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B Carrasco

Publications and source records attributed to B Carrasco.

At least 19 recordsLinked to original sources
PubMed2002

Hydrodynamic properties of rigid macromolecules composed of ellipsoidal and cylindrical subunits.

A procedure is devised for the calculation of hydrodynamic properties of rigid macromolecules composed subunits that are modeled as ellipsoids of revolution and cylinders. Owing to the axial symmetry of these shapes, smooth shell models can be constructured for the subunit structure. The bead shell model so constructed is employed for the calculation of the properties. A computer program, HYDROSUB, has been written implementing both the model building and the hydrodynamic calculation. A detailed example of the use of this methodology is presented for the case of the solution properties of the human antibody molecule immunoglobulin G3 (IgG3). Finally, hints are given on other uses and applications of the procedure.

Biophysical Phenomena↗
PubMed2001

Effect of the recU suppressors sms and subA on DNA repair and homologous recombination in Bacillus subtilis.

In Bacillus subtilis, mutant alleles of the genes sms and subA partially suppress the recombination phenotype of recU cells. When present in an otherwise Rec(+) strain, Delta sms and Delta subA alleles render cells slightly sensitive to DNA-damaging agents, and impair chromosomal transformation (3- to 10-fold reduction), but do not affect plasmid transformation (less than 1.5-fold reduction). The Delta sms and Delta subA alleles were introduced into rec-deficient strains representative of the epistatic groups alpha (recF strain), beta (addA addB), gamma (recH), epsilon (recB, Delta recU and recD strains) and zeta (Delta recS). Both the Delta sms and Delta subA mutations were found to increase sensitivity to DNA-damaging agents in recF, Delta recS and addAB cells. In contrast, the Delta sms mutations decreased the sensitivity of recB, Delta recU, recD and recH cells, and the Delta subA mutation decreased the sensitivity of recB and Delta recU cells to DNA-damaging agents. Functions classified within the epistatic groups alpha, epsilon and zeta are required for intramolecular recombination, measured as plasmid transformation. The Delta sms and Delta subA mutations, which partially suppressed the recombinational repair phenotype of mutants for functions within epistatic group epsilon, enhanced plasmid transformation of recU (recB, recD) and recS cells by 10- to 20-fold. In the absence of the proteins Sms and SubA, the recombination machinery is apparently redirected towards (an) alternative pathway(s). Furthermore, the shared ability of the Delta sms and Delta subA mutations to act as indirect suppressors of recB, recU and recD mutations supports the classification of the recBUD genes within epistatic group epsilon.

Alleles↗
PubMed2001

Crystallohydrodynamics for solving the hydration problem for multi-domain proteins: open physiological conformations for human IgG.

Hydrodynamic methods provide a route for studying the low-resolution conformation--in terms of time-averaged spatial orientation of the Fab' and Fc domains relative to each other--of the human IgG subclasses, IgG1, IgG2, IgG3 and IgG4 in the environment in which many exist naturally---a solution. Representative modelling strategies are now available using 'shell-bead' or 'shell' modelling of the surface of the molecules with the size-independent programme SOLPRO [J. Garcia de la Torre, S.E. Harding, B. Carrasco, Eur. Biophys. J. 28 (1999) 119-132]. The shell model fits to the equivalent inertial surface ellipsoids of the published crystal structures for the Fab' and Fc domains of IgG are made and an apparent hydration delta(app) of 0.51g/g for Fab' and 0.70 g/g for the glycoprotein Fc are obtained, which yield an average value of (0.59+/-0.07) g/g for the intact antibody (2 Fab'+1 Fc). The relative orientations of these domains for each of the IgG subclasses is then found (using where appropriate a cylindrical hinge) from SOLPRO by modelling the Perrin function, P (i.e. 'frictional ratio due to shape') using this delta(app) and experimentally measured sedimentation coefficients. All the IgG subclasses appear as open, rather than compact structures with the degree of openness IgG3>IgG1>(IgG2, IgG4), with IgG3 and IgG1 non-coplanar. The hingeless mutant IgGMcg, with s degrees (20,w) approximately 6.8 S yields a coplanar structure rather similar to IgG2 and IgG4 and consistent with its crystallographic structure. The extension of this procedure for representing solution conformations of other antibody classes and other multi-domain proteins is indicated.

Crystallography, X-Ray↗
PubMed2001

The conformation of serum albumin in solution: a combined phosphorescence depolarization-hydrodynamic modeling study.

There is a striking disparity between the heart-shaped structure of human serum albumin (HSA) observed in single crystals and the elongated ellipsoid model used for decades to interpret the protein solution hydrodynamics at neutral pH. These two contrasting views could be reconciled if the protein were flexible enough to change its conformation in solution from that found in the crystal. To investigate this possibility we recorded the rotational motions in real time of an erythrosin-bovine serum albumin complex (Er-BSA) over an extended time range, using phosphorescence depolarization techniques. These measurements are consistent with the absence of independent motions of large protein segments in solution, in the time range from nanoseconds to fractions of milliseconds, and give a single rotational correlation time phi(BSA, 1 cP, 20 degrees C) = 40 +/- 2 ns. In addition, we report a detailed analysis of the protein hydrodynamics based on two bead-modeling methods. In the first, BSA was modeled as a triangular prismatic shell with optimized dimensions of 84 x 84 x 84 x 31.5 A, whereas in the second, the atomic-level structure of HSA obtained from crystallographic data was used to build a much more refined rough-shell model. In both cases, the predicted and experimental rotational diffusion rate and other hydrodynamic parameters were in good agreement. Therefore, the overall conformation in neutral solution of BSA, as of HSA, should be rigid, in the sense indicated above, and very similar to the heart-shaped structure observed in HSA crystals.

Animals↗
PubMed2001

Genetic recombination in Bacillus subtilis 168: effect of DeltahelD on DNA repair and homologous recombination.

The B. subtilis DeltahelD allele rendered cells proficient in transformational recombination and moderately sensitive to methyl methanesulfonate when present in an otherwise Rec(+) strain. The DeltahelD allele was introduced into rec-deficient strains representative of the alpha (recF strain), beta (addA addB), gamma (recH), epsilon (DeltarecU), and zeta (DeltarecS) epistatic groups. The DeltahelD mutation increased the sensitivity to DNA-damaging agents of addAB, DeltarecU, and DeltarecS cells, did not affect the survival of recH cells, and decreased the sensitivity of recF cells. DeltahelD also partially suppressed the DNA repair phenotype of other mutations classified within the alpha epistatic group, namely the recL, DeltarecO, and recR mutations. The DeltahelD allele marginally reduced plasmid transformation (three- to sevenfold) of mutations classified within the alpha, beta, and gamma epistatic groups. Altogether, these data indicate that the loss of helicase IV might stabilize recombination repair intermediates formed in the absence of recFLOR and render recFLOR, addAB, and recH cells impaired in plasmid transformation.

Adenosine Triphosphatases↗
PubMed2001

[Progressive diffuse subretinal fibrosis syndrome: a case report].

CASE REPORT: The case of a 63 year old woman presenting fibrous subretinal lesions in the posterior pole on a routine ocular fundus check up is reported. The angiographic study showed a choroidal origin window defect next to hypofluorescence areas. The patient did not complain of vision loss or scotomas at any time. DISCUSSION: This clinical picture could be classified as a progressive subretinal fibrosis syndrome with atypical features. However, a differential diagnosis with other choroidal inflammatory conditions should be carried out even though many authors may consider them as different developmental phases of the same entity.

Choroiditis↗
PubMed2001

[Acute macular neuroretinopathy: a case report].

CASE REPORT: A 68 year old woman developed a sudden decrease in her visual acuity in both eyes with several central scotomas. Funduscopy demonstrated a motted alteration of the retinal pigment epithelium in both maculae. The fluorescein angiography showed a choroidal ischemia at the macular level in both eyes. DISCUSSION: The patient was diagnosed of acute macular neuroretinopathy. This entity is included among the so-called < >. However, it is important to determine which of these diseases each patient suffers in order to determine if treatment is necessary, the visual prognosis and the possibility of recurrences.

Acute Disease↗
PubMed2000

HYDRONMR: prediction of NMR relaxation of globular proteins from atomic-level structures and hydrodynamic calculations.

The heteronuclear NMR relaxation of globular proteins depends on the anisotropic rotational diffusion tensor. Using our previous developments for prediction of hydrodynamic properties of arbitrarily shaped particles, by means of bead models, we have constructed a computational procedure to calculate the rotational diffusion tensor and other properties of proteins from their detailed, atomic-level structure. From the atomic coordinates file used to build the bead model, the orientation of the pertinent dipoles can be extracted and combined with the hydrodynamic information to predict, for each residue in the protein, the relaxation times. All of these developments have been implemented in a computer program, HYDRONMR, which will be of public domain.

Algorithms↗
PubMed2000

Calculation of hydrodynamic properties of globular proteins from their atomic-level structure.

The solution properties, including hydrodynamic quantities and the radius of gyration, of globular proteins are calculated from their detailed, atomic-level structure, using bead-modeling methodologies described in our previous article (, Biophys. J. 76:3044-3057). We review how this goal has been pursued by other authors in the past. Our procedure starts from a list of atomic coordinates, from which we build a primary hydrodynamic model by replacing nonhydrogen atoms with spherical elements of some fixed radius. The resulting particle, consisting of overlapping spheres, is in turn represented by a shell model treated as described in our previous work. We have applied this procedure to a set of 13 proteins. For each protein, the atomic element radius is adjusted, to fit all of the hydrodynamic properties, taking values close to 3 A, with deviations that fall within the error of experimental data. Some differences are found in the atomic element radius found for each protein, which can be explained in terms of protein hydration. A computational shortcut makes the procedure feasible, even in personal computers. All of the model-building and calculations are carried out with a HYDROPRO public-domain computer program.

Computer Simulation↗
PubMed1999

Calculation of NMR relaxation, covolume, and scattering-related properties of bead models using the SOLPRO computer program.

The hydrodynamic properties of macromolecules and bioparticles, represented by bead models, can be calculated using methods implemented in the computer routine HYDRO. Recently, a new computer routine, SOLPRO, has been presented for the calculation of various SOLution PROperties. These include (1) time-dependent electro-optic and spectroscopic properties related to rotational diffusion, (2) non-dynamic properties like scattering curves, and (3) dimensionless quantities that combine two or more solution properties in a form which depends on the shape of the macromolecule but not on its size. In the present work we describe the inclusion of more of those types of properties in a new version of SOLPRO. Particularly, we describe the calculation of relaxation rates in nuclear magnetic resonance (NMR). For dipolar coupling, given the direction of the dipole the program calculates values of the spectral density, from which the NMR relaxation times can be obtained. We also consider scattering-related properties, namely the distribution of distances for the bead model, which is directly related to the angular dependence of scattered intensity, and the particle's longest distance. We have devised and programmed a procedure to calculate the covolume of the bead model, related to the second virial coefficient and, in general, to the concentration dependence of solution properties. Various shape-dependent dimensionless quantities involving the covolume are calculated. In this paper we also discuss some aspects, namely bead overlapping and hydration, that are not explicitly included in SOLPRO, but should be considered by the user.

Mathematical Computing↗
PubMed1999

Calculation of hydrodynamic properties of macromolecular bead models with overlapping spheres.

For the calculation of hydrodynamic properties of rigid macromolecules using bead modelling, models with overlapping beads of different sizes are used in some applications. The hydrodynamic interaction tensor between unequal overlapping beads is unknown, and an oversimplified treatment with the Oseen tensor may introduce important errors. Here we discuss some aspects of the overlapping problem, and explore an ad hoc form of the interaction tensor, proposed by Zipper and Durchschlag. We carry out a systematic numerical study of the hydrodynamic properties of a two-spheres model, showing how the Zipper-Durchschlag correction removes efficiently the numerical instabilities, and predicts the correct limits.

Biophysical Phenomena↗
PubMed1999

Novel size-independent modeling of the dilute solution conformation of the immunoglobulin IgG Fab' domain using SOLPRO and ELLIPS.

The proliferation of hydrodynamic modeling strategies to represent the shape of quasirigid macromolecules in solution has been hampered by ambiguities caused by size. Universal shape parameters, independent of size, developed originally for ellipsoid modeling, are now available for modeling using the bead-shell approximation via the algorithm SOLPRO. This paper validates such a "size-independent" bead-shell approach by comparison with the exact hydrodynamics of 1) an ellipsoid of revolution and 2) a general triaxial ellipsoid (semiaxial ratios a/b, b/c) based on a fit using the routine ELLIPSE (. J. Mol. Graph. 1:30-38) to the chimeric (human/mouse) IgG Fab' B72.3; a similar fit is obtained for other Fabs. Size-independent application of the bead-shell approximation yields errors of only approximately 1% in frictional ratio based shape functions and approximately 3% in the radius of gyration. With the viscosity increment, errors have been reduced to approximately 3%, representing a significant improvement on earlier procedures. Combination of the Perrin frictional ratio function with the experimentally measured sedimentation coefficient for the same Fab' from B72.3 yields an estimate for the molecular hydration of the Fab' fragment of approximately (0.43 +/- 0.07) g/g. This value is compared to values obtained in a similar way for deoxyhemoglobin (0.44) and ribonuclease (0.27). The application of SOLPRO to the shape analysis of more complex macromolecules is indicated, and we encourage such size-independent strategies. The utility of modern sedimentation data analysis software such as SVEDBERG, DCDT, LAMM, and MSTAR is also clearly demonstrated.

Algorithms↗
PubMed1999

Hydrodynamic properties of rigid particles: comparison of different modeling and computational procedures.

The hydrodynamic properties of rigid particles are calculated from models composed of spherical elements (beads) using theories developed by Kirkwood, Bloomfield, and their coworkers. Bead models have usually been built in such a way that the beads fill the volume occupied by the particles. Sometimes the beads are few and of varying sizes (bead models in the strict sense), and other times there are many small beads (filling models). Because hydrodynamic friction takes place at the molecular surface, another possibility is to use shell models, as originally proposed by Bloomfield. In this work, we have developed procedures to build models of the various kinds, and we describe the theory and methods for calculating their hydrodynamic properties, including approximate methods that may be needed to treat models with a very large number of elements. By combining the various possibilities of model building and hydrodynamic calculation, several strategies can be designed. We have made a quantitative comparison of the performance of the various strategies by applying them to some test cases, for which the properties are known a priori. We provide guidelines and computational tools for bead modeling.

Biophysical Phenomena↗
PubMed1998

Bead modeling using HYDRO and SOLPRO of the conformation of multisubunit proteins: sunflower and rape-seed 11S globulins.

Oil seed globulins from sunflower and rape seed are multi-subunit, oligomeric proteins whose native 11S form is a hexamer. In this work we try to determine the spatial structure in which the six subunits of 11S globulin are arranged. Experimental values of solution properties, including radius of gyration, sedimentation and diffusion coefficients and intrinsic viscosity, are compared with theoretical predictions for hexamers of various geometries. Bead model calculations of solution properties are carried out using the HYDRO and SOLPRO computer programs. A most compact shape, the regular octahedron, is the hexameric structure that fits best the experimental values.

Journal Article↗
PubMed1998

[Serum lipids and blood pressure levels in the +Mapuche population living in the Chilean region of Araucanía].

BACKGROUND: Chilean aboriginal populations (Mapuche) predominantly live in the region of Araucanía, in the southern part of the country. Their cardiovascular risk factors have not been systematically assessed. AIM: To study the prevalence of cardiovascular risk factors in the Mapuche population. SUBJECTS AND METHODS: Blood pressure, weight, height, dietary habits, fasting serum total cholesterol, HDL cholesterol and triglycerides were measured in 1.948 adults living in 28 Mapuche communities. RESULTS: Thirteen percent of males and 16% of females had high blood pressure. Body mass index was 25.5 kg/m2 in males and 28.1 kg/m2 in females. Forty five percent of women and 24% of men were classified as obese. Mean serum total cholesterol was 186.7 +/- 9.6 mg/dl, HDL cholesterol was 58.7 +/- 30.7 mg/dl, total cholesterol/HDL cholesterol was 3.4 +/- 2 and triglycerides were 155.2 +/- 91.2 mg/dl. Twenty eight percent of males and 9.6% of females smoked. CONCLUSIONS: Mapuche individuals have higher levels of HDL cholesterol a better total cholesterol/HDL cholesterol ratio and lower frequency of smoking than non aboriginal Chileans subjects.

Adult↗