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Lysergic acid diethylamide (LSD) is a hallucinogenic compound that binds to and activates the serotonin 2A receptor and is classified as a controlled narcotic in Japan. Recently, MiPLA, an N‐methyl‐N‐isopropyl derivative of LSD, has been detected in paper‐sheet products in several countries. This study focuses on the synthesis of MiPLA and includes a comprehensive analysis involving structural and liquid chromatography–mass spectrometry (LC‐MS). Particularly, MiPLA was synthesized in three‐steps starting from ergometrine maleate, which resulted in the formation of (8S)‐isomer, iso‐MiPLA, as a by‐product. The LC‐MS results showed that LSD, MiPLA, and iso‐MiPLA exhibited different retention times. Their chemical structures were determined using nuclear magnetic resonance spectroscopy, which revealed the presence of rotamers involving the N‐methyl‐N‐isopropyl groups of tertiary amides in MiPLA and iso‐MiPLA. [ABSTRACT FROM AUTHOR]

From the n‐butanol soluble fraction of the ethanol extract of the medicinal plant Olax subscorpioidea, a previously unreported rotameric biflavonoid glycoside constituted of 4′‐O‐methylgallocatechin‐(4α → 8)‐4′‐O‐methylgallocatechin as aglycone named olasubscorpioside C (1) along with the known 4′‐O‐methylgallocatechin (2) were isolated. Their structures were determined on the basis of spectrometric and spectroscopic techniques including HRFABMS, 1H and 13C NMR, DEPT 135o, HSQC, HMBC, ROESY, and CD followed by comparison with the reported data. [ABSTRACT FROM AUTHOR]

Protein fluorescence signals essential information about the conformational dynamics of proteins. Different types of intrinsic fluorophores reflect different protein local or global structural changes. Bovine Serum Albumin (BSA) is a transport protein that contains two intrinsic fluorophores: Tryptophan134 (Trp134) and Tryptophan213 (Trp213). This protein displays an interesting temperature dependence of the tryptophan fluorescence. However, the molecular mechanism of the temperature dependence is still unclear. In this work, we propose a generic rotamer model to explain this phenomenon. The model assumes the presence of rotamer‐specific fluorescence lifetimes. The fluorescence temperature dependence is caused by the population shifts between different rotamers due to thermal effects. As a proof of concept, we show that the tryptophan's two fluorescence lifetimes (휏1 = 0.4–0.5 ns and 휏2 = 2‐4 ns) are sufficient to qualitatively explain the fluorescence intensity change at different temperatures, both in buffer solution (water) and in the protein. To computationally verify our rotamer hypothesis, we use an all‐atom molecular dynamics simulation to study the effects of temperature on the two tryptophans' rotamer dynamics. The simulations show that Trp134 is more sensitive to temperature, consistent with experimental observations. Overall, the results support that the temperature dependence of fluorescence in the protein BSA is due to local conformational changes at the residue level. This work sheds light on the relationship between tryptophan's rotamer dynamics and its ability to fluorescence. [ABSTRACT FROM AUTHOR]

Herein we report a highly efficient and enantiospecific borylation method to synthesize a wide range of enantiopure (>99 % ee) α‐amino tertiary boronic esters. The configurationally stable α‐N‐Boc substituted tertiary organolithium species and pinacolborane (HBpin) underwent enantiospecific borylation at −78 °C with the formation of a new stereogenic C−B bond. This reaction has a broad scope, enabling the synthesis of various α‐amino tertiary boronic esters in excellent yields and, importantly, with universally excellent enantiospecificity (>99 % es) and complete retention of configuration. Enantiospecific borylation: A highly enantiospecific borylation of configurationally stable α‐N‐Boc substituted tertiary organolithium species and HBpin has been developed to synthesize various α‐amino tertiary boronic esters through the formation of a new C−B bond with excellet enantiopurity and complete retention of configuration. [ABSTRACT FROM AUTHOR]

Transition metal complexes containing dimethyl sulfoxide (DMSO) are important precursors in catalysis and metallodrugs. Understanding the solid-state supramolecular structure is crucial for predicting the properties and biological activity of the material. Several crystalline phases of DMSO-coordinated iridium anions with different cations, potassium (1 a) and n-butylammonium (1 b), were obtained and their structures determined by X-ray crystallography. Compound (1 a) is present in two solvatomorphic forms: α and β; the β form contains disordered solvent water. In addition, the structures exhibit different rotamers of the trans-[IrCl4(DMSO)2]− anion with the trans-DMSO ligands being oriented in anti and gauche conformations. In consideration of these various conformers, the effects of the crystallized solvent and intermolecular interactions on the conformational preferences of the anion are discussed. In addition, density functional theory calculations were used to investigate the energies of the anions in the different conformations. It was found that hydrogen bonds between water and the DMSO complex stabilize the gauche conformation which is the least stable form of the trans-DMSO complex. Consequently, by controlling the number of hydrogen-bond donors and acceptors and the amount of water, it may be possible to obtain different solvatomorphs of clinically significant metallodrugs. [ABSTRACT FROM AUTHOR]

Obtaining a quantitative description of the membrane proteins stability is crucial for understanding many biological processes. However the advance in this direction has remained a major challenge for both experimental studies and molecular modeling. One of the possible directions is the use of coarse-grained models but such models must be carefully calibrated and validated. Here we use a recent progress in benchmark studies on the energetics of amino acid residue and peptide membrane insertion and membrane protein stability in refining our previously developed coarse-grained model (Vicatos et al., Proteins 2014;82:1168). Our refined model parameters were fitted and/or tested to reproduce water/membrane partitioning energetics of amino acid side chains and a couple of model peptides. This new model provides a reasonable agreement with experiment for absolute folding free energies of several ??-barrel membrane proteins as well as effects of point mutations on a relative stability for one of those proteins, OmpLA. The consideration and ranking of different rotameric states for a mutated residue was found to be essential to achieve satisfactory agreement with the reference data. [ABSTRACT FROM AUTHOR]

Nonmuscle myosin-2 is the primary enzyme complex powering contractility of the F-actin cytoskeleton in the model organism Drosophila. Despite myosin's essential function in fly development and homeostasis, its kinetic features remain elusive. The purpose of this in vitro study is a detailed steady-state and presteady-state kinetic characterization of the Drosophila nonmuscle myosin-2 motor domain. Kinetic features are a slow steady-state ATPase activity, high affinities for F-actin and ADP, and a low duty ratio. Comparative analysis of the overall enzymatic signatures across the nonmuscle myosin-2 complement from model organisms indicates that the Drosophila protein resembles nonmuscle myosin-2s from metazoa rather than protozoa, though modulatory aspects of myo-sin motor function are distinct. Drosophila nonmuscle myosin-2 is uniquely insensitive toward blebbistatin, a commonly used myosin-2 inhibitor. An in silico modeling approach together with kinetic studies indicate that the nonconsensus amino acid Met466 in the Drosophila nonmuscle myosin-2 active-site loop switch-2 acts as blebbistatin desensitizer. Introduction of the M466I mutation sensitized the protein for blebbistatin, resulting in a half-maximal inhibitory concentration of 36.3 ± 4.1 µM. Together, these data show that Drosophila nonmuscle myosin-2 is a bonafide molecular motor and establish an important link between switch-2 and blebbistatin sensitivity. [ABSTRACT FROM AUTHOR]

ABSTRACT Side chain optimization is an integral component of many protein modeling applications. In these applications, the conformational freedom of the side chains is often explored using libraries of discrete, frequently occurring conformations. Because side chain optimization can pose a computationally intensive combinatorial problem, the nature of these conformer libraries is important for ensuring efficiency and accuracy in side chain prediction. We have previously developed an innovative method to create a conformer library with enhanced performance. The Energy-based Library (EBL) was obtained by analyzing the energetic interactions between conformers and a large number of natural protein environments from crystal structures. This process guided the selection of conformers with the highest propensity to fit into spaces that should accommodate a side chain. Because the method requires a large crystallographic data-set, the EBL was created in a backbone-independent fashion. However, it is well established that side chain conformation is strongly dependent on the local backbone geometry, and that backbone-dependent libraries are more efficient in side chain optimization. Here we present the backbone-dependent EBL (bEBL), whose conformers are independently sorted for each populated region of Ramachandran space. The resulting library closely mirrors the local backbone-dependent distribution of side chain conformation. Compared to the EBL, we demonstrate that the bEBL uses fewer conformers to produce similar side chain prediction outcomes, thus further improving performance with respect to the already efficient backbone-independent version of the library. Proteins 2014; 82:3177-3187. © 2014 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Spinning to improve (band) shape: A blend of theoretical and experimental work demonstrates that the rotational conformation of mixed‐valence complexes influences the low‐energy (NIR) transitions in such molecules. Interpretations of the NIR band shapes are presented. [ABSTRACT FROM AUTHOR]

Protein-protein interactions encode the wiring diagram of cellular signaling pathways and their deregulations underlie a variety of diseases, such as cancer. Inhibiting protein-protein interactions with peptide derivatives is a promising way to develop new biological and therapeutic tools. Here, we develop a general framework to computationally handle hundreds of non-natural amino acid sidechains and predict the effect of inserting them into peptides or proteins. We first generate all structural files (pdb and mol2), as well as parameters and topologies for standard molecular mechanics software (CHARMM and Gromacs). Accurate predictions of rotamer probabilities are provided using a novel combined knowledge and physics based strategy. Non-natural sidechains are useful to increase peptide ligand binding affinity. Our results obtained on non-natural mutants of a BCL9 peptide targeting beta-catenin show very good correlation between predicted and experimental binding free-energies, indicating that such predictions can be used to design new inhibitors. Data generated in this work, as well as PyMOL and UCSF Chimera plug-ins for user-friendly visualization of non-natural sidechains, are all available at . Our results enable researchers to rapidly and efficiently work with hundreds of non-natural sidechains. © 2012 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

The unique biophysical properties of tryptophan residues have been exploited for decades to monitor protein structure and dynamics using a variety of spectroscopic techniques, such as fluorescence and nuclear magnetic resonance (NMR). We recently designed a tryptophan mutant in the regulatory N-domain of cardiac troponin C (F77W-cNTnC) to study the domain orientation of troponin C in muscle fibers using solid-state NMR. In our previous study, we determined the NMR structure of calcium-saturated mutant F77W-V82A-cNTnC in the presence of 19% 2,2,2-trifluoroethanol (TFE). TFE is a widely used cosolvent in the biophysical characterization of the solution structures of peptides and proteins. It is generally assumed that the structures are unchanged in the presence of cosolvents at relatively low concentrations, and this has been verified for TFE at the level of the overall secondary and tertiary structure for several calcium regulatory proteins. Here, we present the NMR solution structure of the calcium saturated F77W-cNTnC in presence of its biological binding partner troponin I peptide (cTnI144-163) and in the absence of TFE. We have also characterized a panel of six F77W-cNTnC structures in the presence and absence TFE, cTnI144-163, and the extra mutation V82A, and used 19F NMR to characterize the effect of TFE on the F77(5fW) analog. Our results show that although TFE did not perturb the overall protein structure, TFE did induce a change in the orientation of the indole ring of the buried tryptophan side chain from the anticipated position based upon homology with other proteins, highlighting the potential dangers of the use of cosolvents. [ABSTRACT FROM AUTHOR]

We present direct evidence for a change in protein structural specificity due to hydrophobic core packing. High resolution structural analysis of a designed core variant of ubiquitin reveals that the protein is in slow exchange between two conformations. Examination of side-chain rotamers indicates that this dynamic response and the lower stability of the protein are coupled to greater strain and mobility in the core. The results suggest that manipulating the level of side-chain strain may be one way of fine tuning the stability and specificity of proteins. [ABSTRACT FROM AUTHOR]

Diethylenetriamines and diethanolamines carrying a carbamate‐protected amine and peripheral reactive units are valuable synthetic building blocks for hydrogel crosslinkers or biohybrid materials because they enable orthogonal functionalization. However, the carbamate unit leads to restricted rotational mobility, affecting both physical and chemical properties of the amines. To gain insight into the rotational behavior of such systems, a series of carbamate‐protected amines with different peripheral units was synthesized and their rotational barriers were studied by dynamic NMR measurements and electronic structure calculations. Experimentally observed barriers were in the range of 61 to 66 kJ/mol and were mostly dependent on the size of the peripheral groups rather than their hydrogen bonding ability. Density functional theory (DFT) and MP2 calculations yielded barriers of similar order of magnitude, albeit differing in the overall trends. The data suggest that for improved theoretical estimates of free energy barriers ab initio molecular dynamics simulations in explicit solvent would be required. [ABSTRACT FROM AUTHOR]