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PubMed1998

Synthesis, Magnetic Properties, and Incomplete Double-Cubane Structure of Manganese(III)-Metal(II) Complexes [Mn(MeOH)L(OH)M(bpy)](2) (M = Zn, Cu, Ni, and Mn; H(4)L = 1,2-Bis(2-hydroxybenzamido)benzene; bpy = 2,2'-Bipyridine).

The manganese(III) complex K[MnL(py)(2)].py (H(4)L = 1,2-bis(2-hydroxybenzamido)benzene, py = pyridine) reacted as a ligand complex at the two phenoxo oxygen atoms with metal(II) ion and 2,2'-bipyridine to give a series of heterometal complexes [Mn(MeOH)L(OH)M(bpy)](2) (M(II) = Zn (1); Cu (2); Ni (3); Mn (4)). X-ray structures were determined 1, C(68)H(74)N(8)O(18)Mn(2)Zn(2): a = 12.367(3) Å, b = 12.844(2) Å, c = 12.262(2) Å, alpha = 106.58(1) degrees, beta = 117.89(1) degrees, gamma = 78.57(2) degrees, triclinic, P&onemacr;, and Z = 1. 2, C(68)H(74)N(8)O(18)Mn(2)Cu(2): a = 13.447(1) Å, b = 12.670(2) Å, c = 21.732(1) Å, beta = 107.076(5) degrees, monoclinic, P2(1)/n, and Z =2. 3, C(68)H(74)N(8)O(18)Mn(2)Ni(2): a = 12.358(3) Å, b = 12.847(3) Å, c = 12.315(3) Å, alpha = 106.63(2) degrees, beta = 118.71(1) degrees, gamma = 78.32(2) degrees, triclinic, P&onemacr;, and Z = 1. 4, C(66)H(66)N(8)O(16)Mn(4): a = 12.511(2) Å, b = 21.129(3) Å, c = 12.811(1) Å, beta = 110.12(1) degrees, monoclinic, P2(1)/n, and Z = 2. The X-ray analyses confirmed that each of the crystals consists of an incomplete double-cubane molecule with a [Mn(2)M(2)O(6)] core, in which two M(II) ions are bridged by two hydroxo groups to form a planar dinuclear moiety bridged by di-&mgr;-hydroxo groups [(bpy)M(OH)(2)M(bpy)](2+) and the dinuclear moiety is sandwiched between two Mn(III) complexes [Mn(MeOH)L](-). The Mn(III) ion and the dinuclear M(II) moiety are triply bridged by the one hydroxo oxygen of the dinuclear moiety and two phenoxo oxygen atoms of the Mn(III) ligand complex. The two phenoxo oxygen atoms of the Mn(III) ligand complex coordinate as an axial ligand to two independent metal(II) ions of the dinuclear moiety. The magnetic susceptibilities of 1-4 were measured in the temperature range of 2-300 K. All the Mn(III) ions in these complexes are in a high-spin state of S(Mn) = 2 with a d(4) electronic configuration, and the metal(II) ions are in the spin states of S(Zn) = 0, S(Cu) = 1/2, S(Ni) = 1, and S(Mn(II)) = 1/2 (low-spin). The magnetic susceptibility data are well reproduced by the following spin Hamiltonian based on the rhombus spin coupling model with spin (S(1), S(2), S(3), S(4)) = (2, S(M), 2, S(M)), including a zero-field splitting term for the Mn(III) centers: H = g(Mn)beta(S(1) + S(3)).H + g(M)beta(S(2) + S(4)).H - 2J(S(1).S(2) + S(2).S(3) + S(3).S(4) + S(4).S(1)) - 2J'(S(2).S(4)) + D(Mn)[S(1z)(2) + S(3z)(2)], in which g(Mn) and g(M) are the g factors of the Mn(III) and M(II) ions, J and J' are the Mn(III)-M(II) and M(II)-M(II) Heisenberg coupling constants, and D is the zero-field splitting parameter of Mn(III). The calculated best-fit parameters are as follows: g(Mn) = 1.91, g(Cu) = 2.39, J = -4.5 cm(-)(1), J' = -8.1 cm(-)(1), and D(Mn) = -4.9 cm(-)(1) for 2; g(Mn) = 1.97, g(Ni) = 2.23, J = -1.5 cm(-)(1), J' = -2.6 cm(-)(1), and D(Mn) = -5.5 cm(-)(1) for 3; and g(Mn) =1.95, g(Mn(II)) = 2.29, J = -3.5 cm(-)(1), J' = -14.1 cm(-)(1), and D(Mn) = -12.0 cm(-)(1) for 4. The spin frustration due to the incomplete double-cubane structure is discussed.

Journal Article↗

PubMed1988

Mass spectrometric evaluation of synthetic peptides for deletions and insertions.

A new technique to evaluate methods for the synthesis of peptides was developed. It is based on the identification and quantitation of peptide by-products by mass spectrometry. Model oligopeptides containing 10 or 20 alanine residues were synthesized by automated solid phase methods using a variety of protocols, and the levels of deletion and insertion peptides were measured by the 252Cf fission fragment ionization time-of-flight spectrometric technique in which the total, unfractionated, synthetic product was deposited on a film of nitrocellulose and analyzed. The introduction of D-alanine at every third residue of the model eliminated peptide conformation problems that led to incomplete reactions in the all L model. Couplings with preformed symmetrical anhydrides in dimethylformamide gave rise to significant levels of both deletion peptides and insertion peptides. The best of the protocols examined was a double coupling of tert-butyloxycarbonyl-alanine by in situ activation with dicyclohexylcarbodiimide in dichloromethane. [D-Ala3,6,9,12,15,18]Ala20-Val was synthesized with an average deletion of only 0.036% per step and an average insertion of only 0.029% per step, which is equivalent to a stepwise yield of 99.93% for the target peptide.

Amino Acids↗

PubMedDate not supplied

Immobilization of pectin fragments on solid supports: novel coupling by thiazolidine formation.

As a prerequisite to solid-phase and sequence analyses and for the study of the fine structure of pectin, we have developed oriented and chemoselective methodologies to couple model pectin fragments onto a solid support. Polyethylene glycol polyacrylamide (PEGA) resins were selected due to their excellent swelling properties in a wide range of solvents, including water, and their easy accessibility to enzymes. Following appropriate derivatization of amino-terminated PEGA resins, oligomers of alpha-D-galacturonic acid (GalA), up to the trimer, were anchored to the support through their reducing end. In addition to reductive amination, the strategies included the formation of an oxime bond, a glycosyl hydrazide, and a pyroglutamyl ring. Further, we developed a new immobilization approach based on the formation of a thiazolidine ring. All methods proved efficient and did not require modification of the GalA oligomers prior to coupling. In addition, very mild conditions and few steps for derivatization of the support were required. Immobilization by thiazolidine ring and oxime bond formation were the preferred methods, given the stability of the linkages formed, their compatibility with aqueous solvents, the few number of steps required, and their potential for application to larger pectin fragments. Thiazolidine and pyroglutamyl anchoring were developed further by the insertion of a disulfide bond which allowed release of the saccharides under mild, selective conditions.

Acrylic Resins↗

PubMed2006

MAGOS: multiple alignment and modelling server.

UNLABELLED: MAGOS is a web server allowing automated protein modelling coupled to the creation of a hierarchical and annotated multiple alignment of complete sequences. MAGOS is designed for an interactive approach of structural information within the framework of the evolutionary relevance of mined and predicted sequence information. AVAILABILITY: The web server is freely available at http://pig-pbil.ibcp.fr/magos.

Algorithms↗

PubMed2004

Predicting GPCR-G-protein coupling using hidden Markov models.

MOTIVATION: Determining the coupling specificity of G-protein coupled receptors (GPCRs) is important for understanding the biology of this class of pharmacologically important proteins. Currently available in silico methods for predicting GPCR-G-protein coupling specificity have high error rate. METHOD: We introduce a new approach for creating hidden Markov models (HMMs) based on a first guess about the importance of various residues. We call these knowledge restricted HMMs to emphasize the fact that the state space of the HMM is restricted by the application of a priori knowledge. Specifically, we use only those amino acid residues of GPCRs which are likely to interact with G-proteins, namely those that are predicted to be in the intra-cellular loops. Furthermore, we concatenate these predicted loops into one sequence rather than considering them as four disparate units. This reduces the HMM state space by drastically decreasing the sequence length. RESULTS: Our knowledge restricted HMM based method to predict GPCR-G-protein coupling specificity has an error rate of <1%, when applied to a test set of GPCRs with known G-protein coupling specificity. AVAILABILITY: Academic users can get the data set mentioned herein and HMMs from the authors.

Binding Sites↗

PubMed2001

Analysis of amide bond formation with an alpha-hydroxy-beta-amino acid derivative, 3-amino-2-hydroxy-4-phenylbutanoic acid, as an acyl component: byproduction of homobislactone.

In the synthesis of peptidomimetics containing alpha-hydroxy-beta-amino acid, the coupling of this N(beta)-protected beta-amino acid with amine components was generally performed without the protection of its alpha-hydroxyl group. However, the formation of dipeptides in low yield was often observed when sterically hindered amine components were used. Boc-Apns-OH [Apns: (2S,3S)-3-amino-2-hydroxy-4-phenylbutanoic acid, allophenylnorstatine] (6), which is one of such beta-amino acid derivatives, is intensively employed as a core structure in the development of HIV-1 protease inhibitors. There have been no precise studies, to date, that have examined amide bond formation with alpha-hydroxy-beta-amino acid derivatives as an acyl component. To determine the cause of this low-yield reaction, we studied the amide bond formation focusing on the activation step of N(beta)-protected alpha-hydroxy-beta-amino acid by using a model coupling reaction between 6 and H-Dmt-OR [Dmt: (R)-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid] (7). A significant amount of homobislactone 9 was formed through the activation of the carboxyl group of 6 to the benzotriazole-type active esters such as OBt and OAt. In addition, this homobislactone formation was markedly increased in the presence of a catalytic amount of a base, which exhibited good correlation with the low yield of the amide bond formation, suggesting that homobislactone formation is one major reason for the low yield of the amide bond formation. Moreover, homobislactones were also formed in other derivatives of the N(beta)-protected alpha-hydroxy-beta-amino acid, suggesting a common feature of this type of amino acids. The use of a strong activation method like EDC--HOAt without base addition enhanced amide bond formation, although a small amount of homobislactone may be formed during the coupling reaction.

Aminocaproates↗

PubMed1981

Studies on racemization during couplings using a series of model tripeptides involving activated residues with unfunctionalized side chains.

Racemization studies have been carried out using as model tests couplings of N-benzyloxycarbonylglycyl-L-X with benzyl NE-benzyloxycarbonyl-L-lysinate followed by deprotection and analysis for the diastereomeric tripeptides with an amino acid analyzer, for X = alanine, leucine, phenylalanine, valine and isoleucine. The order of susceptibility to racemization of residues during these segment couplings depends on whether the solvent is polar or apolar, with isoleucyl and valyl, followed by phenylalanyl, being the most susceptible ones in polar solvents. The racemization depressing effect of some additives on carbodiimide-mediated couplings has been examined. Reconciliation of apparent discrepancies in data in the literature on the relative merits of l-hydroxy-benzotriazole and N-hydroxysuccinimide is made on the basis of the nature of the model tests used in acquiring the data.

Models, Chemical↗

PubMed2002

Focused genetic recombination of bacteriophage t4 initiated by double-strand breaks.

A model system for studying double-strand-break (DSB)-induced genetic recombination in vivo based on the ets1 segCDelta strain of bacteriophage T4 was developed. The ets1, a 66-bp DNA fragment of phage T2L containing the cleavage site for the T4 SegC site-specific endonuclease, was inserted into the proximal part of the T4 rIIB gene. Under segC(+) conditions, the ets1 behaves as a recombination hotspot. Crosses of the ets1 against rII markers located to the left and to the right of ets1 gave similar results, thus demonstrating the equal and symmetrical initiation of recombination by either part of the broken chromosome. Frequency/distance relationships were studied in a series of two- and three-factor crosses with other rIIB and rIIA mutants (all segC(+)) separated from ets1 by 12-2100 bp. The observed relationships were readily interpretable in terms of the modified splice/patch coupling model. The advantages of this localized or focused recombination over that distributed along the chromosome, as a model for studying the recombination-replication pathway in T4 in vivo, are discussed.

Bacteriophage T4↗

PubMed2003

Hydrogen bonding at a conserved threonine in lentivirus capsid is required for virus replication.

The N terminus of the capsid protein (CA) undergoes a considerable conformational change when the human immunodeficiency virus (HIV) protease cleaves it free from the Pr55(Gag) polyprotein. This rearrangement is thought to facilitate the establishment of specific CA-CA interactions that are required for the formation of the mature viral core. Substitution of amino acids that are critical for this refolding of the N terminus is generally detrimental to virus replication and mature virion core morphology. Here, we identify a conserved threonine in simian immunodeficiency virus (SIV) CA, T(47)(CA), that is requisite for viral replication. Replacement of T(47)(CA) in the infectious viral clone SIVmac239 with amino acids with different hydrogen-bonding capabilities and analysis of the effects of these substitutions at key steps in the viral life cycle demonstrate that hydrogen bonding at this position is important for virus infectivity and virion release. In the HIV-based homology model of the mature SIV CA N terminus presented in this study, T(47)(CA) forms several hydrogen bonds with a proximal aspartate, D(50)(CA). This model, coupled with strong phenotypic similarities between viral substitution mutants of each of these two residues in all of the virological assays described herein, indicates that hydrogen bonding between T(47)(CA) and D(50)(CA) is likely required for viral replication. As hydrogen bonding between these two residues is present in HIV CA as well, this interaction presents a potential target for antiviral drug design.

Amino Acid Sequence↗

PubMed2005

Modeling of cadmium bioaccumulation in two populations of the green mussel Perna viridis.

This study attempted to quantify differences in Cd biokinetics from two populations of green mussels (Perna viridis) from two sites (eastern and western) in Hong Kong with contrasting hydrological conditions. Body Cd concentrations were modeled using a simple biokinetic model coupled with measurements of dissolved Cd concentrations at each site. Mussels collected from the western site had three to six times higher Cd tissue concentration than the eastern population collected during two seasons (summer wet and winter dry), but the salinity was only lower in the western site during the summer. More Cd was distributed in the metallothionein-like and heat-sensitive proteins in the western population than the eastern population, and Cd predominantly was distributed in the insoluble fraction during summer. The Cd uptake rate constant from the dissolved phase was higher in the western population during summer due to a much lower salinity, but was comparable during winter. Dietary uptake of Cd was similar in both populations, and assimilation was lower from ingested radiolabeled seston than from diatoms. Efflux of Cd remained comparable between the two populations from two seasons (0.02-0.03 /d). Kinetic modeling demonstrates that the faster influx of Cd from aqueous phase caused the higher body Cd concentrations in the western population. The predicted Cd concentrations in mussels were comparable to those observed in the field. Our study highlights differences in Cd accumulation kinetics in different populations of mussels likely caused by the different physical environments.

Animals↗

PubMed2003

Assessing the impact of airline travel on the geographic spread of pandemic influenza.

The objective of this research is to explore what would happen if the Hong Kong influenza pandemic strain of 1968-1969 returned in 2000. We report the results of a series of simulations of an SEIR epidemic model coupled with air transportation data for 52 global cities. Preliminary results suggest that if the 1968-1969 pandemic strain returned, it would spread concurrently to cities in both the northern and southern hemispheres thereby exhibiting less of the characteristic seasonal swing. In addition, after recognition of pandemic onset in the focal city, the time lag for public health intervention is very short. These findings highlight the importance of coordinated global surveillance and pandemic planning.

Algorithms↗

PubMed2002

Polarization IR spectra of the hydrogen bond in phenylacetic acid crystals: H/D isotopic effects temperature and polarization effects.

This paper deals with experimental studies and with quantitative interpretation of the polarized IR crystalline spectra of phenylacetic acid and of its deuterium isotopomers d2 and d7. The spectra were measured in the v(O-H) and in the v(O-D) band frequency ranges at temperatures of 298 and 77 K. The intensity distribution in the bands was quantitatively reproduced on the basis of the strong-coupling model, when assuming that the isolated (COOH)2 and (COOD)2 cycles were the source of the spectral properties of the crystals. Such approach appeared to be sufficient for explaining most of the isotopic and the temperature effects in the spectra. A vibronic mechanism, promoting the symmetry forbidden transition in the IR for the totally symmetric proton stretching vibrations in centrosymmetric hydrogen bond dimers, was found to be of a considerably minor importance, when compared with analogous properties of arylcarboxylic acid crystals. The spectra of phenylacetic acid crystals, unlike the spectra of arylacetic acid crystals do not exhibit the so-called H/D long-range isotopic effects, depending on an influence of the aromatic ring hydrogen atoms on the v(O-H) band fine structure patterns. Also no Fermi resonance impact on the v(O-H) band shape was identified in the phenylacetic acid crystal spectra. These effects were ascribed to weakening of electronic couplings between the hydrogen bonds and the phenyl rings, due to the separation of these groups in phenylacetic acid molecules by methylene groups.

Carbon Tetrachloride↗

PubMed2004

CompuCell, a multi-model framework for simulation of morphogenesis.

MOTIVATION: CompuCell is a multi-model software framework for simulation of the development of multicellular organisms known as morphogenesis. It models the interaction of the gene regulatory network with generic cellular mechanisms, such as cell adhesion, division, haptotaxis and chemotaxis. A combination of a state automaton with stochastic local rules and a set of differential equations, including subcellular ordinary differential equations and extracellular reaction-diffusion partial differential equations, model gene regulation. This automaton in turn controls the differentiation of the cells, and cell-cell and cell-extracellular matrix interactions that give rise to cell rearrangements and pattern formation, e.g. mesenchymal condensation. The cellular Potts model, a stochastic model that accurately reproduces cell movement and rearrangement, models cell dynamics. All these models couple in a controllable way, resulting in a powerful and flexible computational environment for morphogenesis, which allows for simultaneous incorporation of growth and spatial patterning. RESULTS: We use CompuCell to simulate the formation of the skeletal architecture in the avian limb bud. AVAILABILITY: Binaries and source code for Microsoft Windows, Linux and Solaris are available for download from http://sourceforge.net/projects/compucell/

Animals↗

PubMed2006

Desensitization of mechano-gated K2P channels.

The neuronal mechano-gated K2P channels TREK-1 and TRAAK show pronounced desensitization within 100 ms of membrane stretch. Desensitization persists in the presence of cytoskeleton disrupting agents, upon patch excision, and when channels are expressed in membrane blebs. Mechanosensitive currents evoked with a variety of complex stimulus protocols were globally fit to a four-state cyclic kinetic model in detailed balance, without the need to introduce adaptation of the stimulus. However, we show that patch stress can be a complex function of time and stimulation history. The kinetic model couples desensitization to activation, so that gentle conditioning stimuli do not cause desensitization. Prestressing the channels with pressure, amphipaths, intracellular acidosis, or the E306A mutation reduces the peak-to-steady-state ratio by changing the preexponential terms of the rate constants, increasing the steady-state current amplitude. The mechanical responsivity can be accounted for by a change of in-plane area of approximately 2 nm2 between the closed and open conformations. Desensitization and its regulation by chemical messengers is predicted to condition the physiological role of K2P channels.

Animals↗

PubMed2005

Analytical theory of the stochastic dynamics of the power stroke in nonprocessive motor proteins.

Statistical distributions of the structural states of individual molecules of nonprocessive motor complexes such as actomyosins are examined theoretically by considering a two-state stochastic model coupled by chemical reactions along the reaction coordinate representing the internal conformational states of the motor. The use of a conformational reaction coordinate allows for the approximation of taking the rate constants as local in their dependence on the reaction coordinate, and yields a simple analytic solution of the stationary states. The approximation is also tested against numerical solutions with a nonlocal form of rate constants. The theory is well-suited for computational treatments based on atomic structures of protein constituents using free energy molecular dynamics simulations. With empirical sets of free energy functions, stationary distributions of forces exerted by a motor head compare well with known experimental data.

Actins↗

PubMed1994

Estimated mean flow resistance increase during coronary artery catheterization.

The purpose of this investigation is to examine the influence of the presence and size of the catheter on the measurement of mean pressure drop and, thus, flow resistance in coronary vessels. Relatively large mean translesional pressure gradients have been reported, but they may be due to obstruction effects. To evaluate this hypothesis, analytical flow modeling coupled with in vitro experimental evidence was used to estimate mean flow resistance increases due to the presence of a catheter in a proximal vessel for concentric and eccentric catheter configurations. For an angioplasty catheter, over the relative range of catheter size to coronary vessel size (di/d(o)) from 0.3 to 0.7 (which is currently being used clinically), the flow resistance increased by a large factor of 3-33 for the concentric configuration. For smaller infusion catheters, the flow resistance increase was less, although still appreciable. Very small angioplasty guidewire also leads to sizeable increases in flow resistance. Effects of catheter eccentricity also indicated substantial increases in flow resistance, although the magnitude was less. These initial results might be used by clinicians to obtain rough estimates of actual mean pressure gradients in vivo in relatively straight proximal segments of artery from values measured with catheters. Since catheters are used so widely clinically, these initial results may be useful also for other vessels in the vascular system where the mean flow is describable by the Poiseuille relation. Whereas there is reasonable confidence in the flow modeling methodology, hemodynamic data are needed to evaluate the actual magnitude of the effects of obstruction in vivo.

Blood Flow Velocity↗

PubMed1998

Improving lipase production from Candida rugosa by a biochemical engineering approach.

It has been tested that the use of oleic acid as sole carbon source and as inducer of the production has an important effect in the lipase production by Candida rugosa under aerobic conditions. A simple structured mathematical model coupled with a methodology to estimate biomass, specific growth rate and substrate was developed and applied to the production of Candida rugosa lipase in batch, fed-batch and continuous operation to obtain a reproducible product. The best operation mode tested was a controlled specific growth rate fed-batch with a 10-fold increase in productivity related to batch operation. Downstream of the culture broth has demonstrated that the ratio between the different isoenzymes presented can be modulated by the selection of the operational strategy and this ratio is quite different comparing with commercial lipases. Thus, their catalytic properties in front of chiral reactions could be different.

Biotechnology↗

PubMed2004

Cooperativity can reduce stochasticity in intracellular calcium dynamics.

The opening of inositol (1,4,5)-triphosphate (IP(3)) receptors, clustered at discrete sites on the endoplasmic reticulum, can lead to large-scale intracellular calcium waves. Recent experiments in Xenopus oocytes have shown that the inter-wave intervals for these waves have a standard deviation that is much smaller than their mean and that the background calcium concentration exhibits a slow rise during the interwave interval. Using a simple mathematical model, we examine the possibility that this slow rise increases the cooperativity between the openings of the clusters. We find that our model, coupled to the usual assumption that the pumps on the endoplasmic reticulum are activated instantaneously, is unable to explain the observed data: the clusters are found to fire independently and the inter-wave interval distribution is a Poisson distribution with a standard deviation that is approximately equal to its mean. On the other hand, we find that incorporating pumps that slowly activate leads to a slow increase in the background calcium concentration which makes global events progressively more likely to occur. We show that this cooperativity results in much smaller standard deviations and inter-wave interval distributions that are clearly not Poisson distributions.

Animals↗