Exploring the crystal form landscape

2020 ◽  
pp. 78-135
Author(s):  
Joel Bernstein
Keyword(s):  
High Throughput ◽  
Crystal Form ◽  
Time Frame ◽  
Theoretical Background ◽  
Experimental Techniques ◽  
Crystallization Conditions ◽  
Kinetic Crystallization ◽  
Solid Form ◽  
Evolving Models

Chapter 3 deals with the theoretical background, the strategies, and the experimental techniques for exploring the crystal for landscape. The various and evolving models for aggregation and nucleation are discussed, followed by the description of thermodynamic (i.e., approximately equilibrium) and kinetic crystallization conditions, followed by the use of thermodynamic information obtained in Chapter 2 for designing crystallization strategies. The various aspects of solid form screens—design, composition, time frame, variables to consider, application of high throughput methods—are discussed, followed by a description of the screen on the specific example of axitinib. The chapter closes with discussions of concomitant polymorphs and disappearing polymorphs.

scholarly journals Postmodernism, Postmodernist Fiction, Apocalypse and Fantasy

2019 ◽  
pp. 1-8
Author(s):  
Dr. S. Z. Abbas
Keyword(s):  
Temporal Logic ◽  
Time Scale ◽  
Historical Perspective ◽  
Time Frame ◽  
Experimental Techniques ◽  
Modern Literature ◽  
True Nature ◽  
Avant Garde

Terms like 'modern', 'postmodern' and 'contemporary' are subject-centered, and not based on any historical or objective phenomenon or personality. Everyone feels that something called 'Postmodernism' has happened, but, as regards its true nature and causes, opinion is divided; a few people say postmodernism is a fiction. There is also a problem with the nomenclature. What was referred to as 'contemporary', for example, in 1956 by the writers of that year will not be so to the generation of Y2K. All these terms tend to shift about what is known as PP in temporal logic, which itself keeps moving on the time scale. When we rename modern literature as the age of T.S. Eliot, we assign it a slot in the historical perspective. A further complication is created by the use of ‘modern’ and 'modernist', ‘postmodern’ and ‘postmodernist' as well as ‘contemporary.’ We may, perhaps, safely assume that its element in each case signifies the avant-garde, a group of authors in the respective period that is distinguished by experimentation and innovation. While attempts to accord the postmodern period a definitive time frame (which includes the postmodernist movement in arts and literature) remain in an inconclusive stage, let us assume that postmodernism encompasses the period from the fifties to the present time, which is open-endeded. It should also be noted that some postmodernist writers concentrate on new tones and new reality rather than experimental techniques.

High-throughput identification of purification conditions leads to preliminary crystallization conditions for three inner membrane proteins

2011 ◽  
Vol 28 (7-8) ◽  
pp. 445-453 ◽  
Author(s):  
Mads Gabrielsen ◽  
Frank Kroner ◽  
Isobel Black ◽  
Neil W. Isaacs ◽  
Andrew J. Roe ◽  
...  
Keyword(s):  
Membrane Proteins ◽  
High Throughput ◽  
Inner Membrane ◽  
Crystallization Conditions

1.35 and 2.07 Å resolution structures of the red abalone sperm lysin monomer and dimer reveal features involved in receptor binding

2000 ◽  
Vol 56 (1) ◽  
pp. 34-41 ◽  
Author(s):  
Nicole Kresge ◽  
Victor D. Vacquier ◽  
C. David Stout
Keyword(s):  
High Resolution ◽  
Crystal Form ◽  
Haliotis Rufescens ◽  
Enzymatic Mechanism ◽  
Red Abalone ◽  
New Information ◽  
Local Flexibility ◽  
Crystallization Conditions ◽  
Vitelline Envelope ◽  
Species Specific

Abalone sperm use lysin to make a hole in the egg's protective vitelline envelope (VE). When released from sperm, lysin first binds to the VE receptor for lysin (VERL) then dissolves the VE by a non-enzymatic mechanism. The structures of the monomeric and dimeric forms of Haliotis rufescens (red abalone) lysin, previously solved at 1.90 and 2.75 Å, respectively, have now been refined to 1.35 and 2.07 Å, respectively. The monomeric form of lysin was refined using previously obtained crystallization conditions, while the dimer was solved in a new crystal form with four molecules (two dimers) per asymmetric unit. These high-resolution structures reveal alternate residue conformations, enabling a thorough analysis of the conserved residues contributing to the amphipathic nature of lysin. The availability of five independent high-resolution copies of lysin permits comparisons leading to insights on the local flexibility of lysin and alternative conformations of the hypervariable N-terminus, thought to be involved in species-specific receptor recognition. The new analysis led to the discovery of the basic nature of a cleft formed upon dimerization and a patch of basic residues in the dimer interface. Identification of these features was not possible at lower resolution. In light of this new information, a model explaining the binding of sperm lysin to egg VERL and the subsequent dissolution of the egg VE is proposed.

scholarly journals Structural characterization of the apo form and NADH binary complex of human lactate dehydrogenase

2014 ◽  
Vol 70 (5) ◽  
pp. 1484-1490 ◽  
Author(s):  
Sally Dempster ◽  
Stephen Harper ◽  
John E. Moses ◽  
Ingrid Dreveny
Keyword(s):  
Lactate Dehydrogenase ◽  
Conformational Changes ◽  
Active Site ◽  
Anaerobic Respiration ◽  
Crystal Form ◽  
Binary Complex ◽  
Cofactor Binding ◽  
Key Enzyme ◽  
Crystallization Conditions

Lactate dehydrogenase A (LDH-A) is a key enzyme in anaerobic respiration that is predominantly found in skeletal muscle and catalyses the reversible conversion of pyruvate to lactate in the presence of NADH. LDH-A is overexpressed in many tumours and has therefore emerged as an attractive target for anticancer drug discovery. Crystal structures of human LDH-A in the presence of inhibitors have been described, but currently no structures of the apo or binary NADH-bound forms are available for any mammalian LDH-A. Here, the apo structure of human LDH-A was solved at a resolution of 2.1 Å in space groupP4122. The active-site loop adopts an open conformation and the packing and crystallization conditions suggest that the crystal form is suitable for soaking experiments. The soaking potential was assessed with the cofactor NADH, which yielded a ligand-bound crystal structure in the absence of any inhibitors. The structures show that NADH binding induces small conformational changes in the active-site loop and an adjacent helix. A comparison with other eukaryotic apo LDH structures reveals the conservation of intra-loop interactions. The structures provide novel insight into cofactor binding and provide the foundation for soaking experiments with fragments and inhibitors.

scholarly journals Chemical clustering and visualization applied to macromolecular crystallography

2014 ◽  
Vol 70 (a1) ◽  
pp. C1145-C1145
Author(s):  
Andrew Bruno ◽  
Amanda Ruby ◽  
Joseph Luft ◽  
Thomas Grant ◽  
Jayaraman Seetharaman ◽  
...  
Keyword(s):  
Hierarchical Clustering ◽  
High Throughput ◽  
Active Sites ◽  
X Ray Crystallography ◽  
Rate Limiting Step ◽  
Potential Applications ◽  
Crystallization Conditions ◽  
Electron Density Map ◽  
Distance Coefficient ◽  
Rate Limiting

Many bioscience fields employ high-throughput methods to screen multiple biochemical conditions. The analysis of these becomes tedious without a degree of automation. Crystallization, a rate limiting step in biological X-ray crystallography, is one of these fields. Screening of multiple potential crystallization conditions (cocktails) is the most effective method of probing a proteins phase diagram and guiding crystallization but the interpretation of results can be consuming. To aid this empirical approach a cocktail distance coefficient was developed to quantitatively compare macromolecule crystallization conditions and outcome. These coefficients were evaluated against an existing similarity metric developed for crystallization, the C6 metric, using both virtual crystallization screens and by comparison of two related 1,536-cocktail high-throughput crystallization screens. Hierarchical clustering was employed to visualize one of these screens and the crystallization results from an exopolyphosphatase-related protein from Bacteroides fragilis, (BfR192) overlaid on this clustering. This demonstrated a strong correlation between certain chemically related clusters and crystal lead conditions. While this analysis was not used to guide the initial crystallization optimization, it led to the re-evaluation of unexplained peaks in the electron density map of the protein and the insertion and correct placement of a sodium, potassium and phosphate atoms in the structure. With these in place, the resulting structure of the putative active site demonstrated features consistent with active sites of other phosphatases which are involved in binding the phosphoryl moieties of nucleotide triphosphates. The new distance coefficient appears to be robust in this application and coupled with hierarchical clustering and the overlay of crystallization outcome reveals information of biological relevance. While tested with a single example the potential applications appear promising.

High Throughput Hla Sequence-Based Typing (Sbt) Utilizing the Abi Prism® 3700 Dna Analyzer

2001 ◽  
Vol 87 (2) ◽  
pp. 40-43 ◽  
Author(s):  
Sharon D Adams ◽  
Kathleen C Barracchini ◽  
Toni B Simonis ◽  
David Stroncek ◽  
Francesco M Marincola
Keyword(s):  
High Throughput ◽  
Sequence Data ◽  
Time Frame ◽  
Marrow Transplant ◽  
Negative Control ◽  
Hla Typing ◽  
Null Alleles ◽  
Human Major Histocompatibility Complex ◽  
Genetic Complexity ◽  
Typing Methods

Aims and background The genetic complexity of the human major histocompatibility complex (MHC) has required the development of various molecular typing methods. The purpose of this paper is to compare the results of two of these molecular methods: sequenced based typing (SBT) and polymerase chain reaction (PCR) using sequence specific primers (PCR-SSP). Methods The SBT method described utilizes an ABI Prism® 3700 DNA Analyzer, which has been designed fro high throughput production of sequence data through highly automated operation with significant walk-away time. The ABI Prism® 3700 DNA Analyzer is a 96-capillary electrophoresis instrument with the capability of running four 96-well plates black to back in a sixteen-hour period. Potentially, data from this machine can produce Class I sequences for A or B loci for 64 samples in this time frame. The SBT method encompassed exons 2, 3, and 4 with forward and reverse sequence orientation reactions using the PE Biosystems HLA-A and HLA-B Sequenced Based Typing Kits (PE Applied Biopsystems/Perkin-Elmer, Foster City, CA, USA). Most SBT methods previously employed only gather data from exons 2 and 3 which distinguishes most of the polymorphism necessary to identify the majority of alleles in the HLA region. However, in an effort to discern numerous null alleles in the HLA region, exon 4 data is also included. The PCR-SSP method utilized consists of one 96 well tray, with 95 primer mixes and one negative control, per sample designed to produce an intermediate/high resolution HLA-A, B typing. Results Data from one 96-well capillary run on the ABI Prism® 3700 DNA Analyzer, which consists of results from 16 samples for HLA-A or HLA-B loci, was compared to data derived from sixteen HLA-A and HLA-B PCR-SSP typings. 75% of loci tested achieved a higher resolution HLA typing by the SBT method. Discussion The ability to provide allele level HLA typing results can have significant functional implications for the bone marrow transplant community and numerous vaccine studies.

scholarly journals Structures ofEscherichia colitryptophanase in holo and `semi-holo' forms

2015 ◽  
Vol 71 (3) ◽  
pp. 286-290 ◽  
Author(s):  
Anna Kogan ◽  
Leah Raznov ◽  
Garik Y. Gdalevsky ◽  
Rivka Cohen-Luria ◽  
Orna Almog ◽  
...  
Keyword(s):  
Pyridoxal Phosphate ◽  
Crystal Form ◽  
Asymmetric Unit ◽  
Sulfate Ions ◽  
Crystal Forms ◽  
Cell Parameters ◽  
Open Conformation ◽  
Crystallization Conditions ◽  
Tyrosine Phenol Lyase ◽  
Polypeptide Chains

Two crystal forms ofEscherichia colitryptophanase (tryptophan indole-lyase, Trpase) were obtained under the same crystallization conditions. Both forms belonged to the same space groupP43212 but had slightly different unit-cell parameters. The holo crystal form, with pyridoxal phosphate (PLP) bound to Lys270 of both polypeptide chains in the asymmetric unit, diffracted to 2.9 Å resolution. The second crystal form diffracted to 3.2 Å resolution. Of the two subunits in the asymmetric unit, one was found in the holo form, while the other appeared to be in the apo form in a wide-open conformation with two sulfate ions bound in the vicinity of the active site. The conformation of all holo subunits is the same in both crystal forms. The structures suggest that Trpase is flexible in the apo form. Its conformation partially closes upon binding of PLP. The closed conformation might correspond to the enzyme in its active state with both cofactor and substrate bound in a similar way as in tyrosine phenol-lyase.

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