incidence of focal signs (p = 0.02), hydrocephalus (p = 0.03) and seizures (p = 0.001) during hospital stay, furthermore, a lower leucocyte level, a significantly higher glucose level (p = 0.02) and a lower protein level (p = 0.03) in the first cerebrospinal fluid examination. Of the 43 patients with chronic tuberculous meningitis, only 3 were HIV positive. Focal neurologic deficits were found more frequently in tuberculous meningitis patients (p = 0.001) when compared to cryptococcal meningitis patients without HIV. Cerebral infarction on cerebral CT was indicative of tuberculous meningitis. Cryptococcal meningitis patients with HIV infection had a worse outcome compared to non-AIDS patients. Advanced stage of the disease on admission, decreased level of consciousness prior to and on the admission day and raised intracranial pressure above 40 cm H(2)O at any given time were predictive of a poor outcome in tuberculous meningitis patients.


Assuntos
Meningite/epidemiologia , Adolescente , Adulto , Idoso , Angiostrongylus cantonensis , Animais , Criança , Pré-Escolar , Doença Crônica , Feminino , Infecções por HIV/epidemiologia , Humanos , Lactente , Masculino , Meningite/microbiologia , Meningite/parasitologia , Meningite/fisiopatologia , Meningite Asséptica/epidemiologia , Meningites Bacterianas/epidemiologia , Meningite Criptocócica/epidemiologia , Meningite Criptocócica/microbiologia , Meningite Criptocócica/fisiopatologia , Pessoa de Meia-Idade , Neoplasias/complicações , Estudos Retrospectivos , Infecções Estreptocócicas/epidemiologia , Streptococcus suis , Infecções por Strongylida/epidemiologia , Infecções por Strongylida/parasitologia , Tailândia/epidemiologia , Resultado do Tratamento , Tuberculose Meníngea/epidemiologia , Tuberculose Meníngea/microbiologia , Tuberculose Meníngea/fisiopatologia
15.
Am J Trop Med Hyg ; 72(2): 150-4, 2005 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-15741551

RESUMO

Clinical presentation of Plasmodium falciparum malaria reflects a continuum from asymptomatic to multi-organ manifestation and death. Severe malaria is defined by the World Health Organization as a qualitative variable. We used the multi-organ dysfunction score (MODS) as a quantitative approach for severity in 29 patients with severe and complicated P. falciparum malaria to test its usefulness in discriminating different severity levels. The MODS on admission was highly correlated with the duration of symptoms after admission (r = 0.73, P < 0.001) and the serum level of tumor necrosis factor alpha (r = 0.41, P = 0.03). In addition, the simplified MODS, based mainly on clinical findings, was also correlated with liver and renal dysfunction during hospitalization (alanine transaminase, r = 0.42, P = 0.02; blood urea nitrogen, r = 0.45, P = 0.015). A score >or= 16 was associated with significantly longer disease duration (P = 0.018). Thus, this score might provide a predictive value for morbidity in P. falciparum malaria.


Assuntos
Malária Falciparum/epidemiologia , Malária Falciparum/patologia , Índice de Gravidade de Doença , Adolescente , Adulto , Idoso , Animais , Estudos de Casos e Controles , Intervalo Livre de Doença , Feminino , Humanos , Malária Falciparum/sangue , Malária Falciparum/etiologia , Malária Falciparum/mortalidade , Masculino , Pessoa de Meia-Idade , Insuficiência de Múltiplos Órgãos/patologia , Plasmodium falciparum , Valor Preditivo dos Testes , Tailândia/epidemiologia , Fator de Necrose Tumoral alfa/metabolismo , Organização Mundial da Saúde
16.
Clin Tech Small Anim Pract ; 16(1): 40-50, 2001 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-11373827

RESUMO

The adnexa frequently requires the general practitioner to intervene surgically to manage underlying disease or as an ancillary aid in the management of corneal disease. Both acquired and hereditary disorders are encountered. This article reviews general anatomy and physiology of the eyelids and discusses indications for the more commonly performed surgical procedures and their execution. Procedures include tarsorrhaphy, management of eyelid lacerations, eyelid tumor resection, correction of upper and/or lower lid entropion, ectropion, a medial and lateral canthoplasty, colobomatous syndrome in the cat, management of distichiasis, trichiasis and ectopic ciliae, and reduction of a prolapse of the gland of the third eyelid. Finally a surgical pack inventory useful for adnexal surgery is described.


Assuntos
Doenças do Gato/cirurgia , Doenças do Cão/cirurgia , Doenças Palpebrais/veterinária , Animais , Gatos , Cães , Doenças Palpebrais/cirurgia , Cirurgia Veterinária/métodos
17.
Proteins ; Suppl 5: 55-67, 2001.
Artigo em Inglês | MEDLINE | ID: mdl-11835482

RESUMO

We present the assessment of the CASP4 fold recognition category. The tasks we had to execute include the splitting of multidomain targets into single domains, the classification of target domains in terms of prediction categories, the numerical evaluation of predictions, the mapping of numerical scores to quality indices, the ranking of predictors, the selection of top-performing groups, and the analysis and critical discussion of the state of the art in this field. The 125 fold recognition groups were assessed by a total score that summarizes their performance over all targets and a quality score reflecting the average quality of the submitted models. Most of the top-performing groups achieved respectable results on both scores simultaneously. Several groups submitted models that were much closer to the respective target structures than any of the known folds in the Protein Data Bank. The CASP4 assessment included the automated servers of the parallel CAFASP experiment. For the total score, the highest rank achieved by a fully automated server is 12. Two thirds of the predictors have rather low scores.


Assuntos
Modelos Moleculares , Dobramento de Proteína , Simulação por Computador , Estrutura Terciária de Proteína , Análise de Sequência de Proteína
18.
J Mol Biol ; 297(4): 1003-13, 2000 Apr 07.
Artigo em Inglês | MEDLINE | ID: mdl-10736233

RESUMO

The biological role, biochemical function, and structure of uncharacterized protein sequences is often inferred from their similarity to known proteins. A constant goal is to increase the reliability, sensitivity, and accuracy of alignment techniques to enable the detection of increasingly distant relationships. Development, tuning, and testing of these methods benefit from appropriate benchmarks for the assessment of alignment accuracy.Here, we describe a benchmark protocol to estimate sequence-to-sequence and sequence-to-structure alignment accuracy. The protocol consists of structurally related pairs of proteins and procedures to evaluate alignment accuracy over the whole set. The set of protein pairs covers all the currently known fold types. The benchmark is challenging in the sense that it consists of proteins lacking clear sequence similarity. Correct target alignments are derived from the three-dimensional structures of these pairs by rigid body superposition. An evaluation engine computes the accuracy of alignments obtained from a particular algorithm in terms of alignment shifts with respect to the structure derived alignments. Using this benchmark we estimate that the best results can be obtained from a combination of amino acid residue substitution matrices and knowledge-based potentials.


Assuntos
Biologia Computacional/métodos , Dobramento de Proteína , Proteínas/química , Alinhamento de Sequência/métodos , Algoritmos , Modelos Moleculares , Estrutura Secundária de Proteína , Proteínas/metabolismo , Reprodutibilidade dos Testes , Sensibilidade e Especificidade , Homologia de Sequência de Aminoácidos
19.
J Mol Biol ; 296(4): 1139-52, 2000 Mar 03.
Artigo em Inglês | MEDLINE | ID: mdl-10686110

RESUMO

The genome sciences face the challenge to characterize structure and function of a vast number of novel genes. Sequence search techniques are used to infer functional and structural information from similarities to experimentally characterized genes or proteins. The persistent goal is to refine these techniques and to develop alternative and complementary methods to increase the range of reliable inference.Here, we focus on the structural and functional assignments that can be inferred from the known three-dimensional structures of proteins. The study uses all structures in the Protein Data Bank that were known by the end of 1997. The protein structures released in 1998 were then characterized in terms of functional and structural similarity to the previously known structures, yielding an estimate of the maximum amount of information on novel protein sequences that can be obtained from inference techniques. The 147 globular proteins corresponding to 196 domains released in 1998 have no clear sequence similarity to previously known structures. However, 75 % of the domains have extensive structure similarity to previously known folds, and most importantly, in two out of three cases similarity in structure coincides with related function. In view of this analysis, full utilization of existing structure data bases would provide information for many new targets even if the relationship is not accessible from sequence information alone. Currently, the most sophisticated techniques detect of the order of one-third of these relationships.


Assuntos
Flavoproteínas , Conformação Proteica , Sequência de Aminoácidos , Proteínas de Bactérias/química , Proteínas de Transporte/química , Desulfovibrio vulgaris , Modelos Químicos , Modelos Moleculares , Dados de Sequência Molecular , Homologia de Sequência de Aminoácidos
20.
Protein Eng ; 13(11): 745-52, 2000 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-11161105

RESUMO

We investigated and optimized a method for structure comparison which is based on rigid body superimposition. The method maximizes the number of structurally equivalent residues while keeping the root mean square deviation constant. The resulting number of equivalent residues then provides an adequate similarity measure, which is easy to interpret. We demonstrate that the approach is able to detect remote structural similarity. We show that the number of equivalent residues is a suitable measure for ranking database searches and that the results are in good agreement with expert knowledge protein structure classification. Structure comparison frequently has multiple solutions. The approach that we use provides a range of alternative alignments rather a single solution. We discuss the nature of alternative solutions on several examples.


Assuntos
Algoritmos , Conformação Proteica , Sequência de Aminoácidos , Dados de Sequência Molecular , Alinhamento de Sequência
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