Polycyclic Aromatic Hydrocarbons (PAHs) in Grilled Marshmallows.

The aim of this study was to assess potential health risks among children and adolescents consuming various grilled marshmallows using a survey and to determine polycyclic aromatic hydrocarbons (PAHs) in these food products. PAH analysis in grilled marshmallows included a dilution stage with deionized water and liquid-liquid extraction with cyclohexane and solid-phase extraction (SPE). PAH fractions were initially analyzed via high-performance thin-layer chromatography, and PAH concentrations were determined via gas chromatography with a tandem mass detector using the selective reaction monitoring (SRM) mode. This study on the consumption of grilled marshmallows was conducted among approximately 300 children and adolescents. The preliminary results indicated that "raw" marshmallows did not contain PAHs. However, the obtained data suggested the exposure of young people to carcinogenic PAHs from grilled marshmallows (63.5% of them consumed marshmallows). Carcinogenic benzo(a)pyrene (BaP) was determined in all samples. The profile of PAH concentrations in the extracts isolated from various grilled types of marshmallows was similar (r2 > 0.8000), regardless of the grilling method. Compared to the white sugar confection, higher concentrations of PAHs were determined in multicolored marshmallows. The lack of social awareness about exposure to carcinogenic substances is alarming.

Tautomeric equilibrium and spectroscopic properties of 8-azaguanine revealed by quantum chemistry methods.

8-azaguanine is a triazolopyrimidine nucleobase analog possessing potent antibacterial and antitumor activities, and it has been implicated as a lead molecule in cancer and malaria therapy. Its intrinsic fluorescence properties can be utilized for monitoring its interactions with biological polymers like proteins or nucleic acids. In order to better understand these interactions, it is important to know the tautomeric equilibrium of this compound. In this work, the tautomeric equilibrium of all natural neutral and anionic compound forms (except highly improbable imino-enol tautomers) as well as their methyl derivatives and ribosides was revealed by quantum chemistry methods. It was shown that, as expected, tautomers protonated at positions 1 and 9 dominate neutral forms both in gas phase and in aqueous solution. 8-azaguanines methylated at any position of the triazole ring are protonated at position 1. The computed vertical absorption and emission energies are in very good agreement with the experimental data. They confirm the validity of the assumption that replacing the proton with the methyl group does not significantly change the positions of absorption and fluorescence peaks.

Studies on the Efficiency of Iron Release from Fe(III)-EDTA and Fe(III)-Cit and the Suitability of These Compounds for Tetracycline Degradation.

Iron ions can be used to degrade tetracycline dispersed in nature. Studies of absorption and fluorescence spectra and quantum chemistry calculations showed that iron is more readily released from Fe(III)-citrate than from Fe(III)-EDTA, so Fe(III)-citrate (Fe(III)-Cit) is more suitable for tetracycline (TC) degradation. At 30 °C, a severe degradation of TC by Fe(III)-Cit occurred as early as after 3 days of incubation in the light, and after 5 days in the dark. In contrast, the degradation of TC by Fe(III)-EDTA proceeded very slowly in the dark. By the fifth day of incubation of TC with Fe(III)-Cit in darkness, the concentrations of the former compound dropped by 55% and 75%, at 20 °C and 30 °C, respectively. The decrease in tetracycline concentrations caused by Fe(III)-EDTA in darkness at the same temperatures was only 2% and 6%, respectively. Light increased the degradation rates of TC by Fe(III)-EDTA to 20% and 56% at 20 °C and 30 °C, respectively. The key role of the light in the degradation of tetracycline by Fe(III)-EDTA was thus demonstrated. The TC degradation reaction showed a second-order kinetics. The rate constants of Fe(III)-Cit-induced TC degradation at 20 °C and 30 °C in darkness were k = 4238 M-1day-1 and k = 11,330 M-1day-1, respectively, while for Fe(III)-EDTA were 55 M-1day-1 and 226 M-1day-1. In light, these constants were k = 15,440 M-1day-1 and k = 40,270 M-1day-1 for Fe(III)-Cit and k = 1012 M-1day-1 and 2050 M-1day-1 at 20 °C and 30 °C; respectively. A possible reason for the higher TC degradation rate caused by Fe(III)-Cit can be the result of its lower thermodynamical stability compared with Fe(III)-EDTA, which we confirmed with our quantum chemistry calculations. Two quantum chemistry calculations showed that the iron complex with EDTA is more stable (the free energy of the ensemble is 15.8 kcal/mol lower) than the iron complex with Cit; hence, Fe release from Fe(III)-EDTA is less effective.

The influence of erdosteine administration on lead-induced oxidative stress in rat muscle.

Lead-exposure is known to disrupt the redox balance of tissues leading to oxidative stress. Due to the fact that a mucolytic drug, erdosteine, exerts also antioxidant properties, we decided to perform a pilot study on rats to evaluate its therapeutic potency in lead poisoning. Male Wistar rats were divided randomly into the following seven groups having 10 animals in each. Group I served as the control group. During 8-week period, rats in groups II-IV, except standard alimentation, received: erdosteine in a dose 350 mg/kg (collateral control group), 1200 ppm of lead acetate in drinking water and placebo, as well as the same doses of lead and erdosteine, respectively. Rats in group V-VII received 1200 ppm of lead acetate in drinking water for the initial 6-week period and then administered: placebo, erdosteine and EDTA for 2 weeks, respectively. The levels of malondialdehyde (MDA) were significantly higher in groups III and V compared to the control group. The activities of catalase (CAT) were significantly higher in groups IV, V, and VI compared to the control group. The activities of glutathione-S-transferase (GST) were significantly lower in group II and significantly higher in groups VI and VII compared to the control group, while the activities of glutathione reductase (GR) were significantly lower in group III and significantly higher in group VI. Erdosteine has an effect of protection against lead-induced oxidative stress which is not worse than that of EDTA.

Cadmium ion-chlorophyll interaction - Examination of spectral properties and structure of the cadmium-chlorophyll complex and their relevance to photosynthesis inhibition.

Chlorophyll was shown to spontaneously form a complex with cadmium, which is incorporated at the central position of the chlorophyll molecule porphyrin ring, where it replaces magnesium. The rate of complex formation depended on the ratio of Cd2+ ions to chlorophyll concentration in the solution. In solutions with chlorophyll concentration of C = 1 × 10-5 M and Cd2+ concentrations of C = 1 × 10-5 M, C = 1 × 10-3 M and C = 9 × 10-3 M, Cd-Chl complex formation was completed after 200 h, 50 h and 33 h, respectively. The formation of Cd-Chl complex followed the second order over all substrates reaction order, first order over Cd2+ concentration and first over Chl concentration. The pseudo second order reaction rate constant k, when Cd2+ concentration was equal Chl concentration have been obtained as k = 1.510 ± 0.023 × 10-4 M-1min-1. Quantum chemistry computations showed that Cd-chlorophyll complex existed in two conformations in the methanol solution with cadmium ion placed either below or above the coordination plane. Two times smaller overlap integral of the Chl fluorescence spectrum with the Cd-Chl absorption spectrum IChl,Cd-Chl= 2.4223 × 10-13 cm3/M in comparison with the overlap integral of the Chl fluorescence spectrum with the Chl absorption spectrum IChl,Chl= 4.6210 × 10-13 cm3/M (twice lower probability of energy transfer Chl∗ → Cd-Chl than Chl∗ → Chl) and lower Förster critical distance for resonance energy transfer: RoChl→Cd-Chl= 46.773 Å, RoChl→Chl= 52.086 Å, indicated that in plants intoxicated with cadmium, taken up from the contaminated soil, the energy transfer between Chl and Cd-Chl in antennas will be disturbed, which may be one of the reasons for the inhibition of photosynthesis.

Scale-consistent approach to the derivation of coarse-grained force fields for simulating structure, dynamics, and thermodynamics of biopolymers.

In this chapter the scale-consistent approach to the derivation of coarse-grained force fields developed in our laboratory is presented, in which the effective energy function originates from the potential of mean force of the system under consideration and embeds atomistically detailed interactions in the resulting energy terms through use of Kubo's cluster-cumulant expansion, appropriate selection of the major degrees of freedom to be averaged out in the derivation of analytical approximations to the energy terms, and appropriate expression of the interaction energies at the all-atom level in these degrees of freedom. Our approach enables the developers to find correct functional forms of the effective coarse-grained energy terms, without having to import them from all-atom force fields or deriving them on a heuristic basis. In particular, the energy terms derived in such a way exhibit correct dependence on coarse-grained geometry, in particular on site orientation. Moreover, analytical formulas for the multibody (correlation) terms, which appear to be crucial for coarse-grained modeling of many of the regular structures such as, e.g., protein α-helices and ß-sheets, can be derived in a systematic way. Implementation of the developed theory to the UNIfied COarse-gRaiNed (UNICORN) model of biological macromolecules, which consists of the UNRES (for proteins), NARES-2P (for nucleic acids), and SUGRES-1P (for polysaccharides) components, and is being developed in our laboratory is described. Successful applications of UNICORN to the prediction of protein structure, simulating the folding and stability of proteins and nucleic acids, and solving biological problems are discussed.

Why Purine Nucleoside Phosphorylase Ribosylates 2,6-Diamino-8-azapurine in Noncanonical Positions? A Molecular Modeling Study.

Protein nucleoside phosphorylase (PNP) is an enzyme that catalyzes a reversible conversion process (ribosylation and phosphorolysis) between nucleobases (purines) and their nucleosides. Experimental studies showed that calf PNP ribosylates purine analogues in specific positions: 2,6-diamino-8-azapurine in position 7 or 8 and 8-azaguanine in position 9 of the triazole ring. The reason for this phenomenon can be a result of different expositions of purine substrates to the channel leading to the binding site. This hypothesis was verified by the application of molecular modeling techniques to two complexes of purine analogues 2,6-diamino-azapurine, calf PNP (pdb-code: 1LVU), and 8-azaguanine, calf PNP (pdb-code: 2AI1). The results obtained with a combination of quantum chemistry, docking, and molecular dynamics methods showed qualitative validity of our hypothesis. Binding free energies of protein-ligand systems showed that most probable binding poses expose N8 nitrogen for 2,6-diamino-8-azapurine and N9 nitrogen for 8-azaguanine into the binding channel and ruled out the exposition of N9 for 2,6-diamino-8-azapurine and N7 for 8-azaguanine, partially in agreement with the experimental data. The other important result obtained in this study is a significantly higher population of the protonated form of crucial residue Glu-201 present in the binding pocket, compared to the standard protonation of free glutamic acid in solution. This result combined with populations of tautomeric forms of both investigated systems strongly suggests that 2,6-diamino-8-azapurine and 8-azaguanine are recognized by proteins with deprotonated and protonated Glu-201 residues, respectively. A comparison of computed binding poses of the investigated ligands to the inhibitors present in crystal structures suggests that the modification of the (S)-PMPDAP inhibitor, in which a 2-(phosphonomethoxy)propyl chain is attached at position 8 instead of position 9, might increase its binding affinity.

Metal Exchange in the Interprotein ZnII -Binding Site of the Rad50 Hook Domain: Structural Insights into CdII -Induced DNA-Repair Inhibition.

CdII is a major genotoxic agent that readily displaces ZnII in a multitude of zinc proteins, abrogates redox homeostasis, and deregulates cellular metalloproteome. To date, this displacement has been described mostly for cysteine(Cys)-rich intraprotein binding sites in certain zinc finger domains and metallothioneins. To visualize how a ZnII -to-CdII swap can affect the target protein's status and thus understand the molecular basis of CdII -induced genotoxicity an intermolecular ZnII -binding site from the crucial DNA repair protein Rad50 and its zinc hook domain were examined. By using a length-varied peptide base, ZnII -to-CdII displacement in Rad50's hook domain is demonstrated to alter it in a bimodal fashion: 1) CdII induces around a two-orders-of-magnitude stabilization effect (log K 12 Zn II =20.8 vs. log K 12 Cd II =22.7), which defines an extremely high affinity of a peptide towards a metal ion, and 2) the displacement disrupts the overall assembly of the domain, as shown by NMR spectroscopic and anisotropy decay data. Based on the results, a new model explaining the molecular mechanism of CdII genotoxicity that underlines CdII 's impact on Rad50's dimer stability and quaternary structure that could potentially result in abrogation of the major DNA damage response pathway is proposed.

The impact of ß-azido(or 1-piperidinyl)methylamino acids in position 2 or 3 on biological activity and conformation of dermorphin analogues.

The synthesis of new dermorphin analogues is described. The (R)-alanine or phenylalanine residues of natural dermorphin were substituted by the corresponding α-methyl-ß-azidoalanine or α-benzyl-ß-azido(1-piperidinyl)alanine residues. The potency and selectivity of the new analogues were evaluated by a competitive receptor binding assay in rat brain using [(3) H]DAMGO (a µ ligand) and [(3) H]DELT (a δ ligand). The most active analogue in this series, Tyr-(R)-Ala-(R)-α-benzyl-ß-azidoAla-Gly-Tyr-Pro-Ser-NH2 and its epimer were analysed by (1) H and (13) C NMR spectroscopy and restrained molecular dynamics simulations. The dominant conformation of the investigated peptides depended on the absolute configuration around C(α) in the α-benzyl-ß-azidoAla residue in position 3. The (R) configuration led to the formation of a type I ß-turn, whilst switching to the (S) configuration gave rise to an inverse ß-turn of type I', followed by the formation of a very short ß-sheet. The selectivity of Tyr-(R)-Ala-(R) and (S)-α-benzyl-ß-azidoAla-Gly-Tyr-Pro-Ser-NH2 was shown to be very similar; nevertheless, the two analogues exhibited different conformational preferences. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd.

Coarse-grained modeling of RNA 3D structure.

Functional RNA molecules depend on three-dimensional (3D) structures to carry out their tasks within the cell. Understanding how these molecules interact to carry out their biological roles requires a detailed knowledge of RNA 3D structure and dynamics as well as thermodynamics, which strongly governs the folding of RNA and RNA-RNA interactions as well as a host of other interactions within the cellular environment. Experimental determination of these properties is difficult, and various computational methods have been developed to model the folding of RNA 3D structures and their interactions with other molecules. However, computational methods also have their limitations, especially when the biological effects demand computation of the dynamics beyond a few hundred nanoseconds. For the researcher confronted with such challenges, a more amenable approach is to resort to coarse-grained modeling to reduce the number of data points and computational demand to a more tractable size, while sacrificing as little critical information as possible. This review presents an introduction to the topic of coarse-grained modeling of RNA 3D structures and dynamics, covering both high- and low-resolution strategies. We discuss how physics-based approaches compare with knowledge based methods that rely on databases of information. In the course of this review, we discuss important aspects in the reasoning process behind building different models and the goals and pitfalls that can result.

Synthesis, Biological Activity, and NMR-Based Structural Studies of Deltorphin I Analogs Modified in Message Domain with a New α,α-Disubstituted Glycines.

This article describes new deltorphin I analogs in which phenylalanine residues were replaced by the corresponding (R) or (S)-α-benzyl-ß-azidoalanine, α-benzyl-ß-(1-pyrrolidinyl)alanine, α-benzyl-ß-(1-piperidinyl)alanine, and α-benzyl-ß-(4-morpholinyl)-alanine residues. The potency and selectivity of the new analogs were evaluated by a competitive receptor binding assay in the rat brain using [(3) H]DAMGO (a µ ligand) and [(3) H]DELT (a δ ligand). The affinity of analogs containing (R) or (S)-α-benzyl-ß-azidoalanine in position 3 to δ-receptors strongly depended on the chirality of the α,α-disubstituted residue. The conformational behavior of peptides modified with (R) or (S)-α-benzyl-ß-(1-piperidinyl)Ala, which displays the opposite selectivity, was analyzed by (1) H and (13) C NMR. The µ-selective Tyr-d-Ala-(R)-α-benzyl-ß-(1-piperidinyl)Ala-Asp-Val-Val-Gly-NH2 lacks the helical conformation observed in the δ-selective Tyr-d-Ala-(S)-α-benzyl-ß-(1-piperidinyl)Ala-Asp-Val-Val-Gly-NH2 . Our results support the proposal that differences between δ- and µ-selective opioid peptides are attributable to the presence or absence of a spatial overlap between the N-terminal message domain and the C-terminal address domain.

DNA Duplex Formation with a Coarse-Grained Model.

A middle-resolution coarse-grained model of DNA is proposed. The DNA chain is built of spherical and planar rigid bodies connected by elastic virtual bonds. The bonded part of the potential energy function is fit to potentials of mean force of model systems. The rigid bodies are sets of neutral, charged, and dipolar beads. Electrostatic and van der Waals interactions are parametrized by our recently developed procedure [Maciejczyk, M.; Spasic, A.; Liwo, A.; Scheraga, H.A. J. Comp. Chem.2010, 31, 1644]. Interactions with the solvent and an ionic cloud are approximated by a multipole-multipole Debye-Hückel model. A very efficient R-RATTLE algorithm, for integrating the movement of rigid bodies, is implemented. It is the first coarse-grained model, in which both bonded and nonbonded interactions were parametrized ab initio and which folds stable double helices from separated complementary strands, with the final conformation close to the geometry of experimentally determined structures.

Synthesis, properties, and biological activity of boranophosphate analogs of the mRNA cap: versatile tools for manipulation of therapeutically relevant cap-dependent processes.

Modified mRNA cap analogs aid in the study of mRNA-related processes and may enable creation of novel therapeutic interventions. We report the synthesis and properties of 11 dinucleotide cap analogs bearing a single boranophosphate modification at either the α-, ß- or γ-position of the 5',5'-triphosphate chain. The compounds can potentially serve either as inhibitors of translation in cancer cells or reagents for increasing expression of therapeutic proteins in vivo from exogenous mRNAs. The BH3-analogs were tested as substrates and binding partners for two major cytoplasmic cap-binding proteins, DcpS, a decapping pyrophosphatase, and eIF4E, a translation initiation factor. The susceptibility to DcpS was different between BH3-analogs and the corresponding analogs containing S instead of BH3 (S-analogs). Depending on its placement, the boranophosphate group weakened the interaction with DcpS but stabilized the interaction with eIF4E. The first of the properties makes the BH3-analogs more stable and the second, more potent as inhibitors of protein biosynthesis. Protein expression in dendritic cells was 2.2- and 1.7-fold higher for mRNAs capped with m2 (7,2'-O)GppBH3pG D1 and m2 (7,2'-O)GppBH3pG D2, respectively, than for in vitro transcribed mRNA capped with m2 (7,3'-O)GpppG. Higher expression of cancer antigens would make mRNAs containing m2 (7,2'-O)GppBH3pG D1 and m2 (7,2'-O)GppBH3pG D2 favorable for anticancer immunization.

A unified coarse-grained model of biological macromolecules based on mean-field multipole-multipole interactions.

A unified coarse-grained model of three major classes of biological molecules--proteins, nucleic acids, and polysaccharides--has been developed. It is based on the observations that the repeated units of biopolymers (peptide groups, nucleic acid bases, sugar rings) are highly polar and their charge distributions can be represented crudely as point multipoles. The model is an extension of the united residue (UNRES) coarse-grained model of proteins developed previously in our laboratory. The respective force fields are defined as the potentials of mean force of biomacromolecules immersed in water, where all degrees of freedom not considered in the model have been averaged out. Reducing the representation to one center per polar interaction site leads to the representation of average site-site interactions as mean-field dipole-dipole interactions. Further expansion of the potentials of mean force of biopolymer chains into Kubo's cluster-cumulant series leads to the appearance of mean-field dipole-dipole interactions, averaged in the context of local interactions within a biopolymer unit. These mean-field interactions account for the formation of regular structures encountered in biomacromolecules, e.g., α-helices and ß-sheets in proteins, double helices in nucleic acids, and helicoidally packed structures in polysaccharides, which enables us to use a greatly reduced number of interacting sites without sacrificing the ability to reproduce the correct architecture. This reduction results in an extension of the simulation timescale by more than four orders of magnitude compared to the all-atom representation. Examples of the performance of the model are presented.

Mean-field interactions between nucleic-acid-base dipoles can drive the formation of a double helix.

A proposed coarse-grained model of nucleic acids demonstrates that average interactions between base dipoles, together with chain connectivity and excluded-volume interactions, are sufficient to form double-helical structures of DNA and RNA molecules. Additionally, local interactions determine helix handedness and direction of strand packing. This result, and earlier research on reduced protein models, suggests that mean-field multipole-multipole interactions are the principal factors responsible for the formation of regular structure of biomolecules.

Dynamical insight into Caenorhabditis elegans eIF4E recognition specificity for mono-and trimethylated structures of mRNA 5' cap.

Specific recognition and binding of the ribonucleic acid 5' termini (mRNA 5' cap) by the eukaryotic translation initiation factor 4E (eIF4E) is a key, rate limiting step in translation initiation. Contrary to mammalian and yeast eIF4Es that discriminate in favor of 7-methylguanosine cap, three out of five eIF4E isoforms from the nematode Caenorhabditis elegans as well as eIF4Es from the parasites Schistosome mansoni and Ascaris suum, exhibit dual binding specificity for both 7-methylguanosine-and N(2),N(2),7-trimethylguanosine cap. To address the problem of the differences in the mechanism of the cap recognition by those highly homologic proteins, we carried out molecular dynamics simulations in water of three factors, IFE-3 and IFE-5 isoforms from C. elegans and murine eIF4E, in the apo form as well as in the complexes with 7-methyl-GDP and N(2),N(2),7-trimethyl-GDP. The results clearly pointed to a dynamical mechanism of discrimination between each type of the cap, viz. differences in mobility of the loops located at the entrance into the protein binding pockets during the cap association and dissociation. Additionally, our data showed that the hydrogen bond involving the N(2)-amino group of 7-methylguanosine and the carboxylate of glutamic acid was not stable. The dynamic mechanism proposed here differs from a typical, static one in that the differences in the protein-ligand binding specificity cannot be ascribed to formation and/or disruption of well defined stabilizing contacts.

Zn(II) complexes of glutathione disulfide: structural basis of elevated stabilities.

Glutathione disulfide (GSSG), a long disregarded redox partner of glutathione (GSH), is thought to participate in intracellular zinc homeostasis. We performed a concerted potentiometric and NMR spectroscopic study of protonation and Zn(II) binding properties of GSSG ((γECG)(2)) and a series of its nine analogs with C-terminal modifications, tripeptide disulfides: (γECS)(2), (γECE)(2), (γECG-NH(2))(2), (γECG-OEt)(2), and (γEcG)(2); dipeptide disulfides, (γEC)(2) and (γEC-OEt)(2); and mixed disulfides, γECG-γEC and γECG-γEC-OEt. The acid-base and Zn(II) complexation properties in this group of compounds are strictly correlated to average C-terminal electrostatic charges. In particular, it was demonstrated that GSSG assumes a bent (head-to-tail) conformation in solution at neutral pH, which is controlled by electrostatic attraction between the protonated γ-amino groups of the Glu residue and the deprotonated C-terminal Gly carboxylates. This interaction modulates the ability of GSSG to coordinate Zn(II), both indirectly, by affecting the basicities of the amino groups, and directly, through the participation of the Gly carboxylates in the outer coordination sphere of the Zn(II) ion. A specific coiled structure of the major [Zn-GSSG](2-) complex is additionally stabilized by the formation of hydrogen bonds between glycinyl carboxylates and two Zn(II)-coordinated water molecules. The elevated stability of Zn(II)-GSSG complexes was demonstrated by competition with FluoZin-3, a fluorescent sensor with high Zn(II) affinity, commonly used in in vitro and in vivo studies. The potential biological functions and reactivity of GSSG complexes of Zn(II) ions are discussed.

Coarse-grained model of nucleic acid bases.

Atomistic simulations of nucleic acids are prohibitively expensive and, consequently, reduced models of these compounds are of great interest in the field. In this work, we propose a physics-based coarse-grained model of nucleic-acid bases in which each base is represented by several (3-5) interaction centers. van der Waals interactions are modeled by Lennard-Jones spheres with a 12-6 potential energy function. The charge distribution is modeled by a set of electric dipole moments located at the centers of the Lennard-Jones spheres. The method for computing the Lennard-Jones parameters, electric dipole moments (their magnitude and orientation) and positions of the interaction centers is described. Several models with different numbers of interaction centers were tested. The model with three-center cytosine, four-center guanine, four-center thymine, and five-center adenine satisfactorily reproduces the canonical Watson-Crick hydrogen bonding and stacking interaction energies of the all-atom AMBER model. The computation time with the coarse-grained model is reduced seven times compared with that of the all-atom model.

Free energy of helix propagation in short polyalanine chains determined from peptide growth simulations of La3+-binding model peptides. Comparison with experimental data.

Molecular dynamics (MD) is, at present, a unique tool making it possible to study, at the atomic level, conformational transitions in peptides and proteins. Nevertheless, because MD calculations are always based on a more or less approximate physical model, using a set of approximate parameters, their reliability must be tested by comparison with experimental data. Unfortunately, it is very difficult to find a peptide system in which conformational transitions can be studied both experimentally and using MD simulations so that a direct comparison of the results obtained in both ways could be made. Such a system, containing a rigid alpha-helix nucleus stabilized by La(3+) coordination to a 12-residue sequence taken from an EF-hand protein has recently been used to determine experimentally the helix propagation parameters in very short polyalanine segments (Goch et al. (2003) Biochemistry 42: 6840-6847). The same parameters were calculated here for the same peptide system using the peptide growth simulation method with, alternatively, charmm 22 and cedar potential energy functions. The calculated free energies of the helix-coil transition are about two times too large for cedar and even three times too large for charmm 22, as compared with the experimental values. We suggest that these discrepancies have their origin in the incorrect representation of unfolded peptide backbone in solution by the molecular mechanics force fields.