Cat lung hemodynamics: comparison of experimental results and model predictions

Commonly, attempts have been made to learn about the structure and function of the pulmonary vascular bed from measurements of arterial and venous pressures and blood flow rate under steady-state conditions (e.g., from pressure vs. flow data) or dynamic conditions (e.g., from vascular occlusion data). Zhuang et al. (J. Appl. Physiol. 55: 1341-1348, 1983) have presented a detailed model of steady-state cat lung hemodynamics based on direct measurements of anatomical and elasticity data. This model provides an opportunity to better understand the information content of the hemodynamic data. Therefore, in the present study we carried out a series of steady-state and dynamic experiments on isolated cat lungs. We then compared the results with those predicted by the model. We found that the model provided a good fit to the steady-state data. However, to fit the dynamic data, some modifications were necessary to account for the viscous behavior of the vessel walls and to move the first moment of the distribution of vascular resistance toward the arterial end of the vascular bed relative to that of the distribution of vascular compliance. Due to the sensitivity of the vascular resistance to small changes in vessel diameters and branching ratio, the modifications in morphometry represent small changes in morphometric data and are probably within the range of uncertainty in such data. The modifications had little effect on the steady-state model simulations but substantially improved the dynamic model simulations, suggesting that the dynamic data are quite sensitive to small changes in the relative distributions of vessel diameters and elasticity.     

The optical activity of polypeptides

The present status of the theory of the optical properties of polypeptides is discussed in a general way. Arguments are presented that indicate that the interaction of exciton bands in helices will occur in a tensorial way with the parallel polarized bands normally having stronger interactions than the perpendicular polarized bands, with only small cross-interactions. The net result is an anisotropy of the hyperchromism of the ππ* band and an imbalance of the rotatory strengths of the parallel and perpendicular components. According to the evidence of Mandel and Holzwarth [(1973) Biopolymers 13 , 655–674], this is, in fact, the origin of the strongly nonconservative CD bands of polyproline II and related structures. The implications of anisotropic hyperchromicity on the interpretation of the linear dichroism of crystals is discussed.     

Biodegradation kinetics of naphthalene in nonaqueous phase liquid-water mixed batch systems: comparison of model predictions and experimental results

A model is formulated to describe dissolution of naphthalene from an insoluble nonaqueous phase liquid (NAPL) and its subsequent biodegradation in the aqueous phase in completely mixed batch reactors. The physicochemical processes of equilibrium partitioning and mass transfer of naphthalene between the NAPL and aqueous phases were incorporated into the model. Biodegradation kinetics were described by Monod's microbial growth kinetic model, modified to account for the inhibitory effects of 1,2-naphthoquinone formed during naphthalene degradation under certain conditions. System parameters and biokinetic coefficients pertinent to the NAPL-water systems were determined either by direct measurement or from nonlinear regression of the naphthalene mineralization profiles obtained from batch reactor tests with two-component NAPLs comprised of naphthalene and heptamethylnonane. The NAPLs contained substantial mass of naphthalene, and naphthalene biodegradation kinetics were evaluated over the time required for near complete depletion of naphthalene from the NAPL. Model predictions of naphthalene mineralization time profiles compared favorably to the general trends observed in the data obtained from laboratory experiments with the two-component NAPL, as well as with two coal tars obtained from the subsurface at contaminated sites and composed of many different PAHs (polycyclic aromatic hydrocarbon compounds). The effects of varying the NAPL mass and the naphthalene mole fractions in the NAPL are discussed. It was observed that the time to achieve a given percent removal of naphthalene does not change significantly with the initial mass of naphthalene in a fixed volume of the NAPL. Significant changes in the mineralization profiles are observed when the volume (and mass) of NAPL in the system is changed.     

Reirradiation at long time intervals in mouse kidney: a comparison between experimental results and the predictions of the F-type tissue model

The tolerance of a late-responding tissue to reirradiation after long time intervals has been analysed using the F-type tissue model. In this model the tissue is composed of identical cells, each of which is capable of extensive proliferation and of tissue-specific function. The model was adapted to calculate the response to two fractions of radiation given in a variable overall time. For two equal doses of radiation the repair of tissue damage after the first fraction could be detected theoretically by a change in the rate of cell depletion after retreatment and by an increase in the minimum cell number attained. For an 'experimental set-up', in which a constant first dose was followed by a range of retreatment doses in a variable overall time, the repair of tissue damage theoretically could be detected most sensitively by a shift of the dose-response curves to higher retreatment doses as the time interval between the two doses was increased. A prerequisite for a proper comparison of these dose-response curves was that the responses were evaluated at times after the first dose determined by the minimal latency times after high retreatment doses. From a comparison of these theoretical results with experimental findings for mouse kidneys it was concluded that no recovery of tissue function took place over a 6-month period. Instead it appeared that the kidneys had become more sensitive to irradiation over this period.     

Plasmonic nanoparticles assemblies templated by helical bacteria and resulting optical activity

Plasmonic nanoparticles (NPs) adsorbing onto helical bacteria can lead to formation of NP helicoids with micron scale pitch. Associated chiroptical effects can be utilized as bioanalytical tool for bacterial detection and better understanding of the spectral behavior of helical self-assembled structures with different scales. Here, we report that enantiomerically pure helices with micron scale of chirality can be assembled on Campylobacter jejuni, a helical bacterium known for severe stomach infections. These organisms have right-handed helical shapes with a pitch of 1–2 microns and can serve as versatile templates for a variety of NPs. The bacteria itself shows no observable rotatory activity in the visible, red, and near-IR ranges of electromagnetic spectrum. The bacterial dispersion acquires chiroptical activity at 500–750 nm upon plasmonic functionalization with Au NPs. Finite-difference time-domain simulations confirmed the attribution of the chiroptical activity to the helical assembly of gold nanoparticles. The position of the circular dichroism peaks observed for these chiral structures overlaps with those obtained before for Au NPs and their constructs with molecular and nanoscale chirality. This work provides an experimental and computational pathway to utilize chiroplasmonic particles assembled on bacteria for bioanalytical purposes.     

Critical comparison of consensus methods for molecular sequences.

Consensus methods are recognized as valuable tools for data analysis, especially when some sort of data aggregation is desired. Although consensus methods for sequences play a vital role in molecular biology, researchers pay little heed to the features and limitations of such methods, and so there are risks that criteria for constructing consensus sequences will be misused or misunderstood. To understand better the issues involved, we conducted a critical comparison of nine consensus methods for sequences, of which eight were used in papers appearing in this journal. We report the results of that comparison, and we make recommendations which we hope will assist researchers when they must select particular consensus methods for particular applications.     

Effects of side group functionality and molecular weight on the activity of synthetic antimicrobial polypeptides

The rapid emergence of antibiotic-resistant bacteria along with increasing difficulty in biofilm treatment has caused an immediate need for the development of new classes of antimicrobial therapeutics. We have developed a library of antimicrobial polypeptides, prepared by the ring-opening polymerization of γ-propargyl-L-glutamate N-carboxyanhydride and the alkyne-azide cycloaddition click reaction, which mimic the favorable characteristics of naturally occurring antimicrobial peptides (AmPs). AmPs are known not to cause drug resistance as well as prevent bacteria attachment on surfaces. The ease and scale of synthesis of the antimicrobial polypeptides developed here are significantly improved over the traditional Merrifield synthetic peptide approaches needed for naturally occurring antimicrobial peptides and avoids the unique challenges of biosynthetic pathways. The polypeptides range in length from 30 to 140 repeat units and can have varied side group functionality, including primary, secondary, tertiary, and quaternary amines with hydrocarbon side chains ranging from 1 to 12 carbons long. Overall, we find these polypeptides to exhibit broad-spectrum activity against both Gram positive and Gram negative bacteria, namely, S. aureus and E. coli , while having very low hemolytic activity. Many of the polypeptides can also be used as surface coatings to prevent bacterial attachment. The polypeptide library developed in this work addresses the need for effective biocompatible therapeutics for drug delivery and medical device coatings.     

A comparison of mathematical model predictions to experimental measurements for growth and recombinant protein production in induced cultures of Escherichia coli

Recombinant cell growth and protein synthesis by a recombinant Escherichia coli under various inducing conditions are compared to the predictions of a mathematical model. The mathematical model used was a combination of two literature models: (1) an empirical kinetic model for recombinant growth and product formation and (2) a genetically structured model of the lac promoter-operator on a multicopy plasmid. The experimental system utilized was recombinant E. coli CSH22 bearing the temperature-sensitive plasmid pVH106/172, which codes for the synthesis of beta-galactosidase and the other lac operon genes under the control of a lac promoter. Mathematical model predictions for recombinant beta-galactosidase yield and specific growth rate were compared with fermentation measurements of these same quantities for conditions of chemical induction with cyclic AMP and IPTG, copy number amplification (by shifting culture temperature), and combined chemical induction and copy number amplification. The model successfully predicted experimental product yields for most cases of chemical induction even though the product yields varied from 0.34 x 10(3) to 1500 x 10(3) units/g cell mass. The kinetic model also correctly predicted a decline in the specific growth rate with increasing levels of plasmid and recombinant protein. The model was less successful at predicting product amplification at high copy numbers. A comparison of model predictions and experimental results was also used to investigate some of the assumptions used in constructing the mathematical models.     

An HMM model for coiled-coil domains and a comparison with PSSM-based predictions

MOTIVATION: Large-scale sequence data require methods for the automated annotation of protein domains. Many of the predictive methods are based either on a Position Specific Scoring Matrix (PSSM) of fixed length or on a window-less Hidden Markov Model (HMM). The performance of the two approaches is tested for Coiled-Coil Domains (CCDs). The prediction of CCDs is used frequently, and its optimization seems worthwhile. RESULTS: We have conceived MARCOIL, an HMM for the recognition of proteins with a CCD on a genomic scale. A cross-validated study suggests that MARCOIL improves predictions compared to the traditional PSSM algorithm, especially for some protein families and for short CCDs. The study was designed to reveal differences inherent in the two methods. Potential confounding factors such as differences in the dimension of parameter space and in the parameter values were avoided by using the same amino acid propensities and by keeping the transition probabilities of the HMM constant during cross-validation. AVAILABILTY: The prediction program and the databases are available at http://www.wehi.edu.au/bioweb/Mauro/Marcoil     

Effect of sequence-specific interactions on the stability of helical conformations in polypeptides

A modification of the Zimm–Bragg two-state model for the helix–coil transition in polypeptides, which considers the effect of charge–dipole, charge–charge, and other specific interactions on helix stability, is presented. The new model introduces a series of adjustable parameters whose values are estimated by fitting to recent spectroscopic results on medium-sized peptides. This formalism, based on traditional two-state helix–coil transition models, provides a framework in which data on the helix contents of peptides of specific sequence can be rationalized by a statistical mechanical theory.     

Distance dependency of exciton coupled circular dichroism using turn and helical peptide spacers

Porphyrins are promising chromophores for the investigation of the still unexplored area of 3-dimensional structural studies of proteins by using the exciton coupled circular dichroism (CD) method. The synthesis, conformational characterization by FTIR absorption and (1)H-NMR, and CD properties are described for a model bis-porphyrin system based on homooligo-[L-(alphaMe)Val](n) peptides as rigid spacers. In particular, the coupled CD phenomenon is experimentally detected, the intensity of which is modulated by the interchromophoric distance. These results extend and integrate those already reported with steroid, dimeric steroid, and brevetoxin bridges.     

Rescoring docking hit lists for model cavity sites: predictions and experimental testing

Molecular docking computationally screens thousands to millions of organic molecules against protein structures, looking for those with complementary fits. Many approximations are made, often resulting in low “hit rates.” A strategy to overcome these approximations is to rescore top-ranked docked molecules using a better but slower method. One such is afforded by molecular mechanics-generalized Born surface area (MM-GBSA) techniques. These more physically realistic methods have improved models for solvation and electrostatic interactions and conformational change compared to most docking programs. To investigate MM-GBSA rescoring, we re-ranked docking hit lists in three small buried sites: a hydrophobic cavity that binds apolar ligands, a slightly polar cavity that binds aryl and hydrogen-bonding ligands, and an anionic cavity that binds cationic ligands. These sites are simple; consequently, incorrect predictions can be attributed to particular errors in the method, and many likely ligands may actually be tested. In retrospective calculations, MM-GBSA techniques with binding-site minimization better distinguished the known ligands for each cavity from the known decoys compared to the docking calculation alone. This encouraged us to test rescoring prospectively on molecules that ranked poorly by docking but that ranked well when rescored by MM-GBSA. A total of 33 molecules highly ranked by MM-GBSA for the three cavities were tested experimentally. Of these, 23 were observed to bind—these are docking false negatives rescued by rescoring. The 10 remaining molecules are true negatives by docking and false positives by MM-GBSA. X-ray crystal structures were determined for 21 of these 23 molecules. In many cases, the geometry prediction by MM-GBSA improved the initial docking pose and more closely resembled the crystallographic result; yet in several cases, the rescored geometry failed to capture large conformational changes in the protein. Intriguingly, rescoring not only rescued docking false positives, but also introduced several new false positives into the top-ranking molecules. We consider the origins of the successes and failures in MM-GBSA rescoring in these model cavity sites and the prospects for rescoring in biologically relevant targets.     

Effect of lipid saturation on the topology and oligomeric state of helical membrane polypeptides

Natural liquid crystalline membranes are made up of many different lipids carrying a mixture of saturated and unsaturated fatty acyl chains. Whereas in the past considerable attention has been paid to cholesterol content, the phospholipid head groups and the membrane surface charge the detailed fatty acyl composition was often considered less important. However, recent investigations indicate that the detailed fatty acyl chain composition has pronounced effects on the oligomerization of the transmembrane helical anchoring domains of the MHC II receptor or the membrane alignment of the cationic antimicrobial peptide PGLa. In contrast the antimicrobial peptides magainin 2 and alamethicin are less susceptible to lipid saturation. Using histidine-rich LAH4 designer peptides the high energetic contributions of lipid saturation in stabilizing transmembrane helical alignments are quantitatively evaluated. These observations can have important implications for the biological regulation of membrane proteins and should be taken into considerations during biophysical or structural experiments.     

Anisotropic and inhomogeneous tensile behavior of the human anulus fibrosus: experimental measurement and material model predictions

The anulus fibrosus (AF) of the intervertebral disc exhibits spatial variations in structure and composition that give rise to both anisotropy and inhomogeneity in its material behaviors in tension. In this study, the tensile moduli and Poisson's ratios were measured in samples of human AF along circumferential, axial, and radial directions at inner and outer sites. There was evidence of significant inhomogeneity in the linear-region circumferential tensile modulus (17.4+/-14.3 MPa versus 5.6+/-4.7 MPa, outer versus inner sites) and the Poisson's ratio v21 (0.67+/-0.22 versus 1.6+/-0.7, outer versus inner), but not in the axial modulus (0.8+/-0.9 MPa) or the Poisson's ratios V12 (1.8+/-1.4) or v13 (0.6+/-0.7). These properties were implemented in a linear an isotropic material model of the AF to determine a complete set of model properties and to predict material behaviors for the AF under idealized kinematic states. These predictions demonstrate that interactions between fiber populations in the multilamellae AF significantly contribute to the material behavior, suggesting that a model for th     

Optical activity of polypeptides and proteins

Using methods described in a previous publication the optical activity of a number of polypeptides and proteins has been calculated. The systems included the α-helix, the two β-structures, polyproline I, polyproline II, collagen and collagen models, and poly-N-methylalanine. In addition to these orderded structures, calculations were also performed on the α, β and nonperiodic regions of myoglobin, lysozyme, ribonuclease-S and β-chymotrypsin. The α and β structures in prteins differ from the polypeptide models by being very short and partially disordered. It is concluded that the 222-nm band of the α-helix is a good method for detecting helices in proteins but that the 207-and 191-nm bands of the helix will not fit a linear superposition model. The circular dichroism of the so-called β regions of proteins differs markedly from that for ideal β structure because of breakdownin symmetry. As a result estimates of β-structure in proteins based on polypeptide models are not likely to be quantitative. The theoretical methods give an adequate account of the optical activity of all the ordered polypeptides except polyproline II and collagen and (by inference) the nonperiodic chains in the various proteins. This difficulty is the remaining barrier to a complete theory of the optical activity of the polypeptide backbone in globular proteins.     

Hydrogen bonding in helical polypeptides from molecular dynamics simulations and amide hydrogen exchange analysis: alamethicin and melittin in methanol.

Molecular dynamics simulations of ion channel peptides alamethicin and melittin, solvated in methanol at 27 degrees C, were run with either regular alpha-helical starting structures (alamethicin, 1 ns; melittin 500 ps either with or without chloride counterions), or with the x-ray crystal coordinates of alamethicin as a starting structure (1 ns). The hydrogen bond patterns and stabilities were characterized by analysis of the dynamics trajectories with specified hydrogen bond angle and distance criteria, and were compared with hydrogen bond patterns and stabilities previously determined from high-resolution NMR structural analysis and amide hydrogen exchange measurements in methanol. The two alamethicin simulations rapidly converged to a persistent hydrogen bond pattern with a high level of 3(10) hydrogen bonding involving the amide NH's of residues 3, 4, 9, 15, and 18. The 3(10) hydrogen bonds stabilizing amide NH's of residues C-terminal to P2 and P14 were previously proposed to explain their high amide exchange stabilities. The absence, or low levels of 3(10) hydrogen bonds at the N-terminus or for A15 NH, respectively, in the melittin simulations, is also consistent with interpretations from amide exchange analysis. Perturbation of helical hydrogen bonding in the residues before P14 (Aib10-P14, alamethicin; T11-P14, melittin) was characterized in both peptides by variable hydrogen bond patterns that included pi and gamma hydrogen bonds. The general agreement in hydrogen bond patterns determined in the simulations and from spectroscopic analysis indicates that with suitable conditions (including solvent composition and counterions where required), local hydrogen-bonded secondary structure in helical peptides may be predicted from dynamics simulations from alpha-helical starting structures. Each peptide, particularly alamethicin, underwent some large amplitude structural fluctuations in which several hydrogen bonds were cooperatively broken. The recovery of the persistent hydrogen bonding patterns after these fluctuations demonstrates the stability of intramolecular hydrogen-bonded secondary structure in methanol (consistent with spectroscopic observations), and is promising for simulations on extended timescales to characterize the nature of the backbone fluctuations that underlie amide exchange from isolated helical polypeptides.