The 3′-End of tRNA and Its Role in Protein Biosynthesis

In the course of protein biosynthesis, the 3′-ends of aminoacyl-tRNA (aa-tRNA) and peptidyl-tRNA specifically interact with macromolecules of the protein biosynthesis machinery. The 3′-end of tRNA consists of an invariant C-C-A single strand. Interaction of the aminoacyl-tRNA 3′-end with elongation factor Tu (EF-Tu) containing bound GTP is necessary for the formation of the aa-tRNA·EF-Tu·GTP complex and, after the complex binds to the ribosome, for the GTP hydrolysis. This process is followed by the specific binding of the aminoacyl-tRNA 3′-end to the aminoacyl (A) site of the ribosome. In this review, a model is proposed that involves Watson-Crick base pairing of the C? C sequence of the aminoacyl-tRNA 3′-end with a specific G? G sequence of the ribosomal 23S RNA. Similarly, peptidyl-tRNA binds with its 3′-end to the peptidyl (P) site of the ribosome. This binding may also involve Watson-Crick base pairing of the C-C-A sequence with a complementary sequence of 23S RNA. It is proposed that peptide bond formation is catalyzed by a functional site of the 23S RNA located near the 3′-ends of aminoacyl-tRNA and peptidyl-tRNA. A model is suggested in which two loops of the 23S RNA, brought into close proximity via folding, are involved both in binding the 3′-ends of the tRNAs and in catalyzing peptide bond formation. This model presumes a dynamic structure for ribosomal RNA, which is modulated by interaction with elongation factors and ribosomal proteins.     

Protein biosynthesis: the codon-specific activation of amino acids.

At the start of protein biosynthesis the amino acids are chemically activated by esterification with transfer ribonucleic acids bearing the appropriate anticodons. The esterification is catalyzed with an exceptionally high specificity by aminoacyl-tRNA synthetases. Current knowledge of the structural properties of the reactants, the course of the reaction, and the reasons for its specificity are summarized.     

Second-harmonic generation for studying structural motion of biological molecules in real time and space

SHG and sum-frequency generation (SFG) are surface-selective, nonlinear optical techniques whose ability to measure the average tilt angle of molecules on surfaces is well known in non-biological systems. By labeling molecules with a second-harmonic-active dye probe, SHG detection is extended to any biological molecule. The method has been used in previous work to detect biomolecules at an interface and their ligand-induced conformational changes. Here I demonstrate that SHG can be used to study structural motion quantitatively using a probe placed at a specific site (Cys-77) in adenylate kinase, a protein. The protein is also labeled non-site-specifically via amines. Labeled protein is absorbed to a surface and a baseline SH signal is measured. Upon introducing ATP, AMP or a specific inhibitor, AP(5)A, the baseline signal changes depending on the ligand and the labeling site. In particular, a substantial change in SH intensity is produced upon binding ATP to the amine-labeled protein, consistent with the X-ray crystal structures. In contrast, SHG polarization measurements are used to quantitatively determine that no rotation occurs at site Cys-77, in agreement with the lack of motion observed at this site in the X-ray crystal structures. A method for building a global map of conformational change in real time and space is proposed using a set of probes placed at different sites in a biomolecule. For this purpose, SH-active unnatural amino acids are attractive complements to exogenous labels.     

FT-Raman spectroscopy of biological molecules

Raman spectroscopy of biological molecules is often very difficult if not impossible due to a large fluorescence background from absorbing species, either from the molecule itself or an impurity. Photobleaching is occasionally successful in photochemically removing fluorescent impurities, but the majority of samples are not responsive to such treatment. Resonance enhancement of an absorbing species allows acquisition of Raman spectra in spite of competing fluorescence. However, the resonance Raman spectrum is characteristic of the chromophore only and little structural information is obtained from the spectrum about other parts of the molecule which are not resonantly enhanced. The newly developed technique of FT-Raman spectroscopy proves to be a solution to both of these problems for biological materials. Excitation with infrared wavelengths prevents electronic absorptions which give rise to fluorescence. In addition, the obtained spectra are completely nonresonant, allowing detection of vibrational modes of all parts of the molecule including the chromophore. We will present nonresonant, fluorescence free spectra of a range of biologically significant molecules including phospholipids and porphyrins.     

QM/MM connection atoms for the multistate treatment of organic and biological molecules

We present an extension of our semiempirical floating occupation MO-CI approach for the determination of ground and excited state potential energy surfaces of interest in photochemistry. The QM/MM variant of the method, which allows for electrostatic and van der Waals interactions between the QM and MM subsystems, is supplemented with a treatment of covalent interactions based on Antes and Thiels connection atom approach. We concentrate on the correct treatment of electrostatic interactions concerning the connection atom, on the specific requirements for the representation of excited states, and on the transferability of the optimal parameters. We show the viability of the method with four examples of connection atoms: S in a thioether bridge, acylic C, aliphatic C, and N in a peptide. The results obtained with the QM/MM treatment compare well with all-QM results of the same level.     

Developments in the production of biological and synthetic binders for immunoassay and sensor-based detection of small molecules

The need for chemical and biological entities of predetermined selectivity and affinity towards target analytes is greater than ever, in applications such as environmental monitoring, bioterrorism detection and analysis of natural toxin contaminants in the food chain.In this review, we focus on advances in the production of specific binders, in terms of both natural entities (e.g., antibodies) and synthetic binders (e.g., molecularly-imprinted polymers). We discuss the potential of emerging technologies for integration into immunoassay and sensing techniques. We place special emphasis on use of these technologies in bioanalytical applications.     

Surface characterization and depth profiling of biological molecules by electrospray droplet impact/SIMS

Electrospray droplet impact (EDI) was applied to the analysis of peptides. The etching rate of bradykinin was estimated to be ~2 nm/min. This value is about one order of magnitude greater than the etching rate for SiO₂ (0.2 nm/min). Considering that the etching rate of argon cluster ions Ar₇₀₀⁺ for organic compounds is more than two orders of magnitude larger than that for inorganic materials, the rather small difference in etching rates of EDI for organic and inorganic materials is unique. When water/ethanol (1/1, vol%) solution of gramicidin S and arginine was dried in air, [gramicidin S + H]⁺ was observed as a predominant signal with little [Arg + H]⁺ right after the EDI irradiation, indicating that EDI is capable of detecting the analytes enriched on the sample surface. Copyright © 2011 John Wiley & Sons, Ltd.     

On the investigation of the low-energy conformational space of molecules

A new perspective on traditional energy minimization problems is provided by a connection between statistical thermodynamics and combinatorial optimization (finding the minimum of a function depending on many variables). The joint use of a new method for uncovering the global minimum of intramolecular potential energy functions, based on following the asymptotic behavior of a system of stochastic differential equations, and an iterative-improvement technique, whereby a search for relative minima is made by carrying out local quasi-Newton minimizations starting from many distinct points of the energy hypersurface, proved most effective for investigating the low-energy conformational space of molecules.     

pH dependence of the kinetics of interfacial tension changes during protein adsorption from sessile droplets on FEP-Teflon

Interfacial tension changes during protein adsorption at both the solid-liquid and the liquid-vapor interface were measured simultaneously by ADSA-P from sessile droplets of protein solutions on fluoroethylenepropylene-Teflon. Four globular proteins of similar size, viz. lysozyme, ribonuclease, -lactalbumin and Ca²⁺-free -lactalbumin, and one larger protein, serum albumin, were adsorbed from phosphate solutions at varying pH values (pH 3-12). The kinetics of the interfacial tension changes were described using a model accounting for diffusion-controlled adsorption of protein molecules and conformational changes of already adsorbed molecules. The contribution of conformational changes to the equilibrium interfacial pressure was shown to be relatively small and constant with respect to pH when compared to the contribution of adsorption of the protein molecules. The model also yields the diffusion relaxation time and the rate constant for the conformational changes at the interface. Around the isoelectric point of a protein the calculated diffusion relaxation time was minimal, which is ascribed to the absence of an energy barrier to adsorption. Energy barriers to adsorption become larger at pH values away from the isoelectric point and can therefore become rate-limiting for the adsorption process. The rate constants for conformational changes at the liquid-vapor interface were maximal around the isoelectric point of a protein, suggesting a smaller structural stability of the adsorbed protein. At the solid-liquid interface the rate constants were smaller and independent of pH. indicating that conformational changes more readily occur at the liquid-vapor than at the solid-liquid interface.     

A simple sheathless CE-MS interface with a sub-micrometer electrical contact fracture for sensitive analysis of peptide and protein samples

Online coupling of capillary electrophoresis (CE) to electrospray ionization mass spectrometry (MS) has shown considerable potential, however, technical challenges have limited its use. In this study, we have developed a simple and sensitive sheathless CE-MS interface based on the novel concept of forming a sub-micrometer fracture directly in the capillary. The simple interface design allowed the generation of a stable ESI spray capable of ionization at low nanoliter flow-rates (45–90 nL/min) for high sensitivity MS analysis of challenging samples like those containing proteins and peptides. By analysis of a model peptide (leucine enkephalin), a limit of detection (LOD) of 0.045 pmol/μL (corresponding to 67 attomol in a sample volume of ∼15 nL) was obtained. The merit of the CE-MS approach was demonstrated by analysis of bovine serum albumin (BSA) tryptic peptides. A well-resolved separation profile was achieved and comparable sequence coverage was obtained by the CE-MS method (73%) compared to a representative UPLC-MS method (77%). The CE-MS interface was subsequently used to analyse a more complex sample of pharmaceutically relevant human proteins including insulin, tissue factor and α-synuclein. Efficient separation and protein ESI mass spectra of adequate quality could be achieved using only a small amount of sample (30 fmol). In addition, analysis of ubiquitin samples under both native and denatured conditions, indicate that the CE-MS setup can facilitate native MS applications to probe the conformational properties of proteins. Thus, the described CE-MS setup should be useful for a wide range of high-sensitivity applications in protein research.     

Toward room-temperature optical manipulation of small molecules

Room-temperature optical manipulation of small molecules is a challenging issue in the field of material science. To increase optical force for a single molecule trapping, it has been recognized that resonant excitation of molecules should be controlled under the light illumination. Strongly interacting molecules with solid surfaces at electrified interfaces show the exotic behavior of electronic excitation by localized surface plasmon. In this review, we emphases that surface-enhanced Raman scattering can be used to evaluate the resonant excitation of target molecules at interfaces. Under such excitation, the diffusion of small molecules can be controlled by the optical force generated by the intensity gradient of a highly localized electric field.     

Normal mode analysis based on an elastic network model for biomolecules in the Protein Data Bank,which uses dihedral angles as independent variables

We have developed a computer program, named PDBETA, that performs normal mode analysis (NMA) based on an elastic network model that uses dihedral angles as independent variables. Taking advantage of the relatively small number of degrees of freedom required to describe a molecular structure in dihedral angle space and a simple potential-energy function independent of atom types, we aimed to develop a program applicable to a full-atom system of any molecule in the Protein Data Bank (PDB). The algorithm for NMA used in PDBETA is the same as the computer program FEDER/2, developed previously. Therefore, the main challenge in developing PDBETA was to find a method that can automatically convert PDB data into molecular structure information in dihedral angle space. Here, we illustrate the performance of PDBETA with a protein–DNA complex, a protein–tRNA complex, and some non-protein small molecules, and show that the atomic fluctuations calculated by PDBETA reproduce the temperature factor data of these molecules in the PDB. A comparison was also made with elastic-network-model based NMA in a Cartesian-coordinate system.     

Charge transfer at biotic/abiotic interfaces in biological electrocatalysis

In this opinion paper, we discuss the charge transfer at biotic/abiotic interfaces in man-made and biological electrochemical systems. Specifically, we will first introduce the heterogeneous charge transfer at the bioelectrode interface, followed by the intramolecular change transfer in peptide and protein structures, and finally discuss the extracellular charge transfer in electrogenic microorganisms. In addition to discussion of charge transfer mechanisms and synthetic structures/scaffolds required for it, a particular focus will be given to novel experimental designs that are able to bring new concepts and boost mechanism understanding and applications development. There are also discussions on the combination of modern computational techniques and experimental characterizations.     

Visualization of large elongated DNA molecules

Long and linear DNA molecules are the mainstream single‐molecule analytes for a variety of biochemical analysis within microfluidic devices, including functionalized surfaces and nanostructures. However, for biochemical analysis, large DNA molecules have to be unraveled, elongated, and visualized to obtain biochemical and genomic information. To date, elongated DNA molecules have been exploited in the development of a number of genome analysis systems as well as for the study of polymer physics due to the advantage of direct visualization of single DNA molecule. Moreover, each single DNA molecule provides individual information, which makes it useful for stochastic event analysis. Therefore, numerous studies of enzymatic random motions have been performed on a large elongated DNA molecule. In this review, we introduce mechanisms to elongate DNA molecules using microfluidics and nanostructures in the beginning. Secondly, we discuss how elongated DNA molecules have been utilized to obtain biochemical and genomic information by direct visualization of DNA molecules. Finally, we reviewed the approaches used to study the interaction of proteins and large DNA molecules. Although DNA‐protein interactions have been investigated for many decades, it is noticeable that there have been significant achievements for the last five years. Therefore, we focus mainly on recent developments for monitoring enzymatic activity on large elongated DNA molecules.     

Application of luminescent nanocrystals as labels for biological molecules

Luminescent semiconductor nanocrystals, so called quantum dots (QD), have attracted increasing interest for bioanalytical labeling applications in recent years. This review describes the major optical and (bio)chemical features of this class of label, compared with organic dyes. Different conjugation methods are also discussed and the most important recent applications are presented. An overview over the current state-of-the-art is given, as also is an outlook on possibilities and limitations.     

Chip-based nano-LC-MS/MS identification of proteins in complex biological samples using a novel polymer microfluidic device

Although the proteome of each organism is unambiguously coded in its genome, the proteome shows the real biology in action in each particular organism. New powerful tools are being developed for biochemists and biologists to analyze complex biological samples for studying the complete protein supplement of the genome, i. e., the proteome. There are several methods available for proteome analysis including 2-DE and several forms of MS. In recent years, technologies such as microfluidics and array-based systems have appeared in the field of analysis, identification, and quantification of proteins. These novel approaches might help in solving current technical challenges in proteomics. This paper presents a practical application of the first commercially available microfluidic nano-ESI device coupled with nano-LC (i. e., HPLC-chip) for the analysis of samples of some biological protein mixtures.     

Dynamical and statistical effects of the intrinsic curvature of internal space of molecules

The Hamilton dynamics of a molecule in a translationally and/or rotationally symmetric field is kept rigorously constrained in its phase space. The relevant dynamical laws should therefore be extracted from these constrained motions. An internal space that is induced by a projection of such a limited phase space onto configuration space is an intrinsically curved space even for a system of zero total angular momentum. In this paper we discuss the general effects of this curvedness on dynamics and structures of molecules in such a manner that is invariant with respect to the selection of coordinates. It is shown that the regular coordinate originally defined by Riemann is particularly useful to expose the curvature correction to the dynamics and statistical properties of molecules. These effects are significant both qualitatively and quantitatively and are studied in two aspects. One is the direct effect on dynamics: A trajectory receives a Lorentz-like force from the curved space as though it was placed in a magnetic field. The well-known problem of the trapping phenomenon at the transition state is analyzed from this point of view. By showing that the trapping force is explicitly described in terms of the curvature of the internal space, we clarify that the physical origin of the trapped motion is indeed originated from the curvature of the internal space and hence is not dependent of the selection of coordinate system. The other aspect is the effect of phase space volume arising from the curvedness: We formulate a general expression of the curvature correction of the classical density of states and extract its physical significance in the molecular geometry along with reaction rate in terms of the scalar curvature and volume loss (gain) due to the curvature. The transition state theory is reformulated from this point of view and it is applied to the structural transition of linear chain molecules in the so-called dihedral angle model. It is shown that the curvature effect becomes large roughly linearly with the size of molecule.