RESUMEN
OBJECTIVE: To assess the 10-year outcomes after sleeve gastrectomy (SG). Primary end-points were the long-term weight loss and the need for conversion and one of the secondary end-points was the incidence of gastroesophageal reflux (GERD). MATERIALS AND METHODS: Between 2006 and 2008, 40 consecutive patients had a primary SG. A retrospective analysis of our database and telephone interview of patients who defaulted clinic follow-up was conducted. Success of surgery was defined as percentage of excess weight loss (%EWL) > 50% and no need for conversion. RESULTS: Thirty-four patients (85%) achieved a 10-year follow-up. There were 11 men and 23 women with a mean preoperative body mass index (BMI) of 44 ± 4 kg/m2 and a mean age of 42 ± 8 years. Optimal weight loss was reached after a follow-up of 12 months: the mean BMI was 31 ± 5 kg/m2 and %EWL 70 ± 21%. A progressive weight regain was observed over time. With a median follow-up of 11 years (range 7-12), the mean BMI and %EWL were respectively 36 ± 8 kg/m2 (p < 0.005) and 42 ± 37% (p < 0.001). With a median delay of 9 years (range 7-9), 6 patients (18%) were converted to gastric bypass because of weight regain. On total, SG was successful only in 14 patients (41%). Success rate was particularly high in patients who had a 1-year %EWL > 75%: 10/12 (83%) vs. 4/22 (17%) (p < 0.001). Those 12 patients were only characterized by a lower preoperative BMI: 41 ± 2 vs. 45 ± 4 (p < 0.002). Besides, 22 patients (65%) had long-term GERD requiring medical treatment: the incidence of de novo GERD was 41% (6/14) and of persisting GERD 80% (16/20). CONCLUSIONS: Our 10-year success rate after SG was 41% and the incidence of GERD 65%. SG should preferably be proposed to selected patients. Patients with low preoperative BMI and without preoperative symptoms of GERD appeared as the best candidates for SG.
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Derivación Gástrica , Laparoscopía , Obesidad Mórbida , Adulto , Estudios de Cohortes , Femenino , Gastrectomía , Humanos , Masculino , Persona de Mediana Edad , Obesidad Mórbida/epidemiología , Obesidad Mórbida/cirugía , Estudios Retrospectivos , Resultado del TratamientoRESUMEN
AIM: To assess the long-term incidence and predictive factors for recurrence after laparoscopic ventral hernia repair using a bridging technique. METHODS: The study group consisted of 213 consecutive patients operated by laparoscopy for primary ventral (n = 158) or incisional hernia (n = 55) between 2001 and 2014. Patients had a repair without fascia closure by intra-peritoneal onlay placement of a Parietex® composite mesh centred on the defect with an overlap of at least 3 cm. Clinical outcome was assessed by a combination of office consultation, patient's electronic medical file review and telephone interview. RESULTS: There were 144 men and 69 women with a mean age of 55 ± 12 years and a BMI of 32 ± 6. With a mean follow-up of 69 ± 44 months, a recurrent hernia was noted in 16 patients (7.5%). Univariate analysis showed a statistically significant higher recurrence rate in the following conditions: incisional hernia (15%), BMI ≥ 35 (21%), defect width >4 cm (27%), defect area >20 cm2 (27%), mesh overlap <5 cm (32%) and ratio of mesh area to defect area (M/D ratio) ≤12 (48%). Multivariate logistic analysis revealed that M/D ratio was the only independent predictive factor for recurrence (coefficient -0.79, OR 0.46, p < 0.002). With a M/D ratio ≤8, between 9 and 12, between 13 and 16, and ≥17, the recurrence rate was, respectively, 70, 35, 9 and 0% (p < 0.001). CONCLUSIONS: In laparoscopic repair of ventral hernia using a bridging technique, an overlap of at least 5 cm is not all that is required to prevent hernia recurrence. The M/D ratio is the most important predictive factor for recurrence. A ratio of 13 appears as the threshold under which that technique cannot be recommended and 16 as the threshold over which the risk of recurrence is virtually nil. If a satisfactory M/D ratio cannot be achieved, other surgical repair should be proposed to the patient.
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Hernia Ventral/cirugía , Herniorrafia/métodos , Hernia Incisional/cirugía , Laparoscopía/métodos , Adulto , Anciano , Femenino , Estudios de Seguimiento , Herniorrafia/instrumentación , Humanos , Laparoscopía/instrumentación , Modelos Logísticos , Masculino , Persona de Mediana Edad , Análisis Multivariante , Recurrencia , Estudios Retrospectivos , Factores de Riesgo , Mallas Quirúrgicas , Resultado del TratamientoRESUMEN
OBJECTIVES: To analyse the sound localisation skills of subjects with profound single-sided deafness (SSD) and accompanied ipsilateral tinnitus who are using a cochlear implant (CI) for between 4 and 11 years. DESIGN: Sound localisation skills were tested using nine loudspeakers in a frontal semicircle ranging from -90° to +90°. Subjects were tested in the CION and the CIOFF conditions via 3 localisation stimuli: broadband noise (BB), low-pass noise (LP) and high-pass noise (HP). PARTICIPANTS: The test group consisted of 10 adult subjects with profound sensorineural SSD, ipsilateral tinnitus and a CI. Normative data of a control group of 30 normal hearing subjects were used for comparison. MAIN OUTCOME MEASURES: Sound location accuracy was analysed via the root-mean-square error (RMSE), the mean absolute error (MAE), the localisation bias ('b') and the bias-adjusted deviation ('db '). Subjective dynamic aspects of hearing were assessed via a reduced version of the Speech, Spatial and Qualities of Hearing Scale (SSQ5 ). RESULTS: For all 3 stimuli, the RMSE improved significantly in SSD subjects in the CION condition compared to the CIOFF condition. The localisation accuracy of subjects with SSD improved significantly for BB and HP stimuli. A significant bias-adjusted deviation 'db ' was found for the BB and HP stimuli. Subjects' mean SSQ5 scores were significantly higher in the CION condition at test date than in the CIOFF condition preoperatively. CONCLUSIONS: Subjects can better locate sound in the CION condition than in the CIOFF condition.
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Implantación Coclear , Pérdida Auditiva Unilateral/rehabilitación , Localización de Sonidos , Acúfeno/rehabilitación , Adulto , Anciano , Estudios de Casos y Controles , Femenino , Humanos , Masculino , Persona de Mediana Edad , Estudios ProspectivosRESUMEN
Intravenous lipid emulsion is established therapy for bupivacaine induced cardiotoxicity. The benefit of combined hypertonic saline and lipid treatment is unexplored. In this experiment, sedated rabbits were resuscitated from bupivacaine-induced asystole with intravenous lipid according to the Association of Anaesthetists of Great Britain and Ireland's guideline, or by identical lipid dosing with hypertonic saline: 6 mEq x kg(-1) 21% sodium chloride. Early electrocardiography QRS prolongation was less with lipid plus hypertonic saline (mean (SD) QRS 0.19 (0.07) s lipid only vs 0.09 (0.01) s lipid plus hypertonic saline; p = 0.003) at 9 min though not different from the lipid only group at 20 min. No difference was observed in rates of circulatory return (7/10 lipid only and 9/10 lipid plus hypertonic saline; p = 0.58) or survival (5/10 lipid only and 6/10 lipid plus hypertonic saline; p = 1.00). Some benefit to cardiac conduction may be afforded by hypertonic saline co-administered with lipid emulsion in bupivacaine-induced cardiotoxicity.
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Anestésicos Locales/toxicidad , Bupivacaína/toxicidad , Emulsiones Grasas Intravenosas/uso terapéutico , Paro Cardíaco/terapia , Solución Salina Hipertónica/uso terapéutico , Animales , Presión Sanguínea/efectos de los fármacos , Circulación Coronaria/efectos de los fármacos , Modelos Animales de Enfermedad , Electrocardiografía/efectos de los fármacos , Femenino , Paro Cardíaco/inducido químicamente , Paro Cardíaco/fisiopatología , Frecuencia Cardíaca/efectos de los fármacos , Masculino , ConejosRESUMEN
Ligands specific for B7.1 (CD80) and B7.2 (CD86) have applications in disease indications that require inhibition of T-cell activity. As we observed significant sequence and structural similarity between the B7-binding ligand, cytotoxic T-lymphocyte associated protein-4 (CTLA-4), and antibody variable light chain domains (VLs), we have explored the possibilities of making novel B7 binding molecules based on single VL domains. We first describe the "rational" design and construction of a VL/CTLA-4 hybrid molecule in which we have grafted both the CDR1 and CDR3-like loops of CTLA-4 onto a single VL light chain, at sites determined by sequence and structure-based alignment. This molecule was secreted as a soluble product from Escherichia coli, but did not show any binding to B7.1 and B7.2. In a second approach we constructed a VL library in which human VL genes derived from B-cells were spiked with the CDR3-like loop of CTLA-4 and further diversified by DNA shuffling. This library was displayed on phage, and after selection gave B7.1 binding ligands which competed with CTLA-4. In order to evaluate the possible general utility of VL domains as binding ligands, we have constructed a non-biased VL library. From this DNA-shuffled human VL library we have selected single VL domains specific for B7.1, B7.2 or human IgG. Two B7.1-specific VL ligands and one B7.2-specific VL ligand showed competition with CTLA-4. One candidate VL domain-specific for B7.1 was affinity matured by simultaneous randomisation of all CDR loops using DNA shuffling with degenerate CDR-spiking oligonucleotides. From this library, a single VL domain with affinity of 191 nM for B7.1 was obtained, which also showed binding to B7.1 in situ. This VL had mutations in CDR1 and CDR3, indicating that antigen recognition for this single VL is most likely mediated by the same regions as in the VL domain of whole antibodies. The B7.1 and B7.2-specific VL domains described in this study may form the basis of a new family of immunomodulatory recombinant molecules. Furthermore, our studies suggest that it is feasible to create specific single VL domains to diverse targets as is the case for single VH domains.
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Antígenos CD/metabolismo , Antígeno B7-1/metabolismo , Evolución Molecular Dirigida/métodos , Cadenas Ligeras de Inmunoglobulina/química , Región Variable de Inmunoglobulina/química , Glicoproteínas de Membrana/metabolismo , Biblioteca de Péptidos , Secuencia de Aminoácidos , Afinidad de Anticuerpos , Especificidad de Anticuerpos , Antígenos CD/inmunología , Antígeno B7-1/inmunología , Antígeno B7-2 , Cromatografía en Gel , Clonación Molecular , Regiones Determinantes de Complementariedad/química , Regiones Determinantes de Complementariedad/inmunología , Ensayo de Inmunoadsorción Enzimática , Citometría de Flujo , Humanos , Cadenas Ligeras de Inmunoglobulina/genética , Cadenas Ligeras de Inmunoglobulina/inmunología , Región Variable de Inmunoglobulina/genética , Región Variable de Inmunoglobulina/inmunología , Ligandos , Glicoproteínas de Membrana/inmunología , Datos de Secuencia Molecular , Mutación/genética , Estructura Terciaria de Proteína , Análisis de Secuencia de ADN , Especificidad por Sustrato , Resonancia por Plasmón de SuperficieAsunto(s)
Algoritmos , Péptidos/química , Unión Proteica , Proteínas/química , Sitios de Unión , Simulación por Computador , Antígenos H-2/química , Antígenos H-2/metabolismo , Ligandos , Modelos Moleculares , Oligopéptidos/química , Oligopéptidos/metabolismo , Péptidos/metabolismo , Conformación Proteica , Proteínas/metabolismo , Programas Informáticos , Proteínas Virales/química , Proteínas Virales/metabolismoRESUMEN
We have explored the possibilities of using human cytotoxic T lymphocyte-associated antigen 4 (CTLA-4) as a single immunoglobulin fold-based scaffold for the generation of novel binding ligands. To obtain a suitable protein library selection system, the extracellular domain of CTLA-4 was first displayed on the surface of a filamentous phage as a fusion product of the phage coat protein p3. CTLA-4 was shown to be functionally intact by binding to its natural ligands B7-1 (CD80) and B7-2 (CD86) both in vitro and in situ. Secondly, the complementarity determining region 3 (CDR3) loop of the CTLA-4 extracellular domain was evaluated as a permissive site. We replaced the nine amino acid CDR3-like loop of CTLA-4 with the sequence XXX-RGD-XXX (where X represents any amino acid). Using phage display we selected several CTLA-4-based variants capable of binding to human alphavbeta3 integrin, one of which showed binding to integrins in situ. To explore the construction of bispecific molecules we also evaluated one other potential permissive site diametrically opposite the natural CDR-like loops, which was found to be tolerant of peptide insertion. Our data suggest that CTLA-4 is a suitable human scaffold for engineering single-domain molecules with one or possibly more binding specificities.
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Antígenos de Diferenciación/química , Antígenos de Diferenciación/inmunología , Inmunoconjugados , Linfocitos T Citotóxicos/inmunología , Abatacept , Antígenos CD , Antígenos de Diferenciación/genética , Antígeno CTLA-4 , Diseño de Fármacos , Biblioteca de Genes , Humanos , Ligandos , Pliegue de Proteína , Receptores de Vitronectina/químicaRESUMEN
BACKGROUND: The effects of heparin-coated (HC) circuits have been primarily investigated in routine cardiac operations with limited duration of cardiopulmonary bypass (CPB) and ischemia. Their benefits have not been conclusively proven but could be more significant when CPB and ischemic times are longer, such as during heart transplantation (HTx) or heart-lung transplantation (HLTx). METHODS: In a 22-month period, 29 patients undergoing HTx and HLTx were randomly divided into two groups using HC (Duraflo II, n = 14, 10 HTx and 4 HLTx) or uncoated but identical circuits (NHC group, n = 15, 10 HTx and 5 HLTx). All patients received full systemic heparinization (3 mg/kg) during CPB. Plasma endotoxin, interleukin (IL)-6, IL-8, IL-10, IL-12, and cardiac troponin-I were measured before heparin administration, immediately after aortic cross-clamping, 5, 30, 60, 90, 120 minutes, and 12 and 24 hours after aortic declamping. The intensive care unit (ICU) staff and the laboratory technologists were blinded as to the use of HC circuits. RESULTS: No statistically significant differences between groups were found with respect to all baseline values, duration of CPB and aortic cross-clamping, graft ischemic time, doses of heparin, postoperative blood loss and transfusion, peak lactate and creatine kinase-MB isoenzyme values, duration of mechanical ventilation, or length of ICU stay. One patient in each group died during the hospital stay. Patients in the HC group needed more protamine sulfate after CPB. Although endotoxin levels were similar in the two groups, significantly lower IL-6, IL-8, and IL-10 levels were observed 1 hour after aortic declamping in the HC group. The release of cardiac troponin-I was also significantly reduced in the HC group 12 and 24 hours after reperfusion. CONCLUSIONS: The use of HC circuit limits both pro- and anti-inflammatory responses to CPB. It may also reduce myocardial injury after prolonged duration of CPB and ischemia.
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Puente Cardiopulmonar/instrumentación , Materiales Biocompatibles Revestidos , Trasplante de Corazón-Pulmón/fisiología , Heparina , Complicaciones Posoperatorias/diagnóstico , Síndrome de Respuesta Inflamatoria Sistémica/diagnóstico , Adolescente , Adulto , Anciano , Niño , Endotoxinas/sangre , Femenino , Humanos , Interleucinas/sangre , Masculino , Persona de Mediana Edad , Complicaciones Posoperatorias/inmunología , Estudios Prospectivos , Síndrome de Respuesta Inflamatoria Sistémica/inmunología , Troponina I/sangreRESUMEN
BACKGROUND: Cytokines play an important role in the inflammatory response associated with cardiopulmonary bypass (CPB) and may contribute to postoperative complications. Although it has been shown that the production of tumor necrosis factor a (TNF-a) and interleukin (IL)-6 were higher following normothermic CPB than hypothermic CPB, whether different cardioplegic management could influence the release of cytokines remains unknown. METHODS: We compared the blood concentrations of four cytokines (TNF-a, IL-6, IL-8, and IL-10) in two groups of patients undergoing complete revascularization with CPB in the same study period. Seventeen patients received cold crystalloid cardioplegia at a Belgian center (group-CC), while 21 patients received warm blood cardioplegia at a center in Hong Kong (group-WB). Blood samples were collected before and after surgery in each patient. RESULTS: There were no differences between the 2 groups in terms of age, sex ratio, number of grafts, duration of CPB and aortic crossclamping. All patients survived their hospital stay. The levels of TNF-a, IL-6 and IL-8 after surgery were higher in group-CC than in group-WB. However, IL-10 levels were significantly lower at the end of surgery in group-CC than in group-WB. CONCLUSIONS: Our data suggest that the use of warm blood cardioplegia, rather than cold crystalloid cardioplegia, may reduce the inflammatory response to CPB. This observation warrants future randomized investigation to determine its clinical relevance.
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Puente Cardiopulmonar , Citocinas/sangre , Paro Cardíaco Inducido , Factor de Necrosis Tumoral alfa/análisis , Sangre , Soluciones Cristaloides , Femenino , Humanos , Hipotermia Inducida , Interleucina-10/sangre , Interleucina-6/sangre , Interleucina-8/sangre , Soluciones Isotónicas , Masculino , Persona de Mediana Edad , Sustitutos del PlasmaRESUMEN
OBJECTIVE: The mechanism involved in the endotoxemia frequently recognized during cardiopulmonary bypass remains unclear. It has also been suggested that endotoxin levels were higher in steroid-pretreated patients undergoing cardiopulmonary bypass. METHODS: Twenty patients undergoing cardiopulmonary bypass were randomly pretreated with steroids (methylprednisolone, 30 mg/kg) or placebo. Blood samples for endotoxin measurement were drawn simultaneously from the superior and inferior venae cavae before heparin administration, 5 and 50 minutes after the onset of bypass, 5 minutes after aortic declamping, at the end of bypass, and 1, 2, and 20 hours after the end of cardiopulmonary bypass. RESULTS: The perioperative variables in the two groups were similar. Blood endotoxin levels were higher in the inferior vena cava than in the superior vena cava immediately after the onset of bypass. Endotoxin levels in inferior vena cava blood were significantly lower in steroid-pretreated patients than those in patients not receiving steroids. CONCLUSIONS: Endotoxin is released during cardiopulmonary bypass from the region drained by the inferior vena cava. Steroid pretreatment may actually reduce endotoxin release during bypass.
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Puente Cardiopulmonar/efectos adversos , Endotoxemia/prevención & control , Endotoxinas/sangre , Glucocorticoides/uso terapéutico , Complicaciones Intraoperatorias/prevención & control , Metilprednisolona/uso terapéutico , Anciano , Procedimientos Quirúrgicos Cardíacos , Endotoxemia/sangre , Endotoxemia/etiología , Endotoxinas/antagonistas & inhibidores , Femenino , Estudios de Seguimiento , Humanos , Complicaciones Intraoperatorias/sangre , Prueba de Limulus , Masculino , Cuidados Preoperatorios/métodos , Estudios Prospectivos , Resultado del Tratamiento , Venas CavasRESUMEN
Antigenicity and conformational propensities of synthetic peptides corresponding to the sequential epitope H236-255 of the measles virus hemagglutinin protein were investigated. This epitope corresponds to the neutralising and protective monoclonal antibody BH129 and includes Arg243, implicated in CD46-down-regulation and Arg253 that has been mapped to the putative enzymatic site. Fine mapping with truncation-, elongation-, Gly- and Ala-substitution analogues defined EL-QL as the critical residues of the minimal epitope S244ELSQL249. CD spectra of peptides, comparison with the 3D-structure of homologous sequences, and prediction algorithms suggested a helical structure with the contact residues E245L-QL249 located on the protein surface. Mimotopes obtained with a 6-mer phage display library contained a consensus Pro (important for binding) instead of Ser247 of the wild-type sequence (irrelevant for binding). The kink induced by Pro seemed to be essential to bring the 4 contact-residues in the mimotopes and in the corresponding short peptides together. CD analysis and prediction algorithms suggested that non-helical conformations of the phage insert and of the peptides may favourably mimic the antigenic helical turns of the wild-type sequence, resulting in an up to 135 times higher antigenicity of the mAb towards the mimotope peptides.
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Epítopos/inmunología , Hemaglutininas Virales/inmunología , Virus del Sarampión/química , Biblioteca de Péptidos , Animales , Reacciones Antígeno-Anticuerpo/genética , Bacteriófagos/química , Bacteriófagos/genética , Sitios de Unión/fisiología , Epítopos/biosíntesis , Epítopos/química , Ratones , Imitación Molecular/genética , Estructura Secundaria de Proteína , Homología de Secuencia de AminoácidoRESUMEN
We report on a case of thrombus formation on a native bicuspid aortic valve, which was found during an elective operation for aortic valve replacement. Although no apparent predisposing cause of thrombosis could be ascertained, severe calcific stenosis of the bicuspid valve and cardiac catheterization may have played a role. The patient is in excellent condition 9 months after the operation.
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Estenosis de la Válvula Aórtica/complicaciones , Válvula Aórtica/anomalías , Calcinosis/complicaciones , Trombosis/complicaciones , Anciano , Válvula Aórtica/cirugía , Estenosis de la Válvula Aórtica/cirugía , Humanos , MasculinoRESUMEN
The dead-end elimination algorithm has proven to be a powerful tool in protein homology modeling since it allows one to determine rapidly the global minimum-energy conformation (GMEC) of an arbitrarily large collection of side chains, given fixed backbone coordinates. After introducing briefly the necessary background, we focus on logic arguments that increase the efficacy of the dead-end elimination process. Second, we present new theoretical considerations on the use of the dead-end elimination method as a tool to identify sequences that are compatible with a given scaffold structure. Third, we initiate a search for properties derived from the computed GMEC structure to predict whether a given sequence can be well packed in the core of a protein. Three properties will be considered: the nonbonded energy, the accessible surface area, and the extent by which the GMEC side-chain conformations deviate from a locally optimal conformation.
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Modelos Químicos , Conformación Proteica , Proteínas/química , Secuencia de Aminoácidos , Aminoácidos/química , Pliegue de Proteína , TermodinámicaRESUMEN
With its antiinflammatory properties, interleukin (IL)-10 may play an important role in limiting complications associated with cardiopulmonary bypass (CPB). We previously demonstrated that pretreatment with steroids can significantly increase IL-10 production during CPB, but neither the heart nor the lung was found to be its main source. To define whether the liver is the source of IL-10, hepatic venous cannulation was performed in 12 patients undergoing CPB. Each patient received 30 mg/kg of methylprednisolone before operation. Plasma levels of IL-10 were simultaneously measured in peripheral arterial blood and hepatic venous blood before heparin administration, before aortic cross-clamping, and 5, 30, 60, 90, and 120 minutes after aortic declamping. The duration of CPB and aortic cross-clamping was 113 +/- 7 minutes and 75 +/- 6 minutes (mean +/- SEM), respectively. IL-10 levels 30 minutes after declamping were significantly higher in hepatic venous blood than in arterial blood (1187 +/- 573 pg/ml vs 911 +/- 405 pg/ml, p < 0.01 by Wilcoxon's signed-rank test). To determine whether steroids can also induce the release of another antiinflammatory cytokine, IL-4, plasma IL-4 levels were measured simultaneously. IL-4 was detected in the arterial blood of only 4 of the 12 patients, transiently after aortic declamping. IL-4 was not detected in hepatic venous blood. In conclusion, the liver is a major source of IL-10 during CPB. However, steroid-treated patients do not show an increase in IL-4, and the liver is not the source of IL-4 during and after CPB.
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Antiinflamatorios/farmacología , Puente Cardiopulmonar , Interleucina-10/metabolismo , Hígado/metabolismo , Metilprednisolona/farmacología , Anciano , Puente de Arteria Coronaria , Femenino , Enfermedades de las Válvulas Cardíacas/cirugía , Humanos , Interleucina-10/sangre , Interleucina-4/sangre , Hígado/efectos de los fármacos , Masculino , Persona de Mediana Edad , Estudios ProspectivosRESUMEN
Docking algorithms play an important role in the process of rational drug design and in understanding the mechanism of molecular recognition. An important determinant for successful docking is the extent to which the configurational space (including conformational changes) of the ligand/receptor system is searched. Here we describe a new, combinatorial method for flexible docking of peptides to proteins that allows full rotation around all single bonds of the peptide ligand and around those of a large set of receptor side chains. We have simulated the binding of several viral peptides to murine major histocompatibility complex class I H-2Kb. In addition, we have explored the limits of our method by simulating a complex between calmodulin and an 18-residue long helical peptide from calmodulin-dependent protein kinase IIalpha. The calculated peptide conformations generally matched well with the X-ray structures. Essential information about local flexibility and about residues that are responsible for strong binding was obtained. We have frequently observed considerable side-chain flexibility during the simulations, showing the need for a flexible treatment of the receptor. Our method may also be useful whenever the receptor side-chain conformation is not available or uncertain, as illustrated by the docking of an H-2Kb binding nonapeptide to the receptor structure taken from an octapeptide/H-2Kb complex.
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Simulación por Computador , Proteínas de la Nucleocápside , Oligopéptidos/química , Conformación Proteica , Proteínas/química , Alanina/química , Proteína Quinasa Tipo 2 Dependiente de Calcio Calmodulina , Proteínas Quinasas Dependientes de Calcio-Calmodulina , Calmodulina/química , Antígenos H-2/química , Cómputos Matemáticos , Modelos Moleculares , Nucleocápside/química , Unión Proteica , Respirovirus , Virus de la Estomatitis Vesicular IndianaRESUMEN
The dead-end elimination theorem has proved to be a powerful method to reduce the theoretically accessible conformational space when modeling protein side chains by using a rotameric representation of possible conformations. In this work, theoretical details about variants to the original criterion are discussed. We also provide information on how the equations can be algorithmically implemented in such a way that both computational performance and structural accuracy are optimized. In addition, we discuss the theoretical and practical aspects of three new methods called the "bottom line theorem", dead-end elimination assisted by local modeling and a combinatorial search combined with conventional dead-end elimination. It is shown that the algorithm in its current from enables the determination of the global minimum energy side chain conformation of large proteins on a time scale of hours while for small proteins of up to 30 residues the calculations are done on a time scale of seconds. The latter opens a way to combine a main chain sampling algorithm with the dead-end elimination method to locally model entire fragments of a protein chain.
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Simulación por Computador , Modelos Moleculares , Conformación Proteica , Proteínas/química , Algoritmos , Modelos QuímicosRESUMEN
BACKGROUND: About a decade ago, the concept of rotamer libraries was introduced to model sidechains given known mainchain coordinates. Since then, several groups have developed methods to handle the challenging combinatorial problem that is faced when searching rotamer libraries. To avoid a combinatorial explosion, the dead-end elimination method detects and eliminates rotamers that cannot be members of the global minimum energy conformation (GMEC). Several groups have applied and further developed this method in the fields of homology modelling and protein design. RESULTS: This work addresses at the same time increased prediction accuracy and calculation speed improvements. The proposed enhancements allow the elimination of more than one-third of the possible rotameric states before applying the dead-end elimination method. This is achieved by using a highly detailed rotamer library allowing the safe application of an energy-based rejection criterion without risking the elimination of a GMEC rotamer. As a result, we gain both in modelling accuracy and in computational speed. Being completely automated, the current implementation of the dead-end elimination prediction of protein sidechains can be applied to the modelling of sidechains of proteins of any size on the high-end computer systems currently used in molecular modelling. The improved accuracy is highlighted in a comparative study on a collection of proteins of varying size for which score results have previously been published by multiple groups. Furthermore, we propose a new validation method for the scoring of the modelled structure versus the experimental data based upon the volume overlap of the predicted and observed sidechains. This overlap criterion is discussed in relation to the classic RMSD and the frequently used +/- 40 degrees window in comparing chi 1 and chi 2 angles. CONCLUSIONS: We have shown that a very detailed library allows the introduction of a safe energy threshold rejection criterion, thereby increasing both the execution speed and the accuracy of the modelling program. We speculate that the current method will allow the sidechain prediction of medium-sized proteins and complex protein interfaces involving up to 150 residues on low-end desktop computers.
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Modelos Químicos , Pliegue de Proteína , Algoritmos , Modelos Estructurales , Conformación ProteicaRESUMEN
Proinflammatory cytokines, such as tumor necrosis factor-alpha, interleukin-6, and interleukin-8, and anti unflammatory cytokines, such as interleukin-10, may play an important role in patient responses to cardiopulmonary bypass. We sought to define whether the myocardium and the lungs serve as important sources of these cytokines under conditions of cardiopulmonary bypass. Ten patients (age 64 +/- 3 years, mean +/- standard error of the mean) undergoing elective coronary artery bypass grafting were monitored with an arterial catheter, a coronary sinus catheter, and pulmonary artery catheter. Plasma levels of tumor necrosis factor-alpha, interleukin-6, interleukin-8, and interleukin-10 were measured simultaneously in peripheral arterial blood, coronary sinus blood, and mixed venous blood before heparin administration, 1 minute before aortic crossclamping, 5 minutes after aortic declamping, and at 0.5, 1, 1.5 and 2 hours after aortic declamping. The durations of cardiopulmonary bypass and aortic crossclamping were 114 +/- 9 and 64 +/- 5 minutes, respectively. Levels of tumor necrosis factor-alpha and interleukin-6 were significantly higher in coronary sinus blood than in arterial blood after aortic declamping. Tumor necrosis factor-alpha and interleukin-6 levels were also higher in mixed venous blood than in arterial blood within 1 hour after declamping. There were no significant differences among the three sampling sites with respect to interleukin-8 and interleukin-10 levels. In one patient who had postoperative myocardial infarction, however, interleukin-8 levels were three times as high as in coronary sinus blood than in arterial blood. These data indicate that the myocardium is a major source of tumor necrosis factor-alpha and interleukin-6 in patients undergoing cardiopulmonary bypass. The lungs may consume rather than release proinflammatory cytokines in the early phase of reperfusion. The source under these conditions of the antünflammatory cytokine interleukin-10 remains to be determined.