In silico analysis of the thermodynamic stability changes of psychrophilic and mesophilic alpha-amylases upon exhaustive single-site mutations

Identifying sequence modifications that distinguish psychrophilic from mesophilic proteins is important for designing enzymes with different thermodynamic stabilities and to understand the underlying mechanisms. The PoPMuSiC algorithm is used to introduce, in silico, all the single-site mutations in four mesophilic and one psychrophilic chloride-dependent alpha-amylases and to evaluate the changes in thermodynamic stability. The analysis of the distribution of the sequence positions that could be stabilized upon mutation shows a clear difference between the three domains of psychrophilic and mesophilic alpha-amylases. Most of the mutations stabilizing the psychrophilic enzyme are found in domains B and C, contrary to the mesophilic proteins where they are preferentially situated in the catalytic domain A. Moreover, the calculations show that the environment of some residues responsible for the activity of the psychrophilic protein has evolved to reinforce favorable interactions with these residues. In the second part, these results are exploited to propose rationally designed mutations that are predicted to confer to the psychrophilic enzyme mesophilic-like thermodynamic properties. Interestingly, most of the mutations found in domain C strengthen the interactions with domain A, in agreement with suggestions made on the basis of structural analyses. Although this study focuses on single-site mutations, the thermodynamic effects of the recommended mutations should be additive if the mutated residues are not close in space.     

SDOCK: a global protein-protein docking program using stepwise force-field potentials

Fast Fourier transform (FFT) method limits the forms of scoring functions in global protein-protein docking. On the other hand, force field potentials can effectively describe the energy hyper surface of biological macromolecules. In this study, we developed a new protein-protein docking program, SDOCK, that incorporates van der Waals attractive potential, geometric collision, screened electrostatic potential, and Lazaridis-Karplus desolvation energy into the scoring function in the global searching process. Stepwise potentials were generated from the corresponding continuous forms to treat the structure flexibility. After optimization of the atom solvation parameters and the weights of different potential terms based on a new docking test set that contains 142 cases with small or moderate conformational changes upon binding, SDOCK slightly outperformed the well-known FFT based global docking program ZDOCK3.0. Among the 142 cases tested, 52.8% gave at least one near-native solutions in the top 100 solutions. SDOCK was also tested on six blind testing cases in Critical Assessment of Predicted Interactions rounds 13 to 18. In all six cases, the near-native solutions could be found within the top 350 solutions. Because the SDOCK approach performs global docking based on force-field potentials, one of its advantages is that it provides global binding free energy surface profiles for further analysis. The efficiency of the program is also comparable with that of other FFT based protein-protein docking programs. SDOCK is available for noncommercial applications at http://mdl.ipc.pku.edu.cn/cgi-bin/down.cgi.     

Knowledge acquisition and development of accurate rules for predicting protein stability changes

Knowing the mechanisms by which protein stability change is one of the most important and valuable tasks in molecular biology. The conventional methods of predicting protein stability changes mainly focus on improving prediction accuracy. However, it is desirable to extract domain knowledge from large databases that is beneficial to accurate prediction of the protein stability change. This paper presents an interpretable prediction tree method (named iPTREE) that produces explanatory rules to explore hidden knowledge accompanied with high prediction accuracy and consequently analyzes the factors influencing the protein stability changes. To evaluate iPTREE and the knowledge upon protein stability changes, a thermodynamic dataset consisting of 1615 mutants led by single point mutation from ProTherm is adopted. Being as a predictor for protein stability changes, the rule-based approach can achieve a prediction accuracy of 87%, which is better than other methods based on artificial neural networks (ANN) and support vector machines (SVM). Besides, these methods lack the ability in biological knowledge discovery. The human-interpretable rules produced by iPTREE reveal that temperature is a factor of concern in predicting protein stability changes. For example, one of interpretable rules with high support is as follows: if the introduced residue type is Alanine and temperature is between 4 °C and 40 °C, then the stability change will be negative (destabilizing). The present study demonstrates that iPTREE can easily be used in the application of protein stability changes where one requires more understandable knowledge.     

Detection of point mutations using pyrene-labeled DNA probes

Pyrene-labeled oligodeoxyribonucleotide probes were shown to be suitable for the detection of point mutations. Reagents based on homochiral 2,4-dihydroxybutyramides were used to introduce pyrene residues at the 3"- and 5"- ends of oligonucleotide pairs. The oligonucleotide pair forms a tandem complex with a complementary target, giving rise to an excimer signal (_max 470—490 nm) in the fluorescence spectra when the pyrene residues come into close proximity. The maximum ratio of the intensity of the excimer signal to the monomer signal (_max 380—400 nm) is attained when (S)-N-(1-pyrenylmethyl)-3,3-dimethyl-2,4-dihydroxybutyramide is used to introduce the pyrene residue. The excimer fluorescence completely disappears with an increase in the distance between the pyrene residues (upon the introduction of an additional nucleotide in the target) or in the presence of a mismatch near the contact site of the probes.     

Prediction of protein structure using a knowledge-based off-lattice united-residue force field and global optimization methods

A united-residue model of polypeptide chains developed in our laboratories with united side-chains and united peptide groups as interaction sites is presented. The model is designed to work in continuous space; hence efficient global-optimization methods can be applied. In this work, we adopted the distance-scaling method that is based on continuous deformation of the original rugged energy hypersurface to obtain a smoothed surface. The method has been applied successfully to predict the structures of simple motifs, such as the three-helix bundle structure of the 10-58 fragment of staphylococcal protein A in de novo folding simulations and more complicated motifs in inverse-folding simulations. Received: 24 April 1998 / Accepted: 4 August 1998 / Published online: 2 November 1998     

Investigating effects of sample pretreatment on protein stability using size‐exclusion chromatography and high‐resolution continuum source atomic absorption spectrometry

In this study, size‐exclusion chromatography and high‐resolution atomic absorption spectrometry methods have been developed and evaluated to test the stability of proteins during sample pretreatment. This especially includes different storage conditions but also adsorption before or even during the chromatographic process. For the development of the size exclusion method, a Biosep S3000 5 μm column was used for investigating a series of representative model proteins, namely bovine serum albumin, ovalbumin, monoclonal immunoglobulin G antibody, and myoglobin. Ambient temperature storage was found to be harmful to all model proteins, whereas short‐term storage up to 14 days could be done in an ordinary refrigerator. Freezing the protein solutions was always complicated and had to be evaluated for each protein in the corresponding solvent. To keep the proteins in their native state a gentle freezing temperature should be chosen, hence liquid nitrogen should be avoided. Furthermore, a high‐resolution continuum source atomic absorption spectrometry method was developed to observe the adsorption of proteins on container material and chromatographic columns. Adsorption to any container led to a sample loss and lowered the recovery rates. During the pretreatment and high‐performance size‐exclusion chromatography, adsorption caused sample losses of up to 33%.     

Prediction of glycoprotein secondary structure using ATR-FTIR

Glycoproteins are important biomolecules with a diverse array of structural and signaling functions in biology. Determination of glycoprotein secondary structure is becoming increasingly important in aiding the understanding of how these molecules function in biological environments and disease. Furthermore, glycoproteins such as mucins are being evaluated in various nano-engineering processes that require knowledge of how the underlying secondary structure might alter in different target environments. We have developed an analytical procedure for predicting the secondary structures of glycoprotein using ATR-FTIR on dry film. Using Bovine submaxillary mucin (BSM) as a glycoprotein model, we determined the additive infrared spectral pattern of acetyl amino sugars and amino acids that could contribute to the absorbance in the Amide I band of BSM through empirical data. We show through subtraction of these spectra how the absorbance pattern of the protein backbone can be determined in order to predict glycoprotein secondary structure. The analysis predicted a predominant pattern of random coil, beta sheet and beta turn secondary structure for BSM after carbohydrate and amino acid spectral subtraction in agreement with other methods. Our relatively simple approach can be applied to predict secondary structure in other glycoproteins.     

Determination of ascorbic acid in human plasma with a view to stability using HPLC with UV detection

A method for the measurement of ascorbic acid using HPLC with UV detection and investigation into the protein precipitation techniques with regard to stability and recovery are described. The effectiveness of various protein precipitants was tested. Stability of ascorbic acid samples for analysis was investigated over 10 h. Ascorbic acid samples extracted with metaphosphoric acid were stable on a cooled autosampler (4 degrees C) for at least 10 h (with a decline of 1.8% for ascorbic acid solution and 2.8% for plasma). Perchloric acid as protein precipitant for ascorbic acid was unsuitable (with a decline of 36.0% for ascorbic acid solution and 7.3% for plasma). Analytical performance of this method is satisfactory. The intra- and interassay coefficients of variation were 2.1% (n = 10) and 5.8% (n = 12), respectively. The calibration curve was linear with the tested range of 2.0-250.0 micromol/L. The recovery was 96.1% with CV = 4.8% (n = 6) and the LOD was 3 micromol/L. The preliminary reference ranges of ascorbic acid in a group of blood donors are 50.8 +/- 22.4 micromol/L. This assay is a highly sensitive and reproducible HPLC method for the determination of ascorbic acid in human plasma.     

Characterization of thermo-oxidative stability of polymer optical fibers using chemiluminescence technique

The thermo-oxidative stability of commercially available polymer optical fibers (POFs) and their components (cores and claddings) was investigated. All the bare POFs (core and cladding only) studied here were based on poly(methyl methacrylate) (PMMA) core. The fibers were exposed to 100 °C/low humidity for about 4200 h. Chemiluminescence (CL) technique was applied to investigate the thermo-oxidative stability and for measuring the transmission loss during exposure a prototype device called multiplexer was used. POFs exhibited variation in thermo-oxidative stability although they possessed identical core material PMMA. This was due to difference in the chemical compositions of claddings. Claddings were more susceptible to the thermo-oxidative degradation compared to cores. The thermo-oxidative degradation of both the cladding and the core was found in POFs as a result of climatic exposure. POFs showed an early drop-off followed by a slow decline of transmission. The early drop-off of transmission was attributed to physical changes like thermal expansion and the slow decline of transmission to chemical changes like oxidative degradation of POFs. A good linear relationship between optical transmission stability and thermo-oxidative stability of POFs was established from these studies.     

Dynamic imaging of single DNA-protein interactions using atomic force microscopy

Atomic force microscopy (AFM) imaging of static DNA-protein complexes, in air and in liquid, can be used to directly obtain quantitative and qualitative information on the structure of different complexes. For example, DNA length, the location of preferential binding sites for proteins and bending of DNA as a result of the complexation can all be measured. Recording consecutive AFM images of DNA and protein molecules under conditions that they are still able to move and interact, or dynamic AFM imaging, however, can reveal information on the dynamic aspects of the interactions between these molecules. Here, an overview is given of the technical challenges that need to be considered for successful dynamic AFM imaging studies of individual DNA-protein interactions. Necessary technical improvements to the AFM set-up and the development of new sample preparation methods are described in this paper.     

Computational studies of bond dissociation energies, ionization potentials, and heat of formation for NH and NH+. Are hybrid density functional theory methods as accurate as quadratic complete basis set and Gaussian-2 ab initio methods?

Ionization potentials, bond dissociation energies, and heat of formation for NH and NH⁺ molecular species as well as for their elements were computed with highly reliable quadratic complete basis set and Gaussian-2 ab initio methods. The results are compared with experimental results and the assurance of these ab initio approaches is assessed. The same studies were also performed with three hybrid density functional methods (B3LYP, B3P86, and B3PW91) in combination with variously sized basis sets. The computational results are discussed in light of density functional theory reliability for exploring the potential energy of small polar molecular systems. Received: 21 July 1997 / Accepted: 8 December 1997     

Standard potentials of the silver,silver bromide electrode and the thermodynamic properties of hydrobromic acid in 1,2-dimethoxyethane and its aqueous mixtures

The standard potentials of the silver, silver bromide electrode have been determined in 1,2-dimethoxyethane (DME) and in nineteenDME + water solvents from the e.m.f. measurements of cells of the type Pt|H₂(g, 1 atm)|HBr (m), solvent|AgBr|Ag at intervals of 5°C from 5 to 45°C. The molality of HBr covered the range from 0.01 to 0.1 mol kg^–1. In solvents of highDME content, where the dielectric constant is small, it was necessary to correct for ion-pair formation. The temperature variation of the standard potential has been used to evaluate the standard thermodynamic functions for the cell reaction, and the standard quantities for the transfer of HBr from water to the respective solvents. The results have been discussed both in relation to the acid-base nature of the solvent mixtures and also their structural effects on the transfer process.

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Standardpotentiale der Silber, Silberbromid-Elektrode und thermodynamische Eigenschaften von H Br in 1,2-Dimethoxyethan und 1,2-Dimethoxyethan—Wasser-Mischungen

Zusammenfassung Die Standardpotentiale der Silber, Silberbromid-Elektrode wurden in 1,2-Dimethoxyethan (DME) und in 19 verschiedenenDME—Wasser-Gemischen aus EMK-Messungen der Zelle Pt|H₂(g,1 atm)|HBr (m), Lsgsm.|AgBr|Ag in Temperaturintervallen von 5°C zwischen 5 und 45°C bestimmt. Die Molalität von HBr deckte den Bereich von 0,01 bis 0,1 mol kg^–1. Bei Lösungen mit höheremDME-Gehalt — und damit niedrigen Dielektrizitätskonstanten —war es nötig, für die Bildung von Ionenpaaren eine Korrektur einzuführen. Über die Temperaturvariation wurden die thermodynamischen Größen für die Zellenreaktion und die Standardgrößen für den Transfer von HBr aus Wasser in das jeweilige Lösungsmittel bestimmt. Die Ergebnisse werden sowohl im Zusammenhang zur Säure-Base-Natur de Lösungsmittelmischungen als auch in bezug auf strukturelle Effekte im Transferprozeß diskutiert.

     

Improved thermal stability of crosslinked PTFE using fluorine gas treatment

Crosslinked PTFE (XF) samples were fluorinated at 293-593 K under 0.7-101 kPa F₂ and for 1 h to 7 days to improve its thermal stability. Because the weight uptake which may be caused by the fluorine addition was detected at room temperature, CC bonds in XF can be fluorinated and the fluorine content was saturated after 72 h. Weights of all samples increased more than that of original XF through additional fluorination of CC bonds, whereas it decreased by the chain-scission to form gaseous fluorocarbons such as CF₄. The intensity ratio in IR spectra of the peaks correspond to the double bond (CFCF₂) at 1785 cm⁻¹ and the characteristic peaks of PTFE at 1794 cm⁻¹, I_PTFE/I_PTFE was smaller for the fluorinated XF rather than that for XF. Average values of heat of crystallization (ΔH_c) for all fluorinated XF samples were about 2 J/g higher than that of the original XF. The decomposition temperature calculated from the TG curves increased with increasing reaction temperature and reaction time up to 72 h. Thermal stability of XF was improved through fluorine gas treatment.     

The parameterization and validation of generalized born models using the pairwise descreening approximation

Generalized Born Surface Area (GBSA) models for water using the Pairwise Descreening Approximation (PDA) have been parameterized by two different methods. The first method, similar to that used in previously reported parameterizations, optimizes all parameters against the experimental free energies of hydration of organic molecules. The second method optimizes the PDA parameters to compensate only for systematic errors of the PDA. The best models are compared to Poisson-Boltzmann calculations and applied to the computation of potentials of mean force (PMFs) for the association of various molecules. PMFs present a more rigorous test of the ability of a solvation model to correctly reproduce the screening of intermolecular interactions by the solvent, than its accuracy at predicting free energies of hydration of small molecules. Models derived with the first method are sometimes shown to fail to compute accurate potentials of mean force because of large errors in the computation of Born radii, while no such difficulties are observed with the second method. Furthermore, accurate computation of the Born radii appears to be more important than good agreement with experimental free energies of solvation. We discuss the source of errors in the potentials of mean force and suggest means to reduce them. Our findings suggest that Generalized Born models that use the Pairwise Descreening Approximation and that are derived solely by unconstrained optimization of parameters against free energies of hydration should be applied to the modeling of intermolecular interactions with caution.     

The inclusion of electron correlation in intermolecular potentials: applications to the formamide dimer and liquid formamide

A test of the quality of the electrostatic properties and polarizabilities used in the nonempirical molecular orbital (NEMO) potential is carried out for formamide by calculating the molecular dipole moment and polarizability at the second-order M?ller–Plesset (MP2) level of theory. The molecular dipole moment is 11% lower at the MP2 level than at the Hartree–Fock (HF) level, whereas the isotropic part of the polarizability is increased by 36% by adding electron correlation and using a considerably larger basis set. The atomic charges, dipole moments and polarizabilities obtained at the HF level are rescaled to get the correct molecular properties at the MP2 level. The potential minimum for the cyclic dimer of formamide is −17.50 kcal/mol with the MP2-scaled properties and is significantly lower than other potentials give. Two intermolecular potentials are constructed and used in subsequent molecular dynamics simulations: one with the regular NEMO potential and the other with the rescaled MP2 properties. A damping of the electrostatic field at short intermolecular distances is included in the present NEMO model. The average energies for liquid formamide are lower for the MP2-scaled model and are in good agreement with experimental results. The lowering of the simulation energy for the MP2-scaled potential indicates the strong dispersive interactions in liquid formamide. Received: 20 March 2000 / Accepted: 18 April 2000 / Published online: 18 August 2000     

Water stability of cobalt doped ZIF-8: a quantitative study using optical analyses

Zeolitic imidazolate frameworks (ZIFs), in particular ZIF-8 (made of Zn²⁺ and 2-methyilimidazolate) and cobalt-doped-ZIF-8, are found important for many energy and environmental applications. It was reported that ZIFs show excellent structural stability in water and thus ideal for aqueous applications. However, recent studies also found some evidence that ZIF-8 undergoes hydrolysis in water. Despite the importance of ZIF's stability in many aqueous applications, the extent of ZIFs' degradation in water is still not yet fully understood. In this study, we report a quantitative study of the water stability of 0–100 at% cobalt-doped ZIF-8, using a new combination of analytical tools. The study demonstrated the importance of analyzing both filtered powders and the filtrate liquid systematically, in particular by using UV–Vis spectroscopy and thermogravimetric analysis. The combination of analytical tools allowed the study on the effects of ZIF concentrations in water, cobalt doping levels, and amounts of ligands in water on the water stability of ZIF samples. The effect of cobalt-doping was investigated by using ZIF particles with identical sizes (200–400 nm), in order to eliminate the effects of particle size on hydrolysis. Unlike other synthesis methods, a mechanochemical ball milling method allowed the production of nano-scale ZIF-8 particles with similar sizes, independent of cobalt-doping levels. The proposed combination of analytical tools including UV–Vis spectroscopy can be applied to the study of the water stability of other MOF materials.     

Prediction of the non-Newtonian viscosity and shear stability of polymer solutions

The structure-property relationships derived here permit the prediction of both the zero-shear viscosity ₀, as well as the shear rate dependent viscosity . Using this molecular modeling it is now possible to predict over the whole concentration range, independently of the molecular weight, polymer concentration and imposed shear rate. However, the widely accepted concept: dilute — concentrated, is insufficient. Moreover it is necessary to take five distinct states of solution into account if the viscous behavior of polymeric liquids is to be described satisfactorily. For non-homogeneous, semi-dilute (moderately concentrated) solutions the slope in the linear region of the flow curve (= must be standardized against the overlap parameterc · []. As with the ₀-M-c-relationship, a-M -c- relationship can now be formulated for the complete range of concentration and molecular weight. Furthermore, it is possible to predict the onset of shear induced degradation of polymeric liquids subjected to a laminar velocity field on the basis of molecular modeling. These theoretically obtained results lead to the previously made ad hoc conclusion (Kulicke, Porter [32]) that, experimentally, it is not possible to detect the second Newtonian region.Roman and Italian symbols a exponent of the Mark-Houwink relationship - b exponent of the third term of the ₀-M -c relationship - c concentration /g · cm^–3 - E number of entanglements per molecule - F(r) connector tension - f function - G _i ^A shear modulus; A indicates that it /Pa has been evaluated by a transient shear flow experiment; i is the shear rate to whichG ^A refers to - G storage modulus /Pa - G _p plateau modulus /Pa - H() relaxation spectrum /Pa - h shift factor (₀/_r) - K _H Huggins constant - K _b third constant of the ₀-M -c relationship - K constant of the Mark-Houwink relationship - M molecular weight /g · mol^–1 - M _e molecular weight between two /g · mol^–1 entanglement couplings - N number of segments per molecule - n slope in the power-law region of the flow curve - p p-th mode of the relaxation time spectrum - R gas constant /8.314 J·K^–1·mol^–1 - r direction vector - T temperature /K Greek symbols ß reduced shear rate - shear rate /s^–1 - shear viscosity /Pa·s - _s solvent viscosity /Pa·s - _sp specific viscosity - ₀ zero-shear viscosity /Pa·s - apparent viscosity at shear rate - reduced viscosity - viscosity of polymeric liquid in /Pa·s the second Newtonian region - [] intrinsic viscosity/cm³·g^–1 - screening length/m - /g·cm ^–3 density - relaxation time/s - ₀ experimentally derived relaxation time/s - angular frequency of oscillation Indices conc concentrated - corr slope corrected - cr critical - deg degradation - e entanglement - exp experimental - mod moderately concentrated/semi-dilute - n number average - p polymer - R Rouse - rep reptation - s solvent - sp specific - theo theoretical - weight average - relaxation time - o experimental or steady state - * critical - ** transition moderately conc. — conc. - + transition dilute — moderately cone. Paper presented at the 2nd bilateral U.S.-West German Polymer Symposium, Yountville, the 7th–11th September 1987.     

Long-term stability of pure standards and stock standard solutions for the determination of pesticide residues using gas chromatography

The regular replacement of pure standards used in pesticide residue analysis laboratories and frequent preparation of stock standard solutions, both required by many accreditation bodies, impose considerable demands on a laboratory's resources. In this study, pure standards for all but one (heptenophos) of 118 different pesticides amenable to analysis by GC, and stock standard solutions (1000 microg/ml) prepared from these in toluene, acetone or ethyl acetate have been shown to be stable at < or = -20 degrees C over long periods: 4-13 and 2-8 years, respectively, for pure standards and solutions. Suitable solvents, containers and handling procedures are essential to avoid evaporation from solutions.     

Quantitation of a PEGylated protein in monkey serum by UHPLC-HRMS using a surrogate disulfide-containing peptide: A new approach to bioanalysis and in vivo stability evaluation of disulfide-rich protein therapeutics

To quantify a therapeutic PEGylated protein in monkey serum as well as to monitor its potential in vivo instability and methionine oxidation, a novel ultra high performance liquid chromatography-high resolution mass spectrometric (UHPLC-HRMS) assay was developed using a surrogate disulfide-containing peptide, DCP(SS), and a confirmatory peptide, CP, a disulfide-free peptide. DCP(SS) was obtained by eliminating the step of reduction/alkylation before trypsin digestion. It contains an intact disulfide linkage between two peptide sequences that are essential for drug function but susceptible to potential in vivo cleavages. HRMS-based single ion monitoring (SIM) on a Q Exactive™ mass spectrometer was employed to improve assay specificity and sensitivity for DCP(SS) due to its poor fragmentation and low sensitivity with SRM detection. The assay has been validated for the protein drug in monkey serum using both surrogate peptides with excellent accuracy (within ±4.4%Dev) and precision (within 7.5%CV) with a lower limit of quantitation (LLOQ) at 10 ng mL⁻¹. The protein concentrations in monkey serum obtained from the DCP(SS)-based assay not only provided important pharmacokinetic parameters, but also confirmed in vivo stability of the peptide regions of interest by comparing drug concentrations with those obtained from the CP-based assay or from a ligand-binding assay (LBA). Furthermore, UHPLC-HRMS allowed simultaneous monitoring of the oxidized forms of both surrogate peptides to evaluate potential ex vivo/in vivo oxidation of one methionine present in each of both surrogate peptides. To the best of our knowledge, this is the first report of using a surrogate disulfide-containing peptide for LC-MS bioanalysis of a therapeutic protein.     

Origin of intrinsic 3(10)-helix versus strand stability in homopolypeptides and its implications for the accuracy of the Amber force field

Current all-atom force fields often fail to recognize the native structure of a protein as the lowest free energy minimum. One possible cause could be the mathematical form of the potential based on the assumption that the conformation of a residue is independent of its neighbors. Here, using quantum mechanical (QM) methods (MP2/6-31g**//HF/6-31g** and MP2/cc-pVDZ//cc-pVDZ//HF/cc-pVDZ), the intrinsic correctness of the gas phase terms (without solvation) of the Amber ff03 and ff99 potentials are examined by testing their ability to reproduce the relative 3(10)-helix versus extended structure stabilities in the gas phase for 1-7-residue alanine, valine, leucine, and isoleucine homopolypeptides. The 3(10)-helix versus extended state stability strongly depends on chain length and less on the amino acid identity. The helical conformation becomes lower in energy than the extended conformation for all tested peptides longer than two residues, and its stability increases with the increase of chain length. The ff03 potential better describes the 3(10)-helix versus extended state energy than ff99 and also reproduces the curvature of the relative helix-extended state energies. Therefore, the mathematical form of the Amber potential is sufficient to describe the local effect of 3(10)-helix versus extended structure stabilization in the gas phase. However, the energy curves are shifted and the backbone geometries differ compared with the QM results. This may cause significant geometric discrepancies between native and predicted structures. Therefore, extant molecular mechanics force fields, such as Amber, need refinement of their parameters to correctly describe helix-extended state energetics and geometry of major conformations.