931 resultados para free energy of binding
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Introducción. La obesidad puede definirse como una enfermedad metabólica crónica de origen multifactorial, lo que provoca trastornos o problemas físicos y psicológicos a la persona, con patologías asociadas que limitan la esperanza de vida y deterioran la calidad de la misma, siendo determinante para sus áreas sociales y laborales. Este trastorno metabólico crónico se caracteriza por una acumulación excesiva de energía en el cuerpo en forma de grasa, lo que lleva a un aumento de peso con respecto al valor esperado por sexo, edad y altura. La gestión y el tratamiento de la obesidad tienen objetivos más amplios que la pérdida de peso e incluyen la reducción del riesgo y la mejora de la salud. Estos pueden ser alcanzados por la pérdida modesta de peso (es decir, 10.5% del peso corporal inicial), la mejora del contenido nutricional de la dieta y un modesto incremento en la actividad física y condición física. La dieta es uno de los métodos más populares para perder peso corporal. El ejercicio es otra alternativa para perder peso corporal. El aumento de ejercicio provoca un desequilibrio cuando se mantiene la ingesta calórica. También tiene ventajas, como la mejora del tono muscular, la capacidad cardiovascular, fuerza y flexibilidad, aumenta el metabolismo basal y mejora el sistema inmunológico. Objetivos. El objetivo de esta tesis es contribuir en un estudio de intervención para aclarar la evolución del peso corporal durante una intervención de dieta y ejercicio. Para ello, se evaluaron los efectos de la edad, sexo, índice de masa corporal inicial y el tipo de tratamiento en las tendencias de pérdida de peso. Otro objetivo de la tesis era crear un modelo de regresión lineal múltiple capaz de predecir la pérdida de peso corporal después del periodo de intervención. Y, por último, determinar el efecto sobre la composición corporal (peso corporal, índice de masa corporal, la masa grasa, y la masa libre de grasa) de las diferentes intervenciones basadas en ejercicios (fuerza, resistencia, resistencia combinada con fuerza, y las recomendaciones de actividad física (grupo control)) en combinación con dieta de adultos con sobrepeso y obesidad, después de la intervención, así como los cambios de la composición corporal 3 años más tarde. Diseño de la investigación. Los datos empleados en el análisis de esta tesis son parte del proyecto “Programas de Nutrición y Actividad Física para el tratamiento de la obesidad” (PRONAF). El proyecto PRONAF es un estudio clínico sobre programas de nutrición y actividad física para el sobrepeso y la obesidad, desarrollado en España durante varios años de intervención. Fue diseñado, en parte, para comparar diferentes tipos de intervención, con el objetivo de evaluar su impacto en las dinámicas de pérdida de peso, en personas con sobrepeso y obesidad. Como diseño experimental, el estudio se basó en una restricción calórica, a la que, en algunos casos, se le añadió un protocolo de entrenamiento (fuerza, resistencia, o combinado, en igualdad de volumen e intensidad). Las principales variables para la investigación que comprende esta tesis fueron: el peso corporal y la composición corporal (masa grasa y masa libre de grasa). Conclusiones. En esta tesis, para los programas de pérdida de peso en personas con sobrepeso y obesidad con un 25-30% de la restricción calórica, el peso corporal se redujo significativamente en ambos sexos, sin tener en cuenta la edad y el tipo de tratamiento seguido. Según los resultados del estudio, la pérdida de peso realizada por un individuo (hombre o mujer) durante los seis meses puede ser representada por cualquiera de las cinco funciones (lineal, potencial, exponencial, logarítmica y cuadrática) en ambos sexos, siendo la cuadrática la que tiende a representarlo mejor. Además, se puede concluir que la pérdida de peso corporal se ve afectada por el índice de masa corporal inicial y el sexo, siendo mayor para las personas obesas que para las de sobrepeso, que muestran diferencias entre sexos sólo en la condición de sobrepeso. Además, es posible calcular el peso corporal final de cualquier participante involucrado en una intervención utilizando la metodología del proyecto PRONAF sólo conociendo sus variables iniciales de composición corporal. Además, los cuatro tipos de tratamientos tuvieron resultados similares en cambios en la composición corporal al final del período de intervención, con la única excepción de la masa libre de grasa, siendo los grupos de entrenamiento los que la mantuvieron durante la restricción calórica. Por otro lado, sólo el grupo combinado logra mantener la reducción de la masa grasa (%) 3 años después del final de la intervención. ABSTRACT Introduction. Obesity can be defined as a chronic metabolic disease from a multifactorial origin, which leads to physical and psychological impacts to the person, with associated pathologies that limit the life expectancy and deteriorate the quality of it, being determinant for the social and labor areas of the person. This chronic metabolic disorder is characterized by an excessive accumulation of energy in the body as fat, leading to increased weight relative to the value expected by sex, age and height. The management and treatment of obesity have wider objectives than weight loss alone and include risk reduction and health improvement. These may be achieved by modest weight loss (i.e. 5–10% of initial body weight), improved nutritional content of the diet and modest increases in physical activity and fitness. Weight loss through diet is one of the most popular approaches to lose body weight. Exercise is another alternative to lose body weight. The increase of exercise causes an imbalance when the caloric intake is maintained. It also has advantages such as improved muscle tone, cardiovascular fitness, strength and flexibility, increases the basal metabolism and improves immune system. Objectives. The aim of this thesis is to contribute with an interventional study to clarify the evolution of the body weight during a diet and exercise intervention. For this, the effects of age, sex, initial body mass index and type of treatment on weight loss tendencies were evaluated. Another objective of the thesis was to create a multiple linear regression model able to predict the body weight loss after the intervention period. And, finally, to determine the effect upon body composition (body weight, body mass index, fat mass, and fat-free mass of different exercise-based interventions (strength, endurance, combined endurance and strength, and physical activity recommendations group (control group)) combined with diet in overweight and obese adults, after intervention as well as body composition changes 3 years later. Research Design. The data used in the analysis of this thesis are part of the project "Programs of Nutrition and Physical Activity for the treatment of obesity" (PRONAF). The PRONAF project is a clinical trial program about nutrition and physical activity for overweight and obesity, developed in Spain for several years of intervention. It was designed, in part, to compare different types of intervention, in order to assess their impact on the dynamics of weight loss in overweight and obese people. As experimental design, the study was based on caloric restriction, which, in some cases, added a training protocol (strength, endurance, or combined in equal volume and intensity). The main research variables comprising this thesis were: body weight and body composition outcomes (fat mass and fat-free mass). Conclusions. In this thesis, for weight loss programs in overweight and obese people with 25-30% of caloric restriction, the body weight was significantly decreased in both sexes, regardless the age and type of followed treatment. According to the results of the study, the weight loss performed by an individual (male or female) during six months can be represented by any of the five functions (linear, power law, exponential, logarithmic and quadratic) in both sexes, being the quadratic one which tends to represent it better. In addition, it can be concluded that the body weight loss is affected by the initial body mass index and sex condition, being greater for the obese people than for the overweight one, showing differences between sexes only in the overweight condition. Moreover, it is possible to calculate the final body weight of any participant engaged in an intervention using the PRONAF Project methodology only knowing their initial body composition variables. Furthermore, the four types of treatments had similar results on body composition changes at the end of the intervention period, with the only exception of fat-free mass, being the training groups the ones that maintained it during the caloric restriction. On the other hand, only the combined group achieved to maintain the fat mass (%) reduced 3 years after the end of the intervention.
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The electronic structure and properties of the orthorhombic phase of the CH 3 NH 3 PbI 3 perovskite are computed with density functional theory. The structure, optimized using a van der Waals functional, reproduces closely the unit cell volume. The experimental band gap is reproduced accurately by combining spin-orbit effects and a hybrid functional in which the fraction of exact exchange is tuned self-consistently to the optical dielectric constant. Including spin-orbit coupling strongly reduces the anisotropy of the effective mass tensor, predicting a low electron effective mass in all crystal directions. The computed binding energy of the unrelaxed exciton agrees with experimental data, and the values found imply a fast exciton dissociation at ambient temperature. Also polaron masses for the separated carriers are estimated. The values of all these parameters agree with recent indications that fast dynamics and large carrier diffusion lengths are key in the high photovoltaic efficiencies shown by these materials.
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En la presente tesis desarrollamos una estrategia para la simulación numérica del comportamiento mecánico de la aorta humana usando modelos de elementos finitos no lineales. Prestamos especial atención a tres aspectos claves relacionados con la biomecánica de los tejidos blandos. Primero, el análisis del comportamiento anisótropo característico de los tejidos blandos debido a las familias de fibras de colágeno. Segundo, el análisis del ablandamiento presentado por los vasos sanguíneos cuando estos soportan cargas fuera del rango de funcionamiento fisiológico. Y finalmente, la inclusión de las tensiones residuales en las simulaciones en concordancia con el experimento de apertura de ángulo. El análisis del daño se aborda mediante dos aproximaciones diferentes. En la primera aproximación se presenta una formulación de daño local con regularización. Esta formulación tiene dos ingredientes principales. Por una parte, usa los principios de la teoría de la fisura difusa para garantizar la objetividad de los resultados con diferentes mallas. Por otra parte, usa el modelo bidimensional de Hodge-Petruska para describir el comportamiento mesoscópico de los fibriles. Partiendo de este modelo mesoscópico, las propiedades macroscópicas de las fibras de colágeno son obtenidas a través de un proceso de homogenización. En la segunda aproximación se presenta un modelo de daño no-local enriquecido con el gradiente de la variable de daño. El modelo se construye a partir del enriquecimiento de la función de energía con un término que contiene el gradiente material de la variable de daño no-local. La inclusión de este término asegura una regularización implícita de la implementación por elementos finitos, dando lugar a resultados de las simulaciones que no dependen de la malla. La aplicabilidad de este último modelo a problemas de biomecánica se estudia por medio de una simulación de un procedimiento quirúrgico típico conocido como angioplastia de balón. In the present thesis we develop a framework for the numerical simulation of the mechanical behaviour of the human aorta using non-linear finite element models. Special attention is paid to three key aspects related to the biomechanics of soft tissues. First, the modelling of the characteristic anisotropic behaviour of the softue due to the collagen fibre families. Secondly, the modelling of damage-related softening that blood vessels exhibit when subjected to loads beyond their physiological range. And finally, the inclusion of the residual stresses in the simulations in accordance with the opening-angle experiment The modelling of damage is addressed with two major and different approaches. In the first approach a continuum local damage formulation with regularisation is presented. This formulation has two principal ingredients. On the one hand, it makes use of the principles of the smeared crack theory to avoid the mesh size dependence of the structural response in softening. On the other hand, it uses a Hodge-Petruska bidimensional model to describe the fibrils as staggered arrays of tropocollagen molecules, and from this mesoscopic model the macroscopic material properties of the collagen fibres are obtained using an homogenisation process. In the second approach a non-local gradient-enhanced damage formulation is introduced. The model is built around the enhancement of the free energy function by means of a term that contains the referential gradient of the non-local damage variable. The inclusion of this term ensures an implicit regularisation of the finite element implementation, yielding mesh-objective results of the simulations. The applicability of the later model to biomechanically-related problems is studied by means of the simulation of a typical surgical procedure, namely, the balloon angioplasty.
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A numerical method to analyse the stability of transverse galloping based on experimental measurements, as an alternative method to polynomial fitting of the transverse force coefficient Cz, is proposed in this paper. The Glauert–Den Hartog criterion is used to determine the region of angles of attack (pitch angles) prone to present galloping. An analytic solution (based on a polynomial curve of Cz) is used to validate the method and to evaluate the discretization errors. Several bodies (of biconvex, D-shape and rhomboidal cross sections) have been tested in a wind tunnel and the stability of the galloping region has been analysed with the new method. An algorithm to determine the pitch angle of the body that allows the maximum value of the kinetic energy of the flow to be extracted is presented.
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Protein folding occurs on a time scale ranging from milliseconds to minutes for a majority of proteins. Computer simulation of protein folding, from a random configuration to the native structure, is nontrivial owing to the large disparity between the simulation and folding time scales. As an effort to overcome this limitation, simple models with idealized protein subdomains, e.g., the diffusion–collision model of Karplus and Weaver, have gained some popularity. We present here new results for the folding of a four-helix bundle within the framework of the diffusion–collision model. Even with such simplifying assumptions, a direct application of standard Brownian dynamics methods would consume 10,000 processor-years on current supercomputers. We circumvent this difficulty by invoking a special Brownian dynamics simulation. The method features the calculation of the mean passage time of an event from the flux overpopulation method and the sampling of events that lead to productive collisions even if their probability is extremely small (because of large free-energy barriers that separate them from the higher probability events). Using these developments, we demonstrate that a coarse-grained model of the four-helix bundle can be simulated in several days on current supercomputers. Furthermore, such simulations yield folding times that are in the range of time scales observed in experiments.
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Defined model systems consisting of physiologically spaced arrays of H3/H4 tetramer⋅5S rDNA complexes have been assembled in vitro from pure components. Analytical hydrodynamic and electrophoretic studies have revealed that the structural features of H3/H4 tetramer arrays closely resemble those of naked DNA. The reptation in agarose gels of H3/H4 tetramer arrays is essentially indistinguishable from naked DNA, the gel-free mobility of H3/H4 tetramer arrays relative to naked DNA is reduced by only 6% compared with 20% for nucleosomal arrays, and H3/H4 tetramer arrays are incapable of folding under ionic conditions where nucleosomal arrays are extensively folded. We further show that the cognate binding sites for transcription factor TFIIIA are significantly more accessible when the rDNA is complexed with H3/H4 tetramers than with histone octamers. These results suggest that the processes of DNA replication and transcription have evolved to exploit the unique structural properties of H3/H4 tetramer arrays.
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Proteins can be very tolerant to amino acid substitution, even within their core. Understanding the factors responsible for this behavior is of critical importance for protein engineering and design. Mutations in proteins have been quantified in terms of the changes in stability they induce. For example, guest residues in specific secondary structures have been used as probes of conformational preferences of amino acids, yielding propensity scales. Predicting these amino acid propensities would be a good test of any new potential energy functions used to mimic protein stability. We have recently developed a protein design procedure that optimizes whole sequences for a given target conformation based on the knowledge of the template backbone and on a semiempirical potential energy function. This energy function is purely physical, including steric interactions based on a Lennard-Jones potential, electrostatics based on a Coulomb potential, and hydrophobicity in the form of an environment free energy based on accessible surface area and interatomic contact areas. Sequences designed by this procedure for 10 different proteins were analyzed to extract conformational preferences for amino acids. The resulting structure-based propensity scales show significant agreements with experimental propensity scale values, both for α-helices and β-sheets. These results indicate that amino acid conformational preferences are a natural consequence of the potential energy we use. This confirms the accuracy of our potential and indicates that such preferences should not be added as a design criterion.
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The mouse p53 protein generated by alternative splicing (p53as) has amino acid substitutions at its C terminus that result in constitutively active sequence-specific DNA binding (active form), whereas p53 protein itself binds inefficiently (latent form) unless activated by C-terminal modification. Exogenous p53as expression activated transcription of reporter plasmids containing p53 binding sequences and inhibited growth of mouse and human cells lacking functional endogenous p53. Inducible p53as in stably transfected p53 null fibroblasts increased p21WAF1/Cip-1/Sdi and decreased bcl-2 protein steady-state levels. Endogenous p53as and p53 proteins differed in response to cellular DNA damage. p53 protein was induced transiently in normal keratinocytes and fibroblasts whereas p53as protein accumulation was sustained in parallel with induction of p21WAF1/Cip-1/Sdi protein and mRNA, in support of p53as transcriptional activity. Endogenous p53 and p53as proteins in epidermal tumor cells responded to DNA damage with different kinetics of nuclear accumulation and efficiencies of binding to a p53 consensus DNA sequence. A model is proposed in which C-terminally distinct p53 protein forms specialize in functions, with latent p53 forms primarily for rapid non-sequence-specific binding to sites of DNA damage and active p53 forms for sustained regulation of transcription and growth.
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We report the crystal structures of the copper and nickel complexes of RNase A. The overall topology of these two complexes is similar to that of other RNase A structures. However, there are significant differences in the mode of binding of copper and nickel. There are two copper ions per molecule of the protein, but there is only one nickel ion per molecule of the protein. Significant changes occur in the interprotein interactions as a result of differences in the coordinating groups at the common binding site around His-105. Consequently, the copper- and nickel-ion-bound dimers of RNase A act as nucleation sites for generating different crystal lattices for the two complexes. A second copper ion is present at an active site residue His-119 for which all the ligands are from one molecule of the protein. At this second site, His-119 adopts an inactive conformation (B) induced by the copper. We have identified a novel copper binding motif involving the α-amino group and the N-terminal residues.
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A novel atomic force microscope with a magnetically oscillated tip has provided unprecedented resolution of small DNA fragments spontaneously adsorbed to mica and imaged in situ in the presence of divalent ions. Kinks (localized bends of average angle 78°) were observed in axially strained minicircles consisting of tandemly repeated d(A)5 and d(GGGCC[C]) sequences. The frequency of kinks in identical minicircles increased 4-fold in the presence of 1 mM Zn2+ compared with 1 mM Mg2+. Kinking persisted in mixed Mg2+/Zn2+ electrolytes until the Zn2+ concentration dropped below 100 μM, indicating that this type of kinking may occur under physiological conditions. Kinking appears to replace intrinsic bending, and statistical analysis shows that kinks are not localized within any single sequence element. A surprisingly small free energy is associated with kink formation.
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The causal agent of chrysanthemum chlorotic mottle (CChM) disease has been identified, cloned, and sequenced. It is a viroid RNA (CChMVd) of 398–399 nucleotides. In vitro transcripts with the complete CChMVd sequence were infectious and induced the typical symptoms of the CChM disease. CChMVd can form hammerhead structures in both polarity strands. Plus and minus monomeric CChMVd RNAs self-cleaved during in vitro transcription and after purification as predicted by these structures, which are stable and most probably act as single hammerhead structures as in peach latent mosaic viroid (PLMVd), but not in avocado sunblotch viroid (ASBVd). Moreover, the plus CChMVd hammerhead structure also appears to be active in vivo, because the 5′ terminus of the linear plus CChMVd RNA isolated from infected tissue is that predicted by the corresponding hammerhead ribozyme. Both hammerhead structures of CChMVd display some peculiarities: the plus self-cleaving domain has an unpaired A after the conserved A9 residue, and the minus one has an unusually long helix II. The most stable secondary structure predicted for CChMVd is a branched conformation that does not fulfill the rod-like or quasi-rod-like model proposed for the in vitro structure of most viroids with the exception of PLMVd, whose proposed secondary structure of lowest free energy also is branched. The unusual conformation of CChMVd and PLMVd is supported by their insolubility in 2 M LiCl, in contrast to ASBVd and a series of representative non-self-cleaving viroids that are soluble under the same high salt conditions. These results support the classification of self-cleaving viroids into two subgroups, one formed by ASBVd and the other one by PLMVd and CChMVd.
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It has been suggested that the tethering caused by binding of the N-terminal region of smooth muscle caldesmon (CaD) to myosin and its C-terminal region to actin contributes to the inhibition of actin-filament movement over myosin heads in an in vitro motility assay. However, direct evidence for this assumption has been lacking. In this study, analysis of baculovirus-generated N-terminal and C-terminal deletion mutants of chicken-gizzard CaD revealed that the major myosin-binding site on the CaD molecule resides in a 30-amino acid stretch between residues 24 and 53, based on the very low level of binding of CaDΔ24–53 lacking the residues 24–53 to myosin compared with the level of binding of CaDΔ54–85 missing the adjacent residues 54–85 or of the full-length CaD. As expected, deletion of the region between residues 24 and 53 or between residues 54 and 85 had no effect on either actin-binding or inhibition of actomyosin ATPase activity. Deletion of residues 24–53 nearly abolished the ability of CaD to inhibit actin filament velocity in the in vitro motility experiments, whereas CaDΔ54–85 strongly inhibited actin filament velocity in a manner similar to that of full-length CaD. Moreover, CaD1–597, which lacks the major actin-binding site(s), did not inhibit actin-filament velocity despite the presence of the major myosin-binding site. These data provide direct evidence for the inhibition of actin filament velocity in the in vitro motility assay caused by the tethering of myosin to actin through binding of both the CaD N-terminal region to myosin and the C-terminal region to actin.
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Vascular endothelial growth factor (VEGF) is a homodimeric member of the cystine knot family of growth factors, with limited sequence homology to platelet-derived growth factor (PDGF) and transforming growth factor β2 (TGF-β). We have determined its crystal structure at a resolution of 2.5 Å, and identified its kinase domain receptor (KDR) binding site using mutational analysis. Overall, the VEGF monomer resembles that of PDGF, but its N-terminal segment is helical rather than extended. The dimerization mode of VEGF is similar to that of PDGF and very different from that of TGF-β. Mutational analysis of VEGF reveals that symmetrical binding sites for KDR are located at each pole of the VEGF homodimer. Each site contains two functional “hot spots” composed of binding determinants presented across the subunit interface. The two most important determinants are located within the largest hot spot on a short, three-stranded sheet that is conserved in PDGF and TGF-β. Functional analysis of the binding epitopes for two receptor-blocking antibodies reveal different binding determinants near each of the KDR binding hot spots.
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Two variables define the topological state of closed double-stranded DNA: the knot type, K, and ΔLk, the linking number difference from relaxed DNA. The equilibrium distribution of probabilities of these states, P(ΔLk, K), is related to two conditional distributions: P(ΔLk|K), the distribution of ΔLk for a particular K, and P(K|ΔLk) and also to two simple distributions: P(ΔLk), the distribution of ΔLk irrespective of K, and P(K). We explored the relationships between these distributions. P(ΔLk, K), P(ΔLk), and P(K|ΔLk) were calculated from the simulated distributions of P(ΔLk|K) and of P(K). The calculated distributions agreed with previous experimental and theoretical results and greatly advanced on them. Our major focus was on P(K|ΔLk), the distribution of knot types for a particular value of ΔLk, which had not been evaluated previously. We found that unknotted circular DNA is not the most probable state beyond small values of ΔLk. Highly chiral knotted DNA has a lower free energy because it has less torsional deformation. Surprisingly, even at |ΔLk| > 12, only one or two knot types dominate the P(K|ΔLk) distribution despite the huge number of knots of comparable complexity. A large fraction of the knots found belong to the small family of torus knots. The relationship between supercoiling and knotting in vivo is discussed.
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Recent reports have demonstrated beneficial effects of proinsulin C-peptide in the diabetic state, including improvements of kidney and nerve function. To examine the background to these effects, C-peptide binding to cell membranes has been studied by using fluorescence correlation spectroscopy. Measurements of ligand–membrane interactions at single-molecule detection sensitivity in 0.2-fl confocal volume elements show specific binding of fluorescently labeled C-peptide to several human cell types. Full saturation of the C-peptide binding to the cell surface is obtained at low nanomolar concentrations. Scatchard analysis of binding to renal tubular cells indicates the existence of a high-affinity binding process with Kass > 3.3 × 109 M−1. Addition of excess unlabeled C-peptide is accompanied by competitive displacement, yielding a dissociation rate constant of 4.5 × 10−4 s−1. The C-terminal pentapeptide also displaces C-peptide bound to cell membranes, indicating that the binding occurs at this segment of the ligand. Nonnative d-C-peptide and a randomly scrambled C-peptide do not compete for binding with the labeled C-peptide, nor were crossreactions observed with insulin, insulin-like growth factor (IGF)-I, IGF-II, or proinsulin. Pretreatment of cells with pertussis toxin, known to modify receptor-coupled G proteins, abolishes the binding. It is concluded that C-peptide binds to specific G protein-coupled receptors on human cell membranes, thus providing a molecular basis for its biological effects.