Multiple-quantum nuclear magnetic resonance spectroscopy

A nuclear magnetic resonance (NMR) event is popularly viewed as the flip of a single spin in a magnetc field, stimulated by the absorption or emission of only one quantum of radio-frequency energy. Nevertheless, resonances between nuclear spin states that differ by more than one unit in the Zeeman quantum number also can be induced in systems of coupled spins by suitably designed sequences of radio-frequency pulses. Pairs of states excited in this way oscillate coherently at the frequencies of the corresponding multiple-quantum transitions and produce a response that may be monitored indirectly in a two-dimensional time-domain experiment. The pattern of multiple-quantum excitation and response, influenced largely by the concerted interactions of groups of coupled nuclei, simplifies the NMR spectrum in some instances and provides significant new information in others. Applications of multiple-quantum NMR extend to problems in many different areas, ranging from studies of the structure and function of proteins and nucleic acids in solution to investigations of the arrangements of atoms in amorphous semiconductors. The specific spectroscopic techniques are varied as well and include methods designed, for example, to simplify spectral analysis for liquids and liquid crystals, eliminate inhomogeneous broadening, study interatomic connectivity in liquid-state molecules, identify clusters of atoms in solids, enhance the spatial resolution in solid-state imaging experiments, and probe correlated molecular motions.     

Dynamically controlled protein tunneling paths in photosynthetic reaction centers

Marcus theory has explained how thermal nuclear motions modulate the energy gap between donor and acceptor sites in protein electron transfer reactions. Thermal motions, however, may also modulate electron tunneling between these reactions. Here we identify a new mechanism of nuclear dynamics amplification that plays a central role when interference among the dominant tunneling pathway tubes is destructive. In these cases, tunneling takes place in protein conformations far from equilibrium that minimize destructive interference. As an example, we demonstrate how this dynamical amplification mechanism affects certain reaction rates in the photosynthetic reaction center and therefore may be critical for biological function.     

THE TREND OF THOUGHT IN PHYSICS. II

In its fundamental aspects, practically the whole of modern physics is concerned with the discussion of the relations which exist between the motions of two sets of points in such a way as to establish a sort of one-one correspondence between the things which we do, and the behavior of one set of points on the one hand, and the things which we observe and the behavior of the other set of points on the other hand. We send a beam of electrons through an X-ray tube, and certain dark lines appear on photographic plates elsewhere, or electrons are emitted with certain velocities which we measure indirectly. As regards the electrons which are emitted into our apparatus, we can almost say that we observe them directly. As regards the blackening of the photographic plate, we are content if we can account for certain electronic emissions or motions to which we can attribute it. We do not, however, try to establish a direct relation between the original beam of electrons and the photographic plate or photoelectric cell, because we find that certain other apparatus was necessary for the experiment, a calcite grating and X-ray target, and so forth. These pieces of apparatus are replaced in the mind's eye by other sets of points grouped into atoms and molecules, in a manner characteristic of the substances in such a way that we may hope to be able to establish a relation between the first set of points, those in the target, those in the calcite and those in the final photographic plate or photoelectric cell. The whole problem is to discover how the points must be assigned and what function their mutual motions are of each other in order that the correlation may be satisfactorily made.     

Structures of larger proteins in solution: three- and four-dimensional heteronuclear NMR spectroscopy

Three- and four-dimensional heteronuclear nuclear magnetic resonance (NMR) spectroscopy offers dramatic improvements in spectral resolution by spreading through-bond and through-space correlations in three and four orthogonal frequency axes. Simultaneously, large heteronuclear couplings are exploited to circumvent problems due to the larger linewidths that are associated with increasing molecular weight. These novel experiments have been designed to extend the application of NMR as a method for determining three-dimensional structures of proteins in solution beyond the limits of conventional two-dimensional NMR (approximately 100 residues) to molecules in the 150- to 300-residue range. This potential has recently been confirmed with the determination of the high-resolution NMR structure of a protein greater than 150 residues, namely, interleukin-1 beta.     

Laser probing of chemical reaction dynamics

Lasers are used in increasingly sophisticated ways to carry out reactions between molecules in selected vibrational, rotational, and electronic states and to probe the product states of chemical reactions. Such investigations are providing unprecedented insights into chemical reaction dynamics, the study of the detailed motions that molecules undergo in simple chemical reactions. In many cases it is possible to describe the influence that specific types of molecular excitation have on reactive events. Experiments are also being carried out to leam about chemical reactivity as a function of the alignment of reagents. There is increasing excitement concerning the potential of laser methods to interrogate the transition states of molecular reactions.     

Solution structure of the integral human membrane protein VDAC-1 in detergent micelles

The voltage-dependent anion channel (VDAC) mediates trafficking of small molecules and ions across the eukaryotic outer mitochondrial membrane. VDAC also interacts with antiapoptotic proteins from the Bcl-2 family, and this interaction inhibits release of apoptogenic proteins from the mitochondrion. We present the nuclear magnetic resonance (NMR) solution structure of recombinant human VDAC-1 reconstituted in detergent micelles. It forms a 19-stranded beta barrel with the first and last strand parallel. The hydrophobic outside perimeter of the barrel is covered by detergent molecules in a beltlike fashion. In the presence of cholesterol, recombinant VDAC-1 can form voltage-gated channels in phospholipid bilayers similar to those of the native protein. NMR measurements revealed the binding sites of VDAC-1 for the Bcl-2 protein Bcl-x(L), for reduced beta-nicotinamide adenine dinucleotide, and for cholesterol. Bcl-x(L) interacts with the VDAC barrel laterally at strands 17 and 18.     

Protein structure determination in solution by nuclear magnetic resonance spectroscopy

Knowledge of three-dimensional protein structures is one of the foundations of protein design and protein engineering. Nuclear magnetic resonance spectroscopy was recently introduced as a second method for protein structure determination, in addition to the well-established diffraction techniques with protein single crystals. This new approach enables one to carry out detailed structural studies of proteins in solution and other noncrystalline states, which may be similar or identical to the physiological environment, and promises new insights into the dynamics of protein molecules and the protein-folding problem.     

Conformational switches modulate protein interactions in peptide antibiotic synthetases

Protein dynamics plays an important role in protein function. Many functionally important motions occur on the microsecond and low millisecond time scale and can be characterized by nuclear magnetic resonance relaxation experiments. We describe the different states of a peptidyl carrier protein (PCP) that play a crucial role in its function as a peptide shuttle in the nonribosomal peptide synthetases of the tyrocidine A system. Both apo-PCP (without the bound 4'-phosphopantetheine cofactor) and holo-PCP exist in two different stable conformations. We show that one of the apo conformations and one of the holo conformations are identical, whereas the two remaining conformations are only detectable by nuclear magnetic resonance spectroscopy in either the apo or holo form. We further demonstrate that this conformational diversity is an essential prerequisite for the directed movement of the 4'-PP cofactor and its interaction with externally acting proteins such as thioesterases and 4'-PP transferase.     

Biochemistry. All in the ubiquitin family

The job of a protein can be altered by addition of molecules such as ubiquitin or the related ubiquitin-like modifiers, which bring about changes in the protein's localization, conformation, or its interactions with other proteins. In a comprehensive Perspective, Hochstrasser brings us up to date with the many new members of the ubiquitin modifier family and their multitudinous and diverse protein targets.     

A two-stage optimal motion planner for autonomous agricultural vehicles

This paper presents a two-stage motion planning algorithm which can compute low-cost motions for autonomous agricultural vehicles, for a given cost function defined over the entire path (e.g., shortest path, maximum clearance, etc.). In the first stage, the algorithm utilizes randomized motion planning to explore the space of possible motions and computes a feasible sub-optimal trajectory. In the second stage, the optimization of the stage-1 motion is formulated within the optimal control framework and function-space gradient descent is used to minimize the cost of the entire motion. The numerical results suggest that the two-stage motion planner can compute optimal or quasi-optimal motions in free space very quickly. In the presence of obstacles however, the execution time increases significantly. Furthermore, kino-dynamic, or dynamic motion models seem to be necessary in order to produce smooth motion trajectories.     

Some developments in nuclear magnetic resonance of solids

Nuclear magnetic resonance (NMR) spectroscopy continues to evolve as a primary technique in the study of solids. This review briefly describes some developments in modern NMR that demonstrate its exciting potential as an analytical tool in fields as diverse as physics, chemistry, biology, geology, and materials science. Topics covered include motional narrowing by sample reorientation, multiple-quantum and overtone spectroscopy, probing porous solids with guest atoms and molecules, two-dimensional NMR studies of chemical exchange and spin diffusion, experiments at extreme temperatures, NMR imaging of solid materials, and low-frequency and zero-field magnetic resonance. These developments permit increasingly complex structural and dynamical behavior to be probed at a molecular level and thus add to our understanding of macroscopic properties of materials.     

新型食品添加剂谷氨酰胺转胺酶的生产及应用研究进展

谷氨酰胺转胺酶具有催化酰基转移,使蛋白质分子内和分子间交联,提高蛋白质营养价值的功能,是一种应用前景良好的新型食品添加剂。主要介绍了谷氨酰胺转胺酶的作用机理、生产及其在食品工业中的应用。     

Some concepts in reaction dynamics

The objective in this work has been one which I have shared with the two other 1986 Nobel lecturers in chemistry, D. R. Herschbach and Y. T. Lee, as well as with a wide group of colleagues and co-workers who have been responsible for bringing this field to its current state. That state is summarized in the title; we now have some concepts relevant to the motions of atoms and molecules in simple reactions, and some examples of the application of these concepts. We are, however, richer in vocabulary than in literature. The great epics of reaction dynamics remain to be written. I shall confine myself to some simple stories.     

Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution

Protein dynamics are essential for protein function, and yet it has been challenging to access the underlying atomic motions in solution on nanosecond-to-microsecond time scales. We present a structural ensemble of ubiquitin, refined against residual dipolar couplings (RDCs), comprising solution dynamics up to microseconds. The ensemble covers the complete structural heterogeneity observed in 46 ubiquitin crystal structures, most of which are complexes with other proteins. Conformational selection, rather than induced-fit motion, thus suffices to explain the molecular recognition dynamics of ubiquitin. Marked correlations are seen between the flexibility of the ensemble and contacts formed in ubiquitin complexes. A large part of the solution dynamics is concentrated in one concerted mode, which accounts for most of ubiquitin's molecular recognition heterogeneity and ensures a low entropic complex formation cost.     

Solution of a protein crystal structure with a model obtained from NMR interproton distance restraints

Model calculations were performed to test the possibility of solving crystal structures of proteins by Patterson search techniques with three-dimensional structures obtained from nuclear magnetic resonance (NMR) interproton distance restraints. Structures for crambin obtained from simulated NMR data were used as the test system; the root-mean-square deviations of the NMR structures from the x-ray structure were 1.5 to 2.2 A for backbone atoms and 2.0 to 2.8 A for side-chain atoms. Patterson searches were made to determine the orientation and position of the NMR structures in the unit cell. The correct solution was obtained by comparing the rotation function results of several of the NMR structures and the average structure derived from them. Conventional refinement techniques reduced the R factor from 0.43 at 4 A resolution to 0.27 at 2 A resolution without inclusion of water molecules. The partially refined structure has root-mean-square backbone and side-chain atom deviations from the x-ray structure of 0.5 and 1.3 A, respectively.     

适配体的研究进程与思考

适配体（aptamer）是指利用指数富集的配体系统进化（SELEX）技术，从人工合成的寡核苷酸文库中筛选获得的能够与靶分子特异结合的短单链DNA和RNA分子。筛选得到的适配体可以与DNA，RNA，蛋白质或其它靶分子结合，影响这些靶分子的性质，从而起到改变与靶分子相关的生物学功能的效果。而且研究发现，适配体在与靶分子相互作用时，不仅序列，它们所形成的三维结构也尤其重要。同时，适配体在生物医药研究方面显示出广阔的应用前景。介绍了适配体的发展历程，以及一些典型适配体的生物学功效。提出了RNA适配体三维结构在与靶分子进行相互作用时可能发挥重要作用，以期为RNA适配体的筛选提供理论思考。     

Response of high-rise and base-isolated buildings to a hypothetical mw 7.0 blind thrust earthquake

High-rise flexible-frame buildings are commonly considered to be resistant to shaking from the largest earthquakes. In addition, base isolation has become increasingly popular for critical buildings that should still function after an earthquake. How will these two types of buildings perform if a large earthquake occurs beneath a metropolitan area? To answer this question, we simulated the near-source ground motions of a M(w) 7.0 thrust earthquake and then mathematically modeled the response of a 20-story steel-frame building and a 3-story base-isolated building. The synthesized ground motions were characterized by large displacement pulses (up to 2 meters) and large ground velocities. These ground motions caused large deformation and possible collapse of the frame building, and they required exceptional measures in the design of the base-isolated building if it was to remain functional.     

Specific heat and thermal conductivity of solid fullerenes

Evidence is presented that the lattice vibrations of compacted C(60)/C(70) fullerite microcrystals consist predominantly of localized modes. Vibrational motions of the rigid molecules ("buckyballs") have been identified as well as their internal vibrations. Debye waves play only a relatively minor role, except below approximately 4 kelvin. By comparison with other crystalline materials, for these materials the Einstein model of the specific heat and thermal conductivity of solids, which is based on the assumption of atoms (in this case, buckyballs) vibrating with random phases, is in much better agreement with the measurements than the Debye model, which is based on collective excitations.     

Photoprotection by carotenoids during photosynthesis: motional dependence of intramolecular energy transfer

A new carotenoporphyrin has been prepared in which a synthetic carotenoid is joined to a tetraarylporphyrin through a flexible trimethylene linkage. This molecule exists primarily in an extended conformation with the carotenoid chromophore far from the porphyrin pi-electron system. In benzene solution, where large-amplitude molecular motions are rapid, the molecule can momentarily assume less stable conformations which favor triplet energy transfer, and quenching of the porphyrin triplet by the carotenoid is fast. In a polystyrene matrix or frozen glass such motions are slow, and energy transfer cannot compete with other pathways for depopulating the triplet state. These observations help establish the requirements for biological photoprotection.     

Functions of sphingolipids and sphingolipid breakdown products in cellular regulation

The discovery that breakdown products of cellular sphingolipids are biologically active has generated interest in the role of these molecules in cell physiology and pathology. Sphingolipid breakdown products, sphingosine and lysosphingolipids, inhibit protein kinase C, a pivotal enzyme in cell regulation and signal transduction. Sphingolipids and lysosphingolipids affect significant cellular responses and exhibit antitumor promoter activities in various mammalian cells. These molecules may function as endogenous modulators of cell function and possibly as second messengers.