DOMIRE: a web server for identifying structural domains and their neighbors in proteins.

Summary: The DOMIRE web server implements a novel, automatic, protein structural domain assignment procedure based on 3D substructures of the query protein which are also found within structures of a non-redundant protein database. These common 3D substructures are transformed into a co-occurrence matrix that offers a global view of the protein domain organization. Three different algorithms are employed to define structural domain boundaries from this co-occurrence matrix.

The ability of actinic light to modify the bacteriorhodopsin photocycle revisited: heterogeneity vs photocooperativity.

In 1995, evidence both for photocooperativity and for heterogeneity as possible explanations for the ability of actinic light to modify the kinetics and pathways of the bacteriorhodopsin (BR) photocycle was reviewed ( Shrager, R. I., Hendler, R.

Diffusion delays and unstirred layer effects at monolayer cultures of Chinese hamster ovary cells: radioligand binding, confocal microscopy, and mathematical simulations.

Cells grown in monolayer culture offer a convenient system for binding and other experiments under conditions that preserve the complexity of the living state. Kinetics experiments, however, may be distorted by the time course of drug penetration into even so simple a "tissue" as the monolayer. The impediments include unstirred layers both above and between the cells, the congregation of receptors within the confined space between cells, and nonspecific binding to membrane components.

Theory and procedures for finding a correct kinetic model for the bacteriorhodopsin photocycle.

In this paper, we present the implementation and results of new methodology based on linear algebra. The theory behind these methods is covered in detail in the Supporting Information, available electronically (Shragerand Hendler). In brief, the methods presented search through all possible forward sequential submodels in order to find candidates that can be used to construct a complete model for the BR-photocycle.

Optimal time spacings for T2 measurements: monoexponential and biexponential systems.

We have developed an optimal design strategy, i.e. a choice of times at which the magnetization should be measured, in spin-echo measurements, when the number of measurements is fixed in advance.

O2-binding to fully reduced cytochrome aa3 reexamined using SVD analysis of simulated and real data.

Using new time-resolved multichannel experimental and simulated data, analyzed by SVD, it is concluded that the second order binding rate constant for O2-binding to fully reduced mammalian cytochrome aa3 is approximately five times higher than the currently accepted value of approximately 1.5 x 10(8) M-1 s-1.

Some pitfalls in curve-fitting and how to avoid them: a case in point.

When curve-fitting is used to support a complex nonlinear model containing several exponential terms, some of which have closely-spaced time constants, a particular burden of proof must be assumed. Most important, the uniqueness of the solution must be explored and discussed. Statistical tests for the degree of error and independence of the parameters should be provided, as well as information relating to the steps actually used in the fitting procedures.

Anisotropically weighted MRI.

The intensity of an isotropically weighted MR image is proportional to a rotationally invariant measure of bulk diffusion, Trace(D) (where D is the effective diffusion tensor). Such images can be acquired from as few as two diffusion-weighted images (DWIs). Analogously, the intensity of an anisotropically weighted MR image is proportional to a rotationally invariant measure of diffusion anisotropy derived from D, such as the variance of the principal diffusivities of D.

Multichannel analysis of single-turnover kinetics of cytochrome aa3 reduction of O2.

The single-turnover kinetics of the oxidation of cytochrome aa3 by O2 have been studied using a new approach. Up to 1000 whole spectra covering both the Soret and alpha regions were sequentially collected at room temperature from single samples with a time resolution of 10 microns. All of the spectral and time information were used in analyses based on singular value decomposition.

HIV-1 infection kinetics in tissue cultures.

Despite intensive experimental work on HIV-1, very little theoretical work has focused on HIV-1 spread in tissue culture. This article uses two systems of ordinary differential equations to model two modes of viral spread, cell-free virus and cell-to-cell contact. The two models produce remarkably similar qualitative results.

KINFIT II: a nonlinear least-squares program for analysis of kinetic binding data.

We describe a versatile computer program for least-squares fitting of ligand/receptor association and dissociation curves from several experiments simultaneously. The program is designed to handle any number of classes of binding sites reacting with a single ligand that may have two forms: labeled and unlabeled. For a single class of binding sites, the exact, analytical solution is used to generate the computed curves.

The ability of actinic light to modify the bacteriorhodopsin photocycle. Heterogeneity and/or photocooperativity?

The focus of this paper is on the established observation that the bacteriorhodopsin (BR) photocycle responds to the level of actinic light by altering the proportions of two forms of the M intermediate. The first form of M, called M-fast or MF, decays to the O intermediate. In contrast, the second form of M, called M-slow or MS, decays directly to the ground state, and its decay rate is slower than that of MF.

Exact conditional distribution of a three-phase invariant in space group P1. IV. Further improvements of Cochran-like approximations.

A new approximate method of computing the conditional probability density function (c.p.d.

Influence of excitation energy on the bacteriorhodopsin photocycle.

Kinetic curves for the bacteriorhodopsin (BR) photocycle were obtained both at 570 and at 412 nm at a series of increasing levels of intensity of the exciting laser. Singular value decomposition (SVD) of these curves showed two transitions in the kinetic profiles that occurred at specific levels of actinic light. This means that the photocycle was influenced by photon density in two ways.

Deconvolutions based on singular value decomposition and the pseudoinverse: a guide for beginners.

Singular value decomposition (SVD) is deeply rooted in the theory of linear algebra, and because of this is not readily understood by a large group of researchers who could profit from its application. In this paper, we discuss the subject on a level that should be understandable to scientists who are not well versed in linear algebra. However, because it is necessary that certain key concepts in linear algebra be appreciated in order to comprehend what is accomplished by SVD, we present the section, 'Bare basics of linear algebra'.

Multiwavelength analysis of the kinetics of reduction of cytochrome aa3 by cytochrome c.

Some new approaches to the kinetic study of the reduction of cytochrome aa3 by cytochrome c are presented. The primary innovations are the use of a spectrometer which can acquire multiwavelength data as fast as every 10 microseconds, and the application of a variety of analytical methods which can utilize simultaneously all of the time-resolved spectral data. These techniques include singular value decomposition (SVD), deconvolutions based on pure Gaussian models for absorption peaks, deconvolutions based on isolated absorption spectra for the pure components, and simulations of SVD-deduced and actual experimental difference spectra.

Reversal of caldesmon binding to myosin with calcium-calmodulin or by phosphorylating caldesmon.

Caldesmon, an actin-binding protein from smooth muscle and non-muscle cells, has previously been shown to bind stoichiometrically to smooth muscle myosin in an ATP-dependent manner. We now show quantitatively the effects of Ca(2+)-calmodulin and phosphorylation on the binding of caldesmon to myosin. Ca(2+)-calmodulin reduces the binding of caldesmon to myosin with the same effectiveness as it does the binding of caldesmon to actin.

Mechanism of the oxidation reaction of deoxyhemoglobin as studied by isolation of the intermediates suggests tertiary structure dependent cooperativity.

The intermediates in the oxidation of deoxyhemoglobin by ferricyanide in 0.1 M KCl, at 20 degrees C and three pH values, were studied by cryogenic techniques. Data analysis was carried out according to a simple four rate constant model, ignoring the functional heterogeneity of the subunits, to simulate the time courses of the oxidation reaction, as studied by the stopped-flow technique [Antonini et al.

Analytic models for nonlinear curve-fitting of forward-rate binding data, with applications to hemoglobin.

The experimental procedure of Perrella et al. (1983, J. Biol.

An investigation of the thermal unfolding of swine pepsinogen using circular dichroism.

The thermal unfolding of swine pepsinogen is investigated using circular dichroism (CD) in the pH range 6-9. CD spectra and single wavelength melting curves are analyzed to show the presence of two resolvable transitions. Analysis of difference CD spectra by the method of singular value decomposition indicates that the changes in conformation are distinct in the two transitions.

A kinetic model of CD4+ lymphocytes with the human immunodeficiency virus (HIV).

This report describes a kinetic model of in vitro cytopathology involving interactions of human immunodeficiency virus (HIV) with CD4+ helper T lymphocytes. The model uses nonlinearly coupled, ordinary differential equations to simulate the dynamics of infected and uninfected cells and free virions. It is assumed that resting cells are more readily infected than activated cells, but once infected, only activated cells produce more virus.

Phenobarbital does not increase early labeling of bilirubin from 4-[14C]-delta-aminolevulinic acid in man and rat.

delta-Aminolevulinic acid-4-[14C] and [3H]-bilirubin were administered intravenously to five patients with Gilbert's syndrome and four healthy control subjects on two occasions: before and on days 10 through 14 of a course of phenobarbital (2.5 mg/kg/day). The resulting curves of [3H]-bilirubin and [14C]-bilirubin in plasma were analyzed by computer to determine a number of parameters of physiological interest.