Time-dependent intermolecular interaction during protein reactions

A recently developed method to monitor reaction kinetics of intermolecular interaction is presented in this perspective. This method is based on time-dependent diffusion coefficient measurements using the pulsed laser induced transient grating technique. Using this method, time dependent biomolecular interactions, such as transient association and dissociation reactions in solution, have been successfully detected in real time. The principles and particular applications are described. In particular, unique features of this time-dependent diffusion coefficient method are emphasized by comparison with other techniques.     

Incorporation of chlorinated analogues of aliphatic amino acids during cell-free protein synthesis

3-Chloro-Abu and 4-chloro-Nva are biosynthetically incorporated into E. coli peptidyl-Pro cis-trans isomerase B, as substitutes for Val and Leu, respectively. The extent of incorporation is up to ~90%, and substituted protein is catalytically active. By contrast, 4-chloro-Val is not an effective replacement for Ile.     

Fluorinated amino acids in protein design and engineering

Selective incorporation of unnatural amino acids into proteins is a powerful tool for illuminating the principles of protein design. In particular, fluorinated amino acids have recently emerged as valuable building blocks for designing hyperstable protein folds, as well as directing highly specific protein-protein interactions. We review the collagen mimetic and coiled coil peptide systems that exemplify generalizable paradigms for future design. The unique electronic and phase properties of fluorocarbons are discussed, and protein synthesis using unnatural amino acids is briefly reviewed.     

The effects of individual amino acids on the fast folding dynamics of alpha-helical peptides

Nanosecond temperature jump experiments coupled to time-resolved infrared spectroscopy were carried out on a series of alanine-based peptides containing different guest amino acids to study the effects of residues with different helix propensities on the helix-coil dynamics.     

A facile and efficient method for the incorporation of multiple unnatural amino acids into a single protein

One stone, two birds: Here, we have developed a simple and efficient method for the incorporation of multiple unnatural amino acids in a single protein. This single protein exhibited two different novel functionalities acquired from the genetically incorporated unnatural amino acids, which is an interesting and not an inherent property of the protein.     

In vivo incorporation of multiple noncanonical amino acids into proteins

Expansion of the standard genetic code enables the design of recombinant proteins with novel and unusual properties. Traditionally, such proteins have contained only a single type of noncanonical amino acid (NCAA) in their amino acid sequence. However, recently reported initial efforts demonstrate that it is possible with suppression-based methods to translate two chemically distinct NCAAs into a single recombinant protein by combining the suppression of different termination codons and nontriplet coding units (such as quadruplets). The possibility of expanding the code with various NCAAs simultaneously further increases the toolkit for the generation of multifunctionalized proteins.     

Continuous multiple liquid-liquid separation: diazotization of amino acids in flow

A second-generation laboratory-scale, modular liquid-liquid separation device based on computer-controlled high-pressure pumps and a high-resolution digital camera has been invented. The diazotization of amino acids to produce valuable chiral hydroxyacids is demonstrated in flow for the first time. The use of a triple-separator system in conjuction with the developed diazotization process allows the safe and efficient production and automated isolation of multigram quantities of valuable chiral hydroxyacids.     

Predicting protein folding rates using the concept of Chou's pseudo amino acid composition

One of the most important challenges in computational and molecular biology is to understand the relationship between amino acid sequences and the folding rates of proteins. Recent works suggest that topological parameters, amino acid properties, chain length and the composition index relate well with protein folding rates, however, sequence order information has seldom been considered as a property for predicting protein folding rates. In this study, amino acid sequence order was used to derive an effective method, based on an extended version of the pseudo-amino acid composition, for predicting protein folding rates without any explicit structural information. Using the jackknife cross validation test, the method was demonstrated on the largest dataset (99 proteins) reported. The method was found to provide a good correlation between the predicted and experimental folding rates. The correlation coefficient is 0.81 (with a highly significant level) and the standard error is 2.46. The reported algorithm was found to perform better than several representative sequence-based approaches using the same dataset. The results indicate that sequence order information is an important determinant of protein folding rates.     

Gold nanoparticle formation during bromoaurate reduction by amino acids

The synthesis and characterization of water-soluble dispersions of gold nanoparticles by the reduction of a potassium tetrabromoaurate precursor solution using the amino acids L-tyrosine, glycyl-L-tyrosine, and L-arginine using alkaline synthesis conditions are reported. The particle sizes determined by small-angle X-ray scattering (SAXS) and high-resolution transmission electron microscopy (HRTEM) measurements are found to be inversely proportional to the rate of particle formation, which was determined by time-resolved UV-visible spectrophotometry measurements, and vary very slowly at intermediate gold concentrations and rapidly at the extremes. Dispersions produced with a mixture of the two amino acids glycyl-L-tyrosine and L-tyrosine showed particle sizes and particle size distributions which were directly proportional to the ratio of the two L-amino acids, thus offering the possibility for control over the properties of the gold nanoparticle dispersions.     

Capillary electrophoresis of nonprotein and protein amino acids without derivatization

An efficient separation of eleven nonprotein amino acids (NPAAs) and three protein amino acids containing aromatic moieties was achieved by capillary electrophoresis without derivatization. The fourteen amino acids were well separated with a 100 mM sodium phosphate run buffer (pH 2.0) using a 57 cm fused-silica capillary (50 microm ID, 50 cm effective length) at 20 degrees C. With an electric field of 351 V/cm, the time needed for the separation was less than 20 min. Under optimum conditions, excellent linear responses were obtained in the concentration range of 5-100 microM, with the linear correlation coefficient ranging from 0.9785 or greater. The relative standard deviations of the migration times and the corrected peak areas were found to be 1.5-3.9% and 8.0-11.5%, respectively. In order to improve the limit of detection (LOD), simple stacking and large volume stacking using an EOF pump (LVSEP) methods were used. Improved LODs were about 300 nM in stacking and below 15 nM for five small NPAAs in LVSEP.     

Gas chromatographic separation of protein amino acids in four minutes

A method is presented for analysis of protein amino acids in five minutes, including derivatization. The chemical treatment involves reaction with ethyl chloroformate: if the composition of the reaction medium is optimum this reagent esterifies carboxylic groups simultaneously with derivatization of other reactive groups and the reaction is complete in seconds. The moderately polar silicone OV-1701 was found to be a convenient liquid phase for separation of the derivatives: a five meter capillary column of internal diameter suitable for routine use was able to separate the amino acids in four minutes. Derivatization of arginine was incomplete and it failed to elute from the column.     

Solvent-induced forces in protein folding reflections on the protein folding problem

It is shown that the solvent induced forces on hydrophilic groups are the strongest ones. The relevance of this finding to protein folding is discussed.