scholarly journals ENANTIOMORPHIC PHASE AMBIGUITIES AND THE MODIFIED COMPONENT RELATION——THE APPLICATION OF DIRECT METHODS TO PROTEIN STRUCTURES

1984 ◽  
Vol 33 (3) ◽  
pp. 399
Author(s):  
FAN HAI-FU
Keyword(s):  
Protein Structures ◽  
Direct Methods ◽  
Component Relation

The Pseudo-Atom Approximation in Direct Phase Determination of Protein Structures.

1997 ◽  
Vol 3 (S2) ◽  
pp. 1025-1026
Author(s):  
Douglas L. Dorset
Keyword(s):  
Fourier Transform ◽  
High Resolution ◽  
Protein Structures ◽  
Direct Methods ◽  
Direct Solution ◽  
Phase Problem ◽  
Electron Crystallography ◽  
Phase Determination ◽  
The Fourier Transform

In principle, the availability of high-resolution micrographs in electron crystallography is a direct solution of the phase problem that has been used to great advantage for the study of proteins. However, as the resolution of the determination increases, the Fourier transform of the micrograph becomes a less accurate phase source. Hence, alternative direct methods for phase determination have been evaluated, if only to extend the resolution of most reliable lower resolution phases to the limit of the electron diffraction pattern. The first demonstration of its feasibility was published in a study of bacteriorhodopsin extending 15 Å image phases to beyond 3 Å by maximum entropy and likelihood procedures i. Later studies demonstrated that convolutional methods also can be effective.In protein crystallography, there is always an interest in carrying out a true ab initio determinations, if only because of the challenge to traditional direct methods that become statistically less reliable as the number of atoms in the unit cell increases.

Direct phase extension in protein electron crystallography: tests with data from Escherichia coli omp F porin

1995 ◽  
Vol 53 ◽  
pp. 854-855
Author(s):  
Douglas L. Dorset
Keyword(s):  
Fourier Transforms ◽  
Protein Structures ◽  
Direct Methods ◽  
Crystallographic Analysis ◽  
Resolution Limit ◽  
X Ray Crystallography ◽  
Structure Factors ◽  
Resolution Electron ◽  
Phase Extension ◽  
Access Information

Phase determination in the high-resolution electron crystallographic analysis of membrane protein structures has been based most often on the Fourier transforms of low-dose electron micrographs. With increasing resolution, this task becomes increasingly difficult because of inherent paracrystalline lattice distortions, requiring some ‘unbending’ operation to access information beyond e. g. 6 Å. In addition, the specimen itself will be more prone to radiation damage as the demands for greater resolution are imposed. For this reason, Gilmore, et al. have suggested that direct methods, e. g. maximum entropy and likelihood, be employed to extend easily available lower resolution phase information to the resolution of the electron diffraction pattern. More recently, we have carried out phase extensions for bacteriorhodopsin and halorhodopsin, via the Sayre equation, which is simply a convolution of phased structure factors. Despite pessimistic estimates from x-ray crystallography, the extension, e. g. from 15 to 10 Å to a resolution limit of 6 Å, is relatively easy, so that new phases for bacteriorhodopsin have a mean error of 50°, whereas those corresponding to the most significant magnitudes from halorhodopsin have only a 36° error (but 72° for all new reflections).

Ab initio solution and refinement of two high-potential iron protein structures at atomic resolution

1999 ◽  
Vol 55 (11) ◽  
pp. 1773-1784 ◽  
Author(s):  
Emilio Parisini ◽  
Francesco Capozzi ◽  
Paolo Lubini ◽  
Victor Lamzin ◽  
Claudio Luchinat ◽  
...  
Keyword(s):  
Ab Initio ◽  
Protein Structures ◽  
Direct Methods ◽  
High Potential ◽  
Chromatium Vinosum ◽  
Atomic Resolution ◽  
Crystal Modification ◽  
Redox Potentials ◽  
Asymmetric Unit ◽  
Iron Protein

The crystal structure of the reduced high-potential iron protein (HiPIP) from Chromatium vinosum has been redetermined in a new orthorhombic crystal modification, and the structure of its H42Q mutant has been determined in orthorhombic (H42Q-1) and cubic (H42Q-2) modifications. The first two were solved by ab initio direct methods using data collected to atomic resolution (1.20 and 0.93 Å, respectively). The recombinant wild type (rc-WT) with two HiPIP molecules in the asymmetric unit has 1264 protein atoms and 335 solvent sites, and is the second largest structure reported so far that has been solved by pure direct methods. The solutions were obtained in a fully automated way and included more than 80% of the protein atoms. Restrained anisotropic refinement for rc-WT and H42Q-1 converged to R_1=\sum\big||F_o|-|F_c|\big|\big/\sum|F_o| of 12.0 and 13.6%, respectively [data with I>2\sigma(I)], and 12.8 and 15.5% (all data). H42Q-2 contains two molecules in the asymmetric unit and diffracted only to 2.6 Å. In both molecules of rc-WT and in the single unique molecule of H42Q-1 the [Fe4S4]2+ cluster dimensions are very similar and show a characteristic tetragonal distortion with four short Fe—S bonds along four approximately parallel cube edges, and eight long Fe—S bonds. The unique protein molecules in H42Q-2 and rc-WT are also very similar in other respects, except for the hydrogen bonding around the mutated residue that is at the surface of the protein, supporting the hypothesis that the difference in redox potentials at lower pH values is caused primarily by differences in the charge distribution near the surface of the protein rather than by structural differences in the cluster region.

Ulrich Wolfgang Arndt. 23 April 1924 — 24 March 2006

2014 ◽  
Vol 60 ◽  
pp. 39-55
Author(s):  
R. A. Crowther ◽  
A. G. W. Leslie
Keyword(s):  
Protein Structures ◽  
Three Dimensional ◽  
Direct Methods ◽  
Biological Molecules ◽  
Data Generation ◽  
Data Set ◽  
X Ray ◽  
X Ray Crystallography ◽  
Whole Process ◽  
Wide Range

Ulrich (Uli) Arndt was a physicist and engineer whose contributions to the development of a wide range of instrumentation for X-ray crystallography played an important part in our ability to solve the atomic structure of large biological molecules. Such detailed information about protein structures has for the past 50 years underpinned the huge advances in the field of molecular biology. His innovations spanned all aspects of data generation and collection, from improvements in X-ray tubes, through novel designs for diffractometers and cameras to film scanners and more direct methods of X-ray detection. When he started in the field, the intensities of individual X-ray reflections were often estimated by eye from films. By the end of his career the whole process of collecting from a crystal a three-dimensional data set, possibly comprising hundreds of thousands of measurements, was fully automated and very rapid.

Solving proteins at non-atomic resolution by direct methods

2015 ◽  
Vol 48 (6) ◽  
pp. 1692-1698 ◽  
Author(s):  
Maria Cristina Burla ◽  
Benedetta Carrozzini ◽  
Giovanni Luca Cascarano ◽  
Carmelo Giacovazzo ◽  
Giampiero Polidori
Keyword(s):  
Ab Initio ◽  
Protein Structures ◽  
Structural Complexity ◽  
Direct Methods ◽  
Atomic Resolution ◽  
Asymmetric Unit ◽  
Hydrogen Atoms ◽  
Heavy Atoms ◽  
Density Map ◽  
Electron Density Map

A new probabilistic formula estimating triplet invariants and capable of exploiting a model electron-density map gradually created during theab initiophasing process has been tested on a set of protein structures with data at non-atomic resolution. All the structures contain heavy atoms larger than Ca, and show a structural complexity which may attain the level of about 8000 non-hydrogen atoms in the asymmetric unit. It is shown that the majority of such structures may be solved by our direct methods procedure, which, in combination with a number of ancillary phasing tools, weakens the traditional expectation that atomic resolution is a necessary ingredient for the success of a directab initiophasing.

Optimizing Shake-and-Bake for proteins

1999 ◽  
Vol 55 (2) ◽  
pp. 492-500 ◽  
Author(s):  
Charles M. Weeks ◽  
Russ Miller
Keyword(s):  
Protein Structures ◽  
Direct Methods ◽  
Real Space ◽  
Parameter Variation ◽  
Critical Parameters ◽  
Large Structures ◽  
Refinement Method ◽  
Using Data ◽  
Parameter Values ◽  
Space Phase

Shake-and-Bake is a direct-methods procedure which has provided ab initio solutions for protein structures containing as many as 1000 independent non-H atoms. This algorithm extends the range of conventional direct methods by repetitively, unconditionally and automatically alternating reciprocal-space phase refinement with filtering in real space to impose constraints. The application of SnB to protein-sized molecules is significantly affected by the choice made for certain critical parameters, including the number of peaks used for density modification, the choice of phase-refinement method and the number of refinement cycles. The effects of parameter variation have been studied for six protein structures, all of which are solvable by Shake-and-Bake using data at 1.1 Å or higher resolution. Solvability in the resolution range 1.2–1.4 Å appears to be enhanced by the presence of heavier atoms (S, Cl). Furthermore, it appears that in this range the ratio of refinement cycles and triplet phase invariants to atoms in the structure must be increased. Large structures lacking atoms of any element heavier than oxygen also require non-traditional parameter values.

Gold liposomes

1996 ◽  
Vol 54 ◽  
pp. 898-899
Author(s):  
James F. Hainfeld
Keyword(s):  
Direct Methods ◽  
Important Class ◽  
Double Bonds ◽  
Membrane Phospholipids ◽  
Essential Ingredient ◽  
Lipid Structures

Lipids are an important class of molecules, being found in membranes, HDL, LDL, and other natural structures, serving essential roles in structure and with varied functions such as compartmentalization and transport. Synthetic liposomes are also widely used as delivery and release vehicles for drugs, cosmetics, and other chemicals; soap is made from lipids. Lipids may form bilayer or multilammellar vesicles, micelles, sheets, tubes, and other structures. Lipid molecules may be linked to proteins, carbohydrates, or other moieties. EM study of this essential ingredient of life has lagged, due to lack of direct methods to visualize lipids without extensive alteration. OsO4 reacts with double bonds in membrane phospholipids, forming crossbridges. This has been the method of choice to both fix and stain membranes, thus far. An earlier work described the use of tungstate clusters (W11) attached to lipid moieties to form lipid structures and lipid probes.

High performance Nanogold™-in situ hybridzation and its use in the detection of hybridized and PCR-amplified microscopical preparations

1996 ◽  
Vol 54 ◽  
pp. 896-897
Author(s):  
G. W. Hacker ◽  
I. Zehbe ◽  
J. Hainfeld ◽  
A.-H. Graf ◽  
C. Hauser-Kronberger ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Messenger Rna ◽  
High Performance ◽  
Detection System ◽  
Direct Methods ◽  
Genetic Alterations ◽  
Chain Reaction ◽  
Protein Encoding ◽  
Polymerase Chain

In situ hybridization (ISH) with biotin-labeled probes is increasingly used in histology, histopathology and molecular biology, to detect genetic nucleic acid sequences of interest, such as viruses, genetic alterations and peptide-/protein-encoding messenger RNA (mRNA). In situ polymerase chain reaction (PCR) (PCR in situ hybridization = PISH) and the new in situ self-sustained sequence replication-based amplification (3SR) method even allow the detection of single copies of DNA or RNA in cytological and histological material. However, there is a number of considerable problems with the in situ PCR methods available today: False positives due to mis-priming of DNA breakdown products contained in several types of cells causing non-specific incorporation of label in direct methods, and re-diffusion artefacts of amplicons into previously negative cells have been observed. To avoid these problems, super-sensitive ISH procedures can be used, and it is well known that the sensitivity and outcome of these methods partially depend on the detection system used.

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