A statistical model for predicting protein folding rates from amino acid sequence with structural class information

Prediction of protein folding rates from amino acid sequences is one of the most important challenges in molecular biology. In this work, I have related the protein folding rates with physical-chemical, energetic and conformational properties of amino acid residues. I found that the classification of proteins into different structural classes shows an excellent correlation between amino acid properties and folding rates of two- and three-state proteins, indicating the importance of native state topology in determining the protein folding rates. I have formulated a simple linear regression model for predicting the protein folding rates from amino acid sequences along with structural class information and obtained an excellent agreement between predicted and experimentally observed folding rates of proteins; the correlation coefficients are 0.99, 0.96 and 0.95, respectively, for all-alpha, all-beta and mixed class proteins. This is the first available method, which is capable of predicting the protein folding rates just from the amino acid sequence with the aid of generic amino acid properties and structural class information.     

A statistical method for predicting protein unfolding rates from amino acid sequence

The prediction of protein unfolding rates from amino acid sequences is one of the most important challenges in computational biology and chemistry. The analysis on the relationship between protein unfolding rates and physical-chemical, energetic, and conformational properties of amino acid residues provides valuable information to understand and predict the unfolding rates of two- and three-state proteins. We found that the classification of proteins into different structural classes shows an excellent correlation between amino acid properties and unfolding rates of two- and three-state proteins, indicating the importance of native-state topology in determining the protein unfolding rates. We have formulated three independent linear regression equations to different structural classes of proteins for predicting their unfolding rates from amino acid sequences and obtained an excellent agreement between predicted and experimentally observed unfolding rates of proteins; the correlation coefficients are 0.999, 0.990, and 0.992, respectively, for all-alpha, all-beta, and mixed-class proteins. Further, we have derived a general equation applicable to all structural classes of proteins, which can be used for predicting the unfolding rates for proteins of an unknown structural class. We observed a correlation of 0.987 and 0.930, respectively, for back-check and jack-knife tests. These accuracy levels are better than those of other methods in the literature.     

Extraction of information attributes from the mass spectrometric signals of air

The paper describes a new method of the extraction of information attributes from the processed signals, generalized spectral analysis in an adapted basis. Studies of the functional structure of mathematical foundations and an adaptable classification system of different signal types, including the quadrupole mass spectra of air, were carried out. Algorithms for the synthesis of basis functions adapted to orthogonal transforms of process signals were developed. The use of the method for analytical instrumentation was demonstrated by the processing of mass spectra recorded on a quadrupole mass spectrometer in the analysis of gases exhaled by humans.     

A mass spectrometric study of the pyrolysis of gibberellic acid

The behaviour of gibberellic acid (GA₃) under electron impact and chemical ionization conditions has been examined. The tendency of GA₃ to undergo pyrolysis by the loss of the elements of water and carbon dioxide has been identified. Two methods of sample introduction can be used to minimize the occurrence of this pyrolysis. Accurate mass measurement allows the composition of the pyrolysis product to be determined and metastable techniques confirm the structure of this product to be epi-allogibberic acid rather than its isomer allogibberic acid. This result corrects a misconception in the literature and illustrates the advantage of metastable methods compared with accurate mass measurements, for the determination of small structural differences within a molecule.     

omega-(Bis(trifluoromethyl)amino)alkane-1-sulfonates: synthesis and mass spectrometric study of the biotransformation products

In search of fluorinated functional groups which could undergo defluorination, and therefore be included in novel non-polluting fluorinated surfactants, omega-(bis(trifluoromethyl)amino)alkane-1-sulfonates (BTFMA-AS) with a homologue distribution from seven to thirteen methylene groups were synthesized and investigated for aerobic biodegradation applying both a standardized test and a fixed-bed bioreactor (FBBR). These compounds were prepared as part of a screening study for potentially mineralizable fluorinated endgroups.Application of hybrid triple quadrupole-linear ion trap mass spectrometry (QqQ(LIT)-MS) coupled to high-performance liquid chromatography (HPLC) allowed the tracking of primary degradation as well as the detection and structural elucidation of biotransformation intermediates. An understanding of the fragmentation pathway of the test compounds allowed selective precursor ion scans to reveal the presence of stable fluorinated metabolites. Structures were confirmed by enhanced product ion scans and MS(3) scans in the linear ion trap mode.The primary biodegradation rate and the extent of biodegradation were found to be chain-length dependent, with higher homologues being completely primarily degraded within 10 days. For the first time, two simultaneous metabolic pathways for substituted linear alkane-1-sulfonates were discovered: Desulfonation, oxidation to a carboxylic acid and subsequent chain-length shortening by beta-oxidation dominated the metabolism. This pathway resulted in the formation of 3-(bis(trifluoromethyl)amino)propionic acid and bis(trifluoromethyl)aminoacetic acid, which showed recalcitrance in this experiment. Oxidation of the alkyl chain to the respective carbonyl derivative represents the minor pathway. Only the long-chain homologues of these oxidized species were partially degraded; the short-chain homologues were not attacked.     

Design of amino acid sequences to fold into C(alpha)-model proteins

In order to extend the results obtained with minimal lattice models to more realistic systems, we study a model where proteins are described as a chain of 20 kinds of structureless amino acids moving in a continuum space and interacting through a contact potential controlled by a 20x20 quenched random matrix. The goal of the present work is to design and characterize amino acid sequences folding to the SH3 conformation, a 60-residue recognition domain common to many regulatory proteins. We show that a number of sequences can fold, starting from a random conformation, to within a distance root-mean-square deviation between 2.6 and 4.0 A from the native state. Good folders are those sequences displaying in the native conformation an energy lower than a sequence-independent threshold energy.     

A computer program for activation analysis

A computer program for calculating activation analysis results is described. The program comprises two gamma spectrum analysis programs, STOAV and SAMPO and one program for calculating elemental concentrations, KVANT. STOAV is based on a simple summation of channels and SAMPO is based on fitting of mathematical functions. The programs are tested by analyzing the IAEA G-1 test spectra. In the determination of peak location SAMPO is somewhat better than STOAV and in the determination of peak area SAMPO is more than twice as accurate as STOAV. On the other hand, SAMPO is three times as expensive to use with a Cyber 170 computer as STOAV.     

A computer program for calculating Ge(Li) detector counting efficiencies for Marinelli beakers

A novel computing method has been developed to calculate the absolute photopeak efficiency of a Ge(Li) detector for Marinelli beakers of different heights and diameters and with variable density. For each point in the cylindrical sample the detection efficiency is calculated taking into account the distance from the detector and gamma-ray attenuation and the efficiency is integrated numerically over the volume of the sample. The detector is approximated as a point detector with an experimentally determined effective interaction depth. It is necessary to measure the absolute efficiency for a point source located on the detector axis and on a line beside the detector parallel to the axis. The computer program calculates the absolute counting efficiency for Marinelli beakers of any geometry and for any density. The measured and calculated values for three different densities give a good (–2.2%) overall agreement.     

Extraction of amino acid (L-aspartic acid) from aqueous stream using trioctylamine

L-aspartic acid is an α-amino acid that is primarily used in protein biosynthesis. It can be manufactured via protein extraction, chemical synthesis, fermentation, and enzymatic processes. L-aspartic acid separation from protein hydrolysates, fermentation broths, and aqueous streams are rather difficult. In the current study, trioctylamine (TOA) is used as an extractant in a variety of solvents, including 1-octanol, 1-decanol, and cyclohexane, to extract aspartic acid from aqueous solutions. Different parameters, including the distribution coefficient, loading ratio, extraction efficiency, and number of stages, were used to explain the results. The maximum extraction efficiencies were found to be 86.25%, 67.25%, and 58.50% with 1-octanol, 1-decanol, and cyclohexane by trioctylamine, respectively.     

A new reversed-phase liquid chromatographic/tandem mass spectrometric method for analysis of underivatised amino acids: evaluation for the diagnosis and the management of inherited disorders of amino acid metabolism

Seventy-six compounds of biological interest for the diagnosis of inherited disorders of amino acids (AA) metabolism have previously been demonstrated to be detectable in positive mode electrospray ionisation tandem mass spectrometry (ESI-MS/MS), after separation by ion-pairing reversed-phase liquid chromatography (RPLC). The separation method used tridecafluoroheptanoic acid as ion-pairing agent, and a gradient of acetonitrile for the elution of the most retained compounds. This method had previously been demonstrated to be suitable for the qualitative diagnosis of many AA disorders, and for the quantitative measurement of 16 AA in biological fluids, using their stable isotope labelled (SIL) AA as internal standard. For quantification of the other AA, an internal standard was chosen among the available SIL-AA, as close as possible to the analyte to be measured, in terms of structural analogy, and of retention time in the chromatographic system. The performances of the quantitative analysis of the other AA to be measured are reported here. They show validated results for several AA, allowing their accurate quantification, with another SIL-AA as internal standard. For some other AA, quantitative results were not accurate, allowing only semi-quantitative or qualitative determination for these parameters.     

A multilayer poly(dimethylsiloxane) electrospray ionization emitter for sample injection and online mass spectrometric detection

An ESI emitter made of poly(dimethylsiloxane) interfaces on-chip sample preparation with MS detection. The unique multilayer design allows both the analyte and the spray solutions to reside on the device simultaneously in discrete microfluidic environments that are spatially separated by a polycarbonate track-etched, nanocapillary array membrane (NCAM). In direct spray mode, voltage is applied to the microchannel containing a spray solution delivered via a syringe pump. For injection, the spray potential is lowered and a voltage is applied that forward biases the membrane and permits the analyte to enter the spray channel. Once the injection is complete, the bias potential is switched off, and the spray voltage is increased to generate the ESI of the injected analyte plug. Consecutive injections of a 10 microM bovine insulin solution are reproducible and produce sample plugs with limited band broadening and high quality mass spectra. Peptide signals are observed following transport through the NCAM, even when the peptide is dissolved in solutions containing up to 20% seawater. The multilayer emitter shows great potential for performing multidimensional chemical manipulations on-chip, followed by direct ESI with negligible dead volume for online MS analysis.     

Chromatographic and mass spectrometric methods for determination of lysergic acid diethylamide (LSD) and metabolites in body fluids.

Continued illicit use of the potent psychedelic drug lysergic acid diethylamide (LSD) has stimulated efforts to develop effective analytical methods for detection of the drug and its metabolites in body fluids from suspected LSD users. Recently reported methods based on gas and liquid chromatography, combined with single- and multiple-stage mass spectral analysis, now permit accurate detection and quantitation of LSD at sub-nanogram/milliliter concentrations.