Contemporary methodology for protein structure determination

The techniques used for the characterization of protein and peptide structure have undergone great changes that have improved the speed, reliability, and applicability of the process. High-performance liquid chromatography and gel electrophoresis have made the purification of proteins and peptides a routine procedure, even when the compound of interest is a minor component of a complex biological mixture. The chemistry and instrumentation used in amino acid analysis and amino acid sequencing now permit the analysis of as little as 5 to 50 picomoles of samples. This represents an increase in sensitivity of more than a thousandfold over the last 10 years and has made possible the structural analysis of a wide variety of scarce but important compounds.     

Glycoprotein structure determination by mass spectrometry

The human genome encodes 30,000 to 40,000 proteins, and a major challenge is to understand how posttranslational events, such as glycosylation, affect the activities and functions of these proteins in health and disease. Glycosylated proteins are ubiquitous components of extracellular matrices and cellular surfaces where their oligosaccharide moieties are implicated in a wide range of cell-cell and cell-matrix recognition events. The power of ultrahigh-sensitivity mass spectrometric strategies for defining the primary structures of highly complex mixtures of glycoprotein glycoforms is set to revolutionize structural glycobiology in the coming postgenomic era.     

Valinomycin crystal structure determination by direct methods

The conformation of an uncomplexed form of the antibiotic valinomycin (C(54)N(6)O(18)H(90)) has been determined by direct methods including a novel technique for strong enantiomorph discrimination via the calculation and systematic analysis of cosine invariants of a special type. The intramolecular hydrogen bonding scheme and the isopropyl group stereochemistry of uncomplexed valinomycin are compatible with interpretations of spectral measurements for the complexed and uncomplexed molecule in solution but are different from any previously proposed structure. The simple conformational change of a hydrogen bond shift, which could be induced by the process of potassium ion complexing, transforms the uncomplexed into the complexed structure.     

Inferential structure determination

Macromolecular structures calculated from nuclear magnetic resonance data are not fully determined by experimental data but depend on subjective choices in data treatment and parameter settings. This makes it difficult to objectively judge the precision of the structures. We used Bayesian inference to derive a probability distribution that represents the unknown structure and its precision. This probability distribution also determines additional unknowns, such as theory parameters, that previously had to be chosen empirically. We implemented this approach by using Markov chain Monte Carlo techniques. Our method provides an objective figure of merit and improves structural quality.     

Watching a protein as it functions with 150-ps time-resolved x-ray crystallography

We report picosecond time-resolved x-ray diffraction from the myoglobin (Mb) mutant in which Leu29 is replaced by Phe (L29Fmutant). The frame-by-frame structural evolution, resolved to 1.8 angstroms, allows one to literally "watch" the protein as it executes its function. Time-resolved mid-infrared spectroscopy of flash-photolyzed L29F MbCO revealed a short-lived CO intermediate whose 140-ps lifetime is shorter than that found in wild-type protein by a factor of 1000. The electron density maps of the protein unveil transient conformational changes far more dramatic than the structural differences between the carboxy and deoxy states and depict the correlated side-chain motion responsible for rapidly sweeping CO away from its primary docking site.     

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.     

Nonequilibrium phase transitions in cuprates observed by ultrafast electron crystallography

Nonequilibrium phase transitions, which are defined by the formation of macroscopic transient domains, are optically dark and cannot be observed through conventional temperature- or pressure-change studies. We have directly determined the structural dynamics of such a nonequilibrium phase transition in a cuprate superconductor. Ultrafast electron crystallography with the use of a tilted optical geometry technique afforded the necessary atomic-scale spatial and temporal resolutions. The observed transient behavior displays a notable "structural isosbestic" point and a threshold effect for the dependence of c-axis expansion (Deltac) on fluence (F), with Deltac/F = 0.02 angstrom/(millijoule per square centimeter). This threshold for photon doping occurs at approximately 0.12 photons per copper site, which is unexpectedly close to the density (per site) of chemically doped carriers needed to induce superconductivity.     

Automatic determination of crystal structure

Several crystallographic computer programs have been organized into one large automatic program for solving crystal structures. The emphasis of this organization has been to produce a noninteractive system, that is, to have all decisions made by the computer. Input data are the raw intensity data, cell constants, space group, chemical formula, and other miscellaneous items. The output is a stereo picture of the contents in a unit cell. The program, operating in a noninteractive mode, has successfully solved compounds of unknown structure; in addition, for a test compound of completely unknown composition, this program deduced the correct structure with an average error in bond distance of 0.05 angstrom and an average error in bond angle of 7 degrees .     

利用毛细管电泳测定牛乳和山羊乳混合乳的蛋白质

采用毛细管区带电泳方法,选择聚丙烯酰胺涂层毛细管对混合乳中的蛋白进行图谱的研究,确定混合乳的定性定量检测方法。该方法对牛乳和山羊乳混合乳中的蛋白进行了很好的分离,确定了牛乳αs1-CN、αs0-CN、κ-CN、β-casein A1和山羊乳的β-CN、β1-casein作为定性检测的酪蛋白,测得了混合乳中不同酪蛋白峰面积的比值与混合比例呈很好的线性关系,相关系数均大于0.997,可以作为定量检测混合乳的指标。本法简便、快速、准确,为乳及乳制品质量的监控提供了一种新的手段,可用于乳的质量监控。     

High-resolution crystal structure of an engineered human beta2-adrenergic G protein-coupled receptor

Heterotrimeric guanine nucleotide-binding protein (G protein)-coupled receptors constitute the largest family of eukaryotic signal transduction proteins that communicate across the membrane. We report the crystal structure of a human beta2-adrenergic receptor-T4 lysozyme fusion protein bound to the partial inverse agonist carazolol at 2.4 angstrom resolution. The structure provides a high-resolution view of a human G protein-coupled receptor bound to a diffusible ligand. Ligand-binding site accessibility is enabled by the second extracellular loop, which is held out of the binding cavity by a pair of closely spaced disulfide bridges and a short helical segment within the loop. Cholesterol, a necessary component for crystallization, mediates an intriguing parallel association of receptor molecules in the crystal lattice. Although the location of carazolol in the beta2-adrenergic receptor is very similar to that of retinal in rhodopsin, structural differences in the ligand-binding site and other regions highlight the challenges in using rhodopsin as a template model for this large receptor family.     

Encephalitogenic protein: structure

Amino acid sequences of encephalitogenic proteins from bovine cord and rabbit brain are reported. The bovine protein contains 45 residues. The rabbit protein is identical except for two isopolar substitutions, a dipeptide and amino acid deletion. Analysis of this protein and a 140-residue myelin basic protein indicates that the smaller protein is a portion of the larger encephalitogen. The larger myelin protein contains at least two encephalitogenic sites.     

High-resolution thin-film device to sense texture by touch

Touch (or tactile) sensors are gaining renewed interest as the level of sophistication in the application of minimum invasive surgery and humanoid robots increases. The spatial resolution of current large-area (greater than 1 cm(2)) tactile sensor lags by more than an order of magnitude compared with the human finger. By using metal and semiconducting nanoparticles, a approximately 100-nm-thick, large-area thin-film device is self-assembled such that the change in current density through the film and the electroluminescent light intensity are linearly proportional to the local stress. A stress image is obtained by pressing a copper grid and a United States 1-cent coin on the device and focusing the resulting electroluminescent light directly on the charge-coupled device. Both the lateral and height resolution of texture are comparable to the human finger at similar stress levels of approximately 10 kilopascals.     

Petrologic history of moon suggested by petrography, mineralogy, and crystallography

Opaque mineral compositions indicate that the fugacity of oxygen is approximately 10(-13) (earth basalts, 10(-10)). Experiments under reducing conditions suggest that the crystallization range is approximately 1140 degrees to 1070 degrees C. Iron-rich pyroxmangite, fayalite, and hedenbergite occur in microgabbro. Ferropseudobrookite rimmed by ilmenite containing rutile and Cr-spinel lamellae occurs in ferrobasalt. Plagioclase vitrophyres in breccia can explain highland Surveyor VII analysis. We suggest crystal-liquid differentiation of out-gassed convecting moon with growing Fe-rich core, olivine-pyroxene mantle, plagioclase-rich dynamic crust underlain by nonspherical, inversely stratified ferrobasalt. Impact-breaking or convection-thrusting of crust releases fraction rich in Fe and Ti. Scanning electron microscopy of glass balls reveals minute depressions consistent with micrometeorite impact.     

Human catechol-O-methyltransferase haplotypes modulate protein expression by altering mRNA secondary structure

Catechol-O-methyltransferase (COMT) is a key regulator of pain perception, cognitive function, and affective mood. Three common haplotypes of the human COMT gene, divergent in two synonymous and one nonsynonymous position, code for differences in COMT enzymatic activity and are associated with pain sensitivity. Haplotypes divergent in synonymous changes exhibited the largest difference in COMT enzymatic activity, due to a reduced amount of translated protein. The major COMT haplotypes varied with respect to messenger RNA local stem-loop structures, such that the most stable structure was associated with the lowest protein levels and enzymatic activity. Site-directed mutagenesis that eliminated the stable structure restored the amount of translated protein. These data highlight the functional significance of synonymous variations and suggest the importance of haplotypes over single-nucleotide polymorphisms for analysis of genetic variations.     

Crystal structure of an ancient protein: evolution by conformational epistasis

The structural mechanisms by which proteins have evolved new functions are known only indirectly. We report x-ray crystal structures of a resurrected ancestral protein-the approximately 450 million-year-old precursor of vertebrate glucocorticoid (GR) and mineralocorticoid (MR) receptors. Using structural, phylogenetic, and functional analysis, we identify the specific set of historical mutations that recapitulate the evolution of GR's hormone specificity from an MR-like ancestor. These substitutions repositioned crucial residues to create new receptor-ligand and intraprotein contacts. Strong epistatic interactions occur because one substitution changes the conformational position of another site. "Permissive" mutations-substitutions of no immediate consequence, which stabilize specific elements of the protein and allow it to tolerate subsequent function-switching changes-played a major role in determining GR's evolutionary trajectory.     

Toward protein tertiary structure recognition by means of associative memory hamiltonians

The statistical mechanics of associative memories and spin glasses suggests ways to design Hamiltonians for protein folding. An associative memory Hamiltonian based on hydrophobicity patterns is shown to have a large capacity for recall and to be capable of recognizing tertiary structure for moderately variant sequences.     

Determination of membrane protein structure by rotational resonance NMR: bacteriorhodopsin

Rotationally resonant magnetization exchange, a new nuclear magnetic resonance (NMR) technique for measuring internuclear distances between like spins in solids, was used to determine the distance between the C-8 and C-18 carbons of retinal in two model compounds and in the membrane protein bacteriorhodopsin. Magnetization transfer between inequivalent spins with an isotropic shift separation, delta, is driven by magic angle spinning at a speed omega r that matches the rotational resonance condition delta = n omega r, where n is a small integer. The distances measured in this way for both the 6-s-cis- and 6-s-trans-retinoic acid model compounds agreed well with crystallographically known distances. In bacteriorhodopsin the exchange trajectory between C-8 and C-18 was in good agreement with the internuclear distance for a 6-s-trans configuration [4.2 angstroms (A)] and inconsistent with that for a 6-s-cis configuration (3.1 A). The results illustrate that rotational resonance can be used for structural studies in membrane proteins and in other situations where diffraction and solution NMR techniques yield limited information.     

High-resolution epitope mapping of hGH-receptor interactions by alanine-scanning mutagenesis

A strategy, called alanine-scanning mutagenesis, was used to identify specific side chains in human growth hormone (hGH) that strongly modulate binding to the hGH receptor cloned from human liver. Single alanine mutations (62 in total) were introduced at every residue contained within the three discontinuous segments of hGH (residues 2 to 19, 54 to 74, and 167 to 191) that have been implicated in receptor recognition. The alanine scan revealed a cluster of a dozen large side chains that when mutated to alanine each showed more than a four times lower binding affinity to the hGH receptor. Many of these residues that promote binding to the hGH receptor are altered in homologs of hGH (such as placental lactogens and prolactins) that do not bind tightly to the hGH receptor. The overall folding of these mutant proteins was indistinguishable from that of the wild-type hGH, as determined by strong cross-reactivities with seven different conformationally sensitive monoclonal antibodies. The alanine scan also identified at least one side chain, Glu174, that hindered binding because when it was mutated to alanine the receptor affinity increased by more than a factor of four.