Using the local elevation method to construct optimized umbrella sampling potentials: Calculation of the relative free energies and interconversion barriers of glucopyranose ring conformers in water

A method is proposed to combine the local elevation (LE) conformational searching and the umbrella sampling (US) conformational sampling approaches into a single local elevation umbrella sampling (LEUS) scheme for (explicit‐solvent) molecular dynamics (MD) simulations. In this approach, an initial (relatively short) LE build‐up (searching) phase is used to construct an optimized biasing potential within a subspace of conformationally relevant degrees of freedom, that is then used in a (comparatively longer) US sampling phase. This scheme dramatically enhances (in comparison with plain MD) the sampling power of MD simulations, taking advantage of the fact that the preoptimized biasing potential represents a reasonable approximation to the negative of the free energy surface in the considered conformational subspace. The method is applied to the calculation of the relative free energies of β‐D ‐glucopyranose ring conformers in water (within the GROMOS 45A4 force field). Different schemes to assign sampled conformational regions to distinct states are also compared. This approach, which bears some analogies with adaptive umbrella sampling and metadynamics (but within a very distinct implementation), is shown to be: (i) efficient (nearly all the computational effort is invested in the actual sampling phase rather than in searching and equilibration); (ii) robust (the method is only weakly sensitive to the details of the build‐up protocol, even for relatively short build‐up times); (iii) versatile (a LEUS biasing potential database could easily be preoptimized for small molecules and assembled on a fragment basis for larger ones). © 2009 Wiley Periodicals, Inc. J Comput Chem 2010     

15N-1H and 15N-13C couplings in 15N-enriched dihydroxamic acids

(15)N-enriched dihydroxamic acids (HONHCO(CH(2))(n)CONHOH, n = 0, 1, and 2) were prepared and their spectra NMR ((1)H, (13)C, (15)N) recorded in dimethyl sulfoxide (DMSO) solutions with the aim of determining (15)N coupling constants ((15)N-(1)H and (15)N-(13)C). The results supplement chemical shifts published earlier and yield additional support to the structural conclusions derived from other NMR parameters. Notably, no trace of hydroximic structures could be found in the (15)N NMR spectra of these acids. The values of (15)N-(13)C coupling constants backed by theoretical calculations support the assignments made earlier for all of the major conformers and for the minor conformer of succinohydroxamic acid. The enrichment revealed that the minor component of malonodihydroxamic acid solution previously considered to be the ZE conformer is in fact the monohydroxamic acid (HOOC-CH(2)-CO-NH-OH).     

Preorganization and protein dynamics in enzyme catalysis

Recently, an alternative has been offered to the concept of transition state (TS) stabilization as an explanation for rate enhancements in enzyme-catalyzed reactions. Instead, most of the rate increase has been ascribed to preorganization of the enzyme active site to bind substrates in a geometry close to that of the TS, which then transit the activation barrier impelled by motions along the reaction coordinate. The question as to how an enzyme achieves such preorganization and concomitant TS stabilization as well as potential coupled motions along the reaction coordinate leads directly to the role of protein dynamic motion. Dihydrofolate reductase (DHFR) is a paradigm in which the role of dynamics in catalysis continues to be unraveled by a wealth of kinetic, structural, and computational studies. DHFR has flexible loop regions adjacent to the active site whose motions modulate passage through the kinetically preferred pathway. The participation of residues distant from the DHFR active site in enhancing the rate of hydride transfer, however, is unanticipated and may signify the importance of long range protein motions. The general significance of protein dynamics in understanding other biological processes is briefly discussed.     

Structures and isomerization of neutral and zwitterion serine–water clusters: Computational study

Calculations are presented for the structure and the isomerization reaction of various conformers of the bare serine, neutral serine–(H₂O)_n and serine zwitterion–(H₂O)_n (n = 1, 2) clusters. The effects of binding water molecules on the relative stability and the isomerization processes are examined. Hydrogen bonding between serine and the water molecule(s) may significantly affect the relative stability of conformers of the neutral serine–(H₂O)_n (n = 1, 2) clusters. The sidechain (OH group) in serine is found to have a profound effect on the structure and isomerization of serine–(H₂O)_n (n = 1, 2) clusters. Conformers with the hydrogen bonding between water and the hydroxyl group of serine are predicted. A detailed analysis is presented of the isomerization (proton transfer) pathways between the neutral serine–(H₂O)₂ and serine zwitterion–(H₂O)₂ clusters by carrying out the intrinsic reaction coordinate analysis. At least two water molecules need to bind to produce the stable serine zwitterion–water cluster in the gas phase. The isomerization for the serine–(H₂O)₂ cluster proceeds by the concerted double and triple proton transfer mechanism occurring via the binding water molecules, or via the hydroxyl group. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Folding structures of isolated peptides as revealed by gas-phase mid-infrared spectroscopy.

To understand the intrinsic properties of peptides, which are determined by factors such as intramolecular hydrogen bonding, van der Waals bonding and electrostatic interactions, the conformational landscape of isolated protein building blocks in the gas phase was investigated. Here, we present IR-UV double-resonance spectra of jet-cooled, uncapped peptides containing a tryptophan (Trp) UV chromophore in the 1000-2000 cm(-1) spectral range. In the series Trp, Trp-Gly and Trp-Gly-Gly (where Gly stands for glycine), the number of detected conformers was found to decrease from six (Snoek et al., PCCP, 2001, 3, 1819) to four and two, respectively, which indicates a trend to relaxation to a global minimum. Density functional theory calculations reveal that the O-H in-plane bending vibration, together with the N-H in-plane bend ing and the peptide C=O stretching vibrations, is a sensitive probe to hydrogen bonding and, thus, to the folding of the peptide backbone in these structures. This enables the identification of spectroscopic fingerprints for the various conformational structures. By comparing the experimentally observed IR spectra with the calculated spectra, a unique conformational assignment can be made in most cases. The IR-UV spectrum of a Trp-containing nonapeptide (Trp-Ala-Gly-Gly-Asp-Ala-Ser-Gly-Glu) was recorded as well and, although the IR spectrum is less well-resolved (and it probably results from different isomers), groups of amide I (peptide C=O stretching) and amide II (N-H in-plane bending) bands can still be recognised, in agreement with predictions at the AM1 level.     

Assessing conformer energies using electronic structure and machine learning methods

We have performed a large‐scale evaluation of current computational methods, including conventional small‐molecule force fields; semiempirical, density functional, ab initio electronic structure methods; and current machine learning (ML) techniques to evaluate relative single‐point energies. Using up to 10 local minima geometries across ~700 molecules, each optimized by B3LYP‐D3BJ with single‐point DLPNO‐CCSD(T) triple‐zeta energies, we consider over 6500 single points to compare the correlation between different methods for both relative energies and ordered rankings of minima. We find that the current ML methods have potential and recommend methods at each tier of the accuracy‐time tradeoff, particularly the recent GFN2 semiempirical method, the B97‐3c density functional approximation, and RI‐MP2 for accurate conformer energies. The ANI family of ML methods shows promise, particularly the ANI‐1ccx variant trained in part on coupled‐cluster energies. Multiple methods suggest continued improvements should be expected in both performance and accuracy.     

Process Development for Separation of Conformers from Derivatives of Resorcin[4]arenes and Pyrogallol[4]arenes

Macrocyclic compounds, such as resorcin[4]arenes and pyrogallol[4]arenes, have proven to be useful building blocks in the construction of supramolecular organic frameworks (SOFs) because of their unique bowl‐like shape and ability to interact through variety of intermolecular interactions. Herein, we report the synthesis and crystal structures of two functionalized resorcin[4]arenes and pyroagllol[4]arenes, 4‐hydroxyphenylresorcin[4]arenes, and 4‐hydroxyphenylpyrogallol[4]arenes. These phenyl‐functionalized macrocycles usually have different conformers, such as cone, boat, chair, saddle, and diamond. The successful separation of predominant conformers from the crude product was carried out with solvent‐extraction technique. The shape and molecular arrangement of these conformers in the individual crystal structure was verified with single‐crystal X‐ray diffraction studies.     

Molecular dynamics of 6‐methyl‐2‐phenyl‐2,3‐dihydro‐4H‐chromen‐4‐one and 6‐methyl‐2‐(4‐nitrophenyl)‐2,3‐dihydro‐4H‐chromen‐4‐one (flavanone) derivatives in a solution studied by NMR spectroscopy

Molecular dynamics of benzoxazepin, oxime, pyrazole, and thiosemicarbazone derivatives of some flavanones have been investigated in a solution using NMR. The results confirm the formation of different O–H···O, O–H···N, N···H–N type intramolecular hydrogen bonds in the pyrazole and oxime molecules. The rotational barrier energy and energy of intramolecular hydrogen bonds have been determined. Copyright © 2013 John Wiley & Sons, Ltd.     

Capillary electrophoresis analysis of different variants of the amyloidogenic protein β2‐microglobulin as a simple tool for misfolding and stability studies

Free solution capillary electrophoresis with UV detection is here used to retrieve information on the conformational changes of wild‐type β₂‐microglobulin and a series of naturally and artificially created variants known to have different stability and amyloidogenic potential. Under nondenaturing conditions, the resolution of at least two folding conformers at equilibrium is obtained and a third species is detected for the less stable isoforms. Partial denaturation by using chaotropic agents such as acetonitrile or trifluoroethanol reveals that the separated peaks are at equilibrium, as the presence of less structured species is either enhanced or induced at the expenses of the native form. Reproducible CE data allow to obtain an interesting semiquantitative correlation between the peak areas observed and the protein stability. Thermal unfolding over the range 25–42°C is induced inside the capillary for the two pathogenic proteins (wtβ₂‐microglobulin and D76N variant): the large differences observed upon small temperature variation draw attention on the robustness of analytical methods when dealing with proteins prone to misfolding and aggregation.