Effect of L-4-Thiazolylalanine (Protinol™) on skin barrier strength and skin protection.

OBJECTIVES: Skin barrier properties are critical for maintaining epidermal water content, protecting from environmental factors and providing the first line of defense against pathogens. In this study, we investigated the non-proteinogenic amino acid L-4-Thiazolylalanine (L4) as a potential active ingredient in skin protection and barrier strength. METHODS: L4 on wound healing, anti-inflammatory and anti-oxidant properties were evaluated using monolayers and 3D skin equivalents. The transepithelial electrical resistance (TEER) value was used in vitro as a strong indicator of barrier strength and integrity. Clinical L4 efficacy was assessed for the evaluation of the skin barrier integrity and soothing benefits. RESULTS: In vitro treatments of L4 show beneficial effects in wound closure mechanism, and we demonstrate that L4 anti-oxidant benefits with markedly increased HSP70 and decreased reactive oxygen species production induced by UVs exposure. Barrier strength and integrity were significantly improved by L4, confirmed clinically by an increase in 12R-lipoxygenase enzymatic activity in the stratum corneum. In addition, soothing benefits of L4 have been shown clinically with the decrease in redness after methyl nicotinate application on the inner arm and the significant reduction of the erythema and the skin desquamation on the scalp. CONCLUSION: L4 delivered multiple skin benefits by strengthening the skin barrier, accelerating the skin repair process as well as soothing the skin and the scalp with anti-inflammaging effects. The observed efficacy validates L4 as a desirable skincare ingredient for topical treatment.

OBJECTIFS: La barrière cutanée est primordiale pour le maintien d'un épiderme hydraté, sa protection contre les facteurs environnementaux et pour conférer une première ligne de défense contre les pathogènes. Dans cette étude, nous nous intéressons à un aminoacide non-proteinogénique, L-4-Thiazolylalanine (L4) comme potentiel actif cosmétique et évaluons ses effets sur la protection de la peau et le renforcement de la barrière cutanée. MÉTHODES: Les propriétés cicatrisantes, anti-inflammatoires et antioxydantes de L4 ont été déterminées par culture cellulaire et sur modèles de peau 3D. La mesure de la résistance électrique transépithéliale a été utilisée in vitro comme indicateur de la résistance de la barrière de la peau. Des études cliniques ont été réalisées pour évaluer L4 sur ses capacités apaisantes et son impact sur l'intégrité de la barrière cutanée. RÉSULTATS: In vitro, nous déterminons qu'un traitement L4 a des effets bénéfiques dans le processus de cicatrisation mais aussi des propriétés antioxydantes, induisant une augmentation de HSP70 ainsi qu'une diminution de la production d'espèces réactives a l'oxygène induite par rayons UV. Un renforcement de la barrière cutanée et une amélioration de son intégrité sont observés après un traitement L4 et confirme cliniquement par une augmentation de l'activité enzymatique de la 12R-lipoxygenase dans le stratum corneum. De plus, les effets protecteurs de L4 ont été confirmes cliniquement avec une rougeur cutanée diminuée après application de nicotinate de methyle sur l'avant-bras interne ainsi qu'une réduction significative d'érythème et de desquamation cutanée du cuir chevelu. CONCLUSION: L4 offre de multiples bénéfices pour la peau en renforçant la barrière cutanée, accélérant le processus de cicatrisation et offrant des actions anti-inflammatoires apaisantes pour la peau et le cuir chevelu. Cela fait de L4 un ingrédient cosmétique intéressant pour une application topic.

Evidence for widespread changes in the structure, composition, and fire regimes of western North American forests.

Implementation of wildfire- and climate-adaptation strategies in seasonally dry forests of western North America is impeded by numerous constraints and uncertainties. After more than a century of resource and land use change, some question the need for proactive management, particularly given novel social, ecological, and climatic conditions. To address this question, we first provide a framework for assessing changes in landscape conditions and fire regimes. Using this framework, we then evaluate evidence of change in contemporary conditions relative to those maintained by active fire regimes, i.e., those uninterrupted by a century or more of human-induced fire exclusion. The cumulative results of more than a century of research document a persistent and substantial fire deficit and widespread alterations to ecological structures and functions. These changes are not necessarily apparent at all spatial scales or in all dimensions of fire regimes and forest and nonforest conditions. Nonetheless, loss of the once abundant influence of low- and moderate-severity fires suggests that even the least fire-prone ecosystems may be affected by alteration of the surrounding landscape and, consequently, ecosystem functions. Vegetation spatial patterns in fire-excluded forested landscapes no longer reflect the heterogeneity maintained by interacting fires of active fire regimes. Live and dead vegetation (surface and canopy fuels) is generally more abundant and continuous than before European colonization. As a result, current conditions are more vulnerable to the direct and indirect effects of seasonal and episodic increases in drought and fire, especially under a rapidly warming climate. Long-term fire exclusion and contemporaneous social-ecological influences continue to extensively modify seasonally dry forested landscapes. Management that realigns or adapts fire-excluded conditions to seasonal and episodic increases in drought and fire can moderate ecosystem transitions as forests and human communities adapt to changing climatic and disturbance regimes. As adaptation strategies are developed, evaluated, and implemented, objective scientific evaluation of ongoing research and monitoring can aid differentiation of warranted and unwarranted uncertainties.

mFES: A Robust Molecular Finite Element Solver for Electrostatic Energy Computations.

We present a robust method for the calculation of electrostatic potentials of large molecular systems using tetrahedral finite elements (FE). Compared to the finite difference (FD) method using a regular simple cubic grid to solve the Poisson equation, the FE method can reach high accuracy and efficiency using an adaptive grid. Here, the grid points can be adjusted and are placed directly on the molecular surfaces to faithfully model surfaces and volumes. The grid point density decreases rapidly toward the asymptotic boundary to reach very large distances with just a few more grid points. A broad set of tools are applied to make the grid more regular and thus provide a more stable linear equation system, while reducing the number of grid points without compromising accuracy. The latter reduces the number of unknowns significantly and yields shorter solver execution times. The accuracy is further enhanced by using second order polynomials as shape functions. Generating the adaptive grid for a molecular system is expensive, but it pays off, if the same molecular geometry is used several times as is the case for pKA and redox potential computations of many charge variable groups in proteins. Application of the mFES method is also advantageous, if the molecular system is too large to reach sufficient accuracy when computing the electrostatic potential with conventional FD methods. The program mFES is free of charge and available at http://agknapp.chemie.fu-berlin.de/mfes .

Trends and causes of severity, size, and number of fires in northwestern California, USA.

Research in the last several years has indicated that fire size and frequency are on the rise in western U.S. forests. Although fire size and frequency are important, they do not necessarily scale with ecosystem effects of fire, as different ecosystems have different ecological and evolutionary relationships with fire. Our study assessed trends and patterns in fire size and frequency from 1910 to 2008 (all fires > 40 ha), and the percentage of high-severity in fires from 1987 to 2008 (all fires > 400 ha) on the four national forests of northwestern California. During 1910-2008, mean and maximum fire size and total annual area burned increased, but we found no temporal trend in the percentage of high-severity fire during 1987-2008. The time series of severity data was strongly influenced by four years with region-wide lightning events that burned huge areas at primarily low-moderate severity. Regional fire rotation reached a high of 974 years in 1984 and fell to 95 years by 2008. The percentage of high-severity fire in conifer-dominated forests was generally higher in areas dominated by smaller-diameter trees than in areas with larger-diameter trees. For Douglas-fir forests, the percentage of high-severity fire did not differ significantly between areas that re-burned and areas that only burned once (10% vs. 9%) when re-burned within 30 years. Percentage of high-severity fire decreased to 5% when intervals between first and second fires were > 30 years. In contrast, in both mixed-conifer and fir/high-elevation conifer forests, the percentage of high-severity fire was less when re-burned within 30 years compared to first-time burned (12% vs. 16% for mixed conifer; 11% vs. 19% for fir/high-elevation conifer). Additionally, the percentage of high-severity fire did not differ whether the re-burn interval was less than or greater than 30 years. Years with larger fires and greatest area burned were produced by region-wide lightning events, and characterized by less winter and spring precipitation than years dominated by smaller human-ignited fires. Overall percentage of high-severity fire was generally less in years characterized by these region-wide lightning events. Our results suggest that, under certain conditions, wildfires could be more extensively used to achieve ecological and management objectives in northwestern California.

Rubredoxin Function: Redox Behavior from Electrostatics.

Continuum electrostatic theory was applied to compute redox potentials of rubredoxin (Rd) proteins. We used multiple side chain conformers of Rd crystal structures, optimized geometries of salt bridges, mutated residues, and residues in the neighborhood of the iron-sulfur complex (FeS complex) self-consistently for given solvent pH and redox potential. The following contributions to Rd redox potentials are discussed: side chain conformations, H-bond geometries of the FeS complex, dielectric environment, charged residues, and salt bridges. We considered 15 different Rd's (of different species/strains and mutants) with available crystal structures whose redox potentials vary between -86 mV and +31 mV. The computed redox potentials deviated by less than 16 mV, root-mean-square deviation (RMSD), from measured values. The amide H-bond geometry is considered to be crucial for the variation of Rd redox potentials. To test this assumption, we considered 14 mutant Rd's for which we modeled the structures based on Rd from WT Clostridium pasterianum (Cp) leaving the amide H-bond geometry of the FeS complex invariant. Here, we obtained an RMSD of only 14 mV with measured values demonstrating that the amide H bond geometries cannot be a major factor determining Rd redox potentials. We analyzed the factors determining the Rd redox potentials of a mesophilic and a thermophilic Rd differing by nearly 90 mV. We found that half of the difference is due to sequence and half is due to backbone variations. Albeit salt-bridge networks vary considerably between these two Rd's and are considered to be responsible for differences in thermostability, their overall influence on Rd redox potentials is small.

Cognitive evaluation in children and adolescents with Möbius sequence.

BACKGROUND: Möbius sequence is a rare condition usually defined as uni- or bilateral congenital facial weakness with impairment of ocular abduction. Mental retardation is estimated to occur in 10-15% of cases, but at present there have been no studies focusing on the intellectual capacities of children and adolescents with Möbius sequence. METHODS: Twenty-three children and adolescents aged 6-16 years could be recruited following a request of the German Möbius foundation. The primary caregivers of all subjects filled out a special questionnaire to compile personal, somatic and psychosocial history of the probands. All subjects had a physical examination. To assess intellectual capacities, the German version of the Wechsler Intelligence Test-III (WISC-III) was administered. In case of a severe mental retardation, the Vineland Adaptive Behavior Rating Form was used as an alternative. RESULTS: Twenty-two subjects [12 males, 10 females; mean age: 11.3 (6-16) years] could be included; 21 could be examined with the WISC-III. Compared with the normative sample, Full Scale IQ (mean: 92.05; standard deviation: 14.84) was significantly lower (P = 0.023) which was the consequence of a very low Performance IQ (mean: 80.48; standard deviation: 15.84). Compared with the normative sample, the results of all performance subtests were significantly lower (P = 0.033-0.000), whereas verbal subtest scores did not differ or were even higher ['Similarities' (P = 0.026) and 'Vocabulary' (P = 0.019)]. Verbal IQ (mean: 106.24; standard deviation: 15.31) was not significantly different from the normative sample. Two boys met ICD-10 criteria for mental retardation. Full Scale IQ was not predictive for academic success. CONCLUSIONS: The WISC-III is not an adequate predictor for academic success in Möbius patients; intelligence tests which are less dependant on time constraints should be preferred for subjects with Möbius sequence.

Bound Ligand Conformer Revealed by Flexible Structure Alignment in Absence of Crystal Structures: Indirect Drug Design Probed for HIV-1 Protease Inhibitors.

In the absence of structural knowledge on the target protein, the bound ligand conformer (BLC) can be constructed approximately by an indirect drug-design approach that uses a set of ligands binding to the same target. Once the bound ligand conformer (BLC) is known, different strategies of drug design can be pursued. The indirect drug-design approach of the present study is based on the assumption that a set of ligands with chemically different architecture binding to the same target protein carry hidden information of their corresponding true BLCs. It is shown how this information can be extracted by pairwise flexible structure alignment (FSA) using molecular dynamics (MD) simulations with attractive intermolecular interactions that derive from the molecular similarity of the ligands and allow the ligands to adopt the same space. The FSA approach is performed with a newly designed module overlap in the experimental CHARMM-29a1, which soon will become publicly available. Combining the conformations obtained from FSA of different ligand pairs yields consensus ligand conformers (CLCs) that should be similar to the BLCs. This procedure was validated on HIV-1 protease (HIV-P), where at present 44 crystal structures with bound ligands of sufficiently diverse chemical composition are available. The FSA approach identifies four different clusters of HIV-P BLCs. These clusters are consistent with the H-bond patterns of the ligands bound to HIV-P in the crystal structures exhibiting four different binding modes. The cluster-specific CLCs are indeed very similar (rmsd ≈ 2 Å) to the corresponding BLCs from the crystal structure, demonstrating the feasibility of the present approach.

PAMAM structure-based multifunctional fluorescent conjugates for improved fluorescent labelling of biomacromolecules.

Fluorescent probes are of increasing interest in medicinal and biological applications for the elucidation of the structures and functions of healthy as well as tumour cells. The quality of these investigations is determined by the intensity of the fluorescence signal. High dye/carrier ratios give strong signals. However, these are achieved by the occupation of a high number of derivatisation sites and therefore are accompanied by strong structural alterations of the carrier. Hence, polyvalent substances containing a high number of fluorescent dyes would be favourable because they would allow the introduction of many dyes at one position of the compound to be labelled.A large number of different dyes have been investigated to determine the efficiency of coupling to a dendrimer scaffold and the fluorescence properties of the oligomeric dyes, but compounds that fulfil the requirements of both strong fluorescence signals and reactivities are rare. Herein we describe the synthesis and characterisation of dye oligomers containing dansyl-, 7-nitro-2,1,3-benzoxadiazol-4-yl- (NBD), coumarin-343, 5(6)-carboxyfluorescein and sulforhodamine B2 moieties based on polyamidoamine (PAMAM) dendrimers. The PAMAM dendrimers were synthesised by an improved protocol that yielded highly homogeneous scaffolds with up to 128 conjugation sites. When comparing the fluorescent properties of the dye oligomers it was found that only the dansylated dendrimers met the requirements of enhanced fluorescence signals. The dendrimer containing 16 fluorescent dyes was conjugated to the anti-epidermal-growth-factor receptor (EGFR) antibody hMAb425 as a model compound to show the applicability of the dye multimer compounds. This conjugate revealed a preserved immunoreactivity of 54%.We demonstrate the applicability of the dye oligomers to the efficient and applicable labelling of proteins and other large molecules that enables high dye concentrations and therefore high contrasts in fluorescence applications.

Statistical thermodynamics of the stability of multivalent ligand-receptor complexes.

Multivalent ligands can form ligand-receptor complexes that are orders of magnitude more stable than their monovalent counterparts. A theory of this "enhancement effect" based on fundamental principles of statistical thermodynamics is presented. A key finding is a simple analytical expression that provides clear and direct insight into the mechanism by which the enhanced stability of the multivalent ligand-receptor complex can be achieved. The theory explains experimental data on the activation of ion channels in the membranes of cells by polymer-linked divalent ligands.

Improved pK(a) prediction: combining empirical and semimicroscopic methods.

Using three different methods we tried to compute 171 experimentally known pK(a) values of ionizable residues from 15 different proteins and compared the accuracies of computed pK(a) values in terms of the root mean square deviation (RMSD) from experiment. One method is based on a continuum electrostatic model of the protein including conformational flexibility (KBPLUS). The others are empirical approaches with PROPKA deploying physically motivated energy terms with adjustable parameters and PKAcal using an empirical function with no physical basis. PROPKA reproduced the pK(a) values with highest overall accuracy. Differentiating the data set into weakly and strongly shifted experimental pK(a) values, however, we found that PROPKA's accuracy is better if the pK(a) values are weakly shifted but on equal footing with that of KBPLUS for more strongly shifted values. On the other hand, PKAcal reproduces strongly shifted pK(a) values badly but weakly shifted values with the same accuracy as PROPKA. We tested different consensus approaches combining data from all three methods to find a general procedure for most accurate pK(a) predictions. In most of the cases we found that the consensus approach reproduced experimental data with better accuracy than any of the individual methods alone.

Combined NMR and computational study for azide binding to human manganese superoxide dismutase.

Human manganese superoxide dismutase (MnSOD) labeled with 3-fluorotyrosine (Tyf) was complexed with the (15)N-labeled inhibitor azide ([(15)N(3)(-)]). The sample was characterized by solid-state NMR (SSNMR) spectroscopy ((19)F-MAS and (15)N-CPMAS). Employing (19)F-(15)N-REDOR spectroscopy, we determined the distances between the fluorine label in Tyrosine-34 and the three (15)N-nuclei of the azide and the relative orientation of the azide in the binding pocket of the MnSOD. A distance of R(1)=4.85A between the (19)F-label of Tyf34 and the nearest (15)N of the azide and an azide-fluorotyrosine Tyf34 angle of 90 degrees were determined. These geometry data are employed as input for molecular modeling of the location of the inhibitor in the active site of the enzyme. In the computations, several possible binding geometries of the azide near the Mn-complex were assumed. Only when the azide replaces the water ligand at the Mn-complex we obtained a geometry of the azide-Mn-complex, which is consistent with the present NMR data. This indicates that the water molecule ligating to the Mn-complex is removed and the azide is placed at this position. As a consequence the azide forms an H bond with Gln143 instead with Tyf34, in contrast to non-(19)F-labeled MnSOD, where the azide is hydrogen bonded to the hydroxy group of Tyr34.

Associative and predictive biomarkers of dementia in HIV-1-infected patients.

BACKGROUND: Infection with HIV can result in a debilitating CNS disorder known as HIV dementia (HIV-D). Since the advent of highly active antiretroviral therapy (HAART), the incidence of HIV-D has declined, but the prevalence continues to increase. In this new era of HIV-D, traditional biomarkers such as CSF viral load and monocyte chemotactic protein 1 levels are less likely to be associated with dementia in patients on HAART and biomarkers that can predict HIV-D have not yet been identified. OBJECTIVE: To identify biomarkers that are associated with and can predict HIV-D. METHODS: We grouped patients with HIV based on changes in cognitive status over a 1-year period and analyzed sphingolipid, sterol, triglyceride, antioxidant, and lipid peroxidation levels in CSF. RESULTS: We found that increased levels of the vitamin E and triglyceride C52 predicted the onset or worsening of dementia. Elevated levels of sphingomyelin were associated with inactive dementia. Elevated levels of ceramide and the accumulation of 4-hydroxynonenals were associated with active dementia. CONCLUSIONS: We interpret these findings to indicate that early in the pathogenesis of HIV dementia, there is an up-regulation of endogenous antioxidant defenses in brain. The failure of this attempted neuroprotective mechanism leads to the accumulation of sphingomyelin and moderate cognitive dysfunction. The breakdown of this enlarged pool of sphingomyelin to ceramide and the accumulation of highly reactive aldehydes are associated with declining cognitive function. Thus, elevations in endogenous protective mechanisms may identify patients who are at increased risk of the development of HIV dementia.

Dynamics of viral and proviral loads of feline immunodeficiency virus within the feline central nervous system during the acute phase following intravenous infection.

Animal models of human immunodeficiency virus 1, such as feline immunodeficiency virus (FIV), provide the opportunities to dissect the mechanisms of early interactions of the virus with the central nervous system (CNS). The aims of the present study were to evaluate viral loads within CNS, cerebrospinal fluid (CSF), ocular fluid, and the plasma of cats in the first 23 weeks after intravenous inoculation with FIV(GL8). Proviral loads were also determined within peripheral blood mononuclear cells (PBMCs) and brain tissue. In this acute phase of infection, virus entered the brain in the majority of animals. Virus distribution was initially in a random fashion, with more diffuse brain involvement as infection progressed. Virus in the CSF was predictive of brain parenchymal infection. While the peak of virus production in blood coincided with proliferation within brain, more sustained production appeared to continue in brain tissue. In contrast, proviral loads in the brain decreased to undetectable levels in the presence of a strengthening PBMC load. A final observation in this study was that there was no direct correlation between viral loads in regions of brain or ocular tissue and the presence of histopathology.

The X-ray absorption spectroscopy Debye-Waller factors of an iron compound and of met-myoglobin as a function of temperature.

Protein dynamics can be characterized by the mean square displacements of the individual atoms of a molecule. This concept is extended to X-ray absorption spectroscopy (XAS) of proteins where the physical information in the Debye-Waller factor is in general neglected. In a first step, a procedure for the investigation of the temperature dependence of XAS spectra has been developed for a small iron compound. Subsequently, experiments have been performed on met-myoglobin. It is shown that the mean square displacements of XAS are smaller than those obtained by Mössbauer spectroscopy and far smaller than crystallographic mean square displacements. This behavior is explained by the different sensitivity of the methods. XAS measures a relative mean square displacement between the absorbing and backscattering atoms only. A comparison with mean square displacements calculated from normal modes shows that static displacements contribute significantly. It becomes obvious that the atoms of the active center show a high correlation of their motions.

Hypersensitivity reactions associated with recombinant tissue-type plasminogen activator and urokinase.

Anaphylaxis or angioedema in response to recombinant tissue-type plasminogen activator or urokinase have been reported in only a few isolated cases. Both agents are endogenous proteins and thus considered non-antigenic. Activation of fibrinolysis may per se facilitate anaphylactoid reactions by pathophysiologic pathways that are not well understood. We report a unique case, review the literature and discuss implication for the clinician. The 25-year-old patient underwent thrombolytic treatment for extensive thrombosis of pelvic and deep lower extremity veins. The patient developed protracted anaphylactoid reactions during recombinant tissue-type plasminogen activator continuous intravenous infusion. After changing treatment to urokinase, the same symptoms recurred with more severe intensity, despite corticosteroid premedication. Symptoms resolved within hours after treatment with histamine receptor blockers. This unique observation, i.e. sequential occurrence of anaphylactoid reactions during recombinant tissue plasminogen activator and urokinase treatments, adds to existing evidence for an unspecific non-antigenic pathomechanism, and for a class effect of thrombolytics. Steroids do not prevent, but histamine receptor blockers seem to be an effective treatment of this unusual complication of thrombolytic therapy.

Factors determining the orientation of axially coordinated imidazoles in heme proteins.

Factors determining conformations of imidazole axially coordinated to heme in heme proteins were investigated by analyzing 693 hemes in 432 different crystal structures of heme proteins from the Protein Data Bank (PDB), where at least one histidine is ligated to heme. The results from a search of the PDB for protein structures were interpreted with molecular force field computations. Analysis of data from these crystal structures indicated that there are two main factors that determine the orientations of imidazole ligated to heme. These are the interactions of imidazole with the propionic acid side chains of heme and with the histidine backbone. From the analysis of the crystal structures of heme proteins, it turned out that the hydrogen bonding pattern is often not decisive, though it is probably used by nature to fine-tune the orientation of imidazole axially ligated to heme. We found that in many heme proteins the NdeltaH group of imidazole ligated to heme can assume a number of different hydrogen bonds and that in mutant structures the orientation of the ligated imidazole often does not change significantly, although the mutant altered the hydrogen bonding scheme involving the imidazole. Data from crystal structures of heme proteins show that there are preferred orientations of imidazoles with respect to heme. Generally, the NdeltaH group of imidazole is oriented toward the propionic acid groups of the heme. In some cases, the NdeltaH group of imidazole is close to only one of the propionic acid groups, but it is practically never oriented in the opposite direction. The imidazole also adopts a preferred orientation with respect to its histidine backbone such that the plane of the imidazole ring is practically never parallel to the Calpha-Cbeta bond of its histidine backbone. For a given conformation of histidine backbone with respect to heme, as well as imidazole with respect to histidine backbone, the orientation of the imidazole with respect to heme is uniquely determined, since the three orientations depend on each other. Hence, the interaction of the imidazole with the backbone also influences the orientation of the imidazole with respect to the heme. Force field computations are in agreement with experimental data. With this method, we showed that there is an energy minimum when the NdeltaH group of the imidazole is oriented toward the propionic acid groups and that there are minima of energy for orientations where the imidazole ring is orthogonal to the plane defined by the Calpha-Cbeta and Cbeta-Cgamma bonds of the histidine. The computations also demonstrated that these interactions are mainly of electrostatic origin. By taking into account these two major factors, we were able to understand the orientations of axially coordinated imidazoles for all groups of heme proteins, except for the group of cytochrome c peroxidase. In this group, the orientation of the imidazole is determined by a strong hydrogen bond of the NdeltaH group with Asp235.

How to guarantee optimal stability for most representative structures in the Protein Data Bank.

We proposed recently an optimization method to derive energy parameters for simplified models of protein folding. The method is based on the maximization of the thermodynamic average of the overlap between protein native structures and a Boltzmann ensemble of alternative structures. Such a condition enforces protein models whose ground states are most similar to the corresponding native states. We present here an extensive testing of the method for a simple residue-residue contact energy function and for alternative structures generated by threading. The optimized energy function guarantees high stability and a well-correlated energy landscape to most representative structures in the PDB database. Failures in the recognition of the native structure can be attributed to the neglect of interactions between different chains in oligomeric proteins or with cofactors. When these are taken into account, only very few X-ray structures are not recognized. Most of them are short inhibitors or fragments and one is a structure that presents serious inconsistencies. Finally, we discuss the reasons that make NMR structures more difficult to recognizeCopyright 2001 Wiley-Liss, Inc.

Artificial cytochrome b: computer modeling and evaluation of redox potentials.

We generated atomic coordinates of an artificial protein that was recently synthesized to model the central part of the native cytochrome b (Cb) subunit consisting of a four-helix bundle with two hemes. Since no X-ray structure is available, the structural elements of the artificial Cb were assembled from scratch using all known chemical and structural information available and avoiding strain as much as possible. Molecular dynamics (MD) simulations applied to this model protein exhibited root-mean-square deviations as small as those obtained from MD simulations starting with the crystal structure of the native Cb subunit. This demonstrates that the modeled structure of the artificial Cb is relatively rigid and strain-free. The model structure of the artificial Cb was used to determine the redox potentials of the two hemes by calculating the electrostatic energies from the solution of the linearized Poisson-Boltzmann equation (LPBE). The calculated redox potentials agree within 20 meV with the experimentally measured values. The dependence of the redox potentials of the hemes on the protein environment was analyzed. Accordingly, the total shift in the redox potentials is mainly due to the low dielectric medium of the protein, the protein backbone charges, and the salt bridges formed between the arginines and the propionic acid groups of the hemes. The difference in the shift of the redox potentials is due to the interactions with the hydrophilic side chains and the salt bridges formed with the propionic acids of the hemes. For comparison and to test the computational procedure, the redox potentials of the two hemes in the native Cb from the cytochrome bc(1) (Cbc(1)) complex were also calculated. Also in this case the computed redox potentials agree well with experiments.

Conundrum of the lack of defective RNAs (dRNAs) associated with tobamovirus Infections: dRNAs that can move are not replicated by the wild-type virus; dRNAs that are replicated by the wild-type virus do not move.

Two classes of artificially constructed defective RNAs (dRNAs) of Tobacco mosaic virus (TMV) were examined in planta with helper viruses that expressed one (183 kDa) or both (126 and 183 kDa) of the replicase-associated proteins. The first class of artificially constructed dRNAs had the helicase and polymerase (POL) domains deleted; the second had an intact 126-kDa protein open reading frame (ORF). Despite extremely high levels of replication in protoplasts, the first class of dRNAs did not accumulate in plants. The dRNAs with an intact 126-kDa protein ORF were replicated at moderate levels in protoplasts and in planta when supported by a TMV mutant that expressed the 183-kDa protein but not the 126-kDa protein (183F). These dRNAs were not supported by helper viruses expressing both replicase-associated proteins. De novo dRNAs were generated in plants infected by 183F but not in plants infected with virus with the wild-type replicase. These novel dRNAs each contained a new stop codon near the location of the wild-type stop codon for the 126-kDa protein and had most of the POL domain deleted. The fact that only dRNAs that contained a complete 126-kDa protein ORF moved systemically suggests that expression of a functional 126-kDa protein or the presence of certain sequences and/or structures within this ORF is required for movement of dRNAs. At least two factors may contribute to the lack of naturally occurring dRNAs in association with wild-type TMV infections: an inability of TMV to support dRNAs that can move in plants and the inability of dRNAs that can be replicated by TMV to move in plants.

Calculated pH-dependent population and protonation of carbon-monoxy-myoglobin conformers.

X-ray structures of carbonmonoxymyoglobin (MbCO) are available for different pH values. We used conventional electrostatic continuum methods to calculate the titration behavior of MbCO in the pH range from 3 to 7. For our calculations, we considered five different x-ray structures determined at pH values of 4, 5, and 6. We developed a Monte Carlo method to sample protonation states and conformations at the same time so that we could calculate the population of the considered MbCO structures at different pH values and the titration behavior of MbCO for an ensemble of conformers. To increase the sampling efficiency, we introduced parallel tempering in our Monte Carlo method. The calculated population probabilities show, as expected, that the x-ray structures determined at pH 4 are most populated at low pH, whereas the x-ray structure determined at pH 6 is most populated at high pH, and the population of the x-ray structures determined at pH 5 possesses a maximum at intermediate pH. The calculated titration behavior is in better agreement with experimental results compared to calculations using only a single conformation. The most striking feature of pH-dependent conformational changes in MbCO-the rotation of His-64 out of the CO binding pocket-is reproduced by our calculations and is correlated with a protonation of His-64, as proposed earlier.