Data mining crystallization databases: knowledge-based approaches to optimize protein crystal screens

Protein crystallization is a major bottleneck in protein X-ray crystallography, the workhorse of most structural proteomics projects. Because the principles that govern protein crystallization are too poorly understood to allow them to be used in a strongly predictive sense, the most common crystallization strategy entails screening a wide variety of solution conditions to identify the small subset that will support crystal nucleation and growth. We tested the hypothesis that more efficient crystallization strategies could be formulated by extracting useful patterns and correlations from the large data sets of crystallization trials created in structural proteomics projects. A database of crystallization conditions was constructed for 755 different proteins purified and crystallized under uniform conditions. Forty-five percent of the proteins formed crystals. Data mining identified the conditions that crystallize the most proteins, revealed that many conditions are highly correlated in their behavior, and showed that the crystallization success rate is markedly dependent on the organism from which proteins derive. Of the proteins that crystallized in a 48-condition experiment, 60% could be crystallized in as few as 6 conditions and 94% in 24 conditions. Consideration of the full range of information coming from crystal screening trials allows one to design screens that are maximally productive while consuming minimal resources, and also suggests further useful conditions for extending existing screens.     

Semliki Forest virus vectors for rapid and high-level expression of integral membrane proteins

Semliki Forest virus (SFV) vectors have been applied for the expression of recombinant integral membrane proteins in a wide range of mammalian host cells. More than 50 G protein-coupled receptors (GPCRs), several ion channels and other types of transmembrane or membrane-associated proteins have been expressed at high levels. The establishment of large-scale SFV technology has facilitated the production of large quantities of recombinant receptors, which have then been subjected to drug screening programs and structure-function studies on purified receptors. The recent Membrane Protein Network (MePNet) structural genomics initiative, where 100 GPCRs are overexpressed from SFV vectors, will further provide new methods and technologies for expression, solubilization, purification and crystallization of GPCRs.     

Semliki Forest virus vectors for rapid and high-level expression of integral membrane proteins

Semliki Forest virus (SFV) vectors have been applied for the expression of recombinant integral membrane proteins in a wide range of mammalian host cells. More than 50 G protein-coupled receptors (GPCRs), several ion channels and other types of transmembrane or membrane-associated proteins have been expressed at high levels. The establishment of large-scale SFV technology has facilitated the production of large quantities of recombinant receptors, which have then been subjected to drug screening programs and structure-function studies on purified receptors. The recent Membrane Protein Network (MePNet) structural genomics initiative, where 100 GPCRs are overexpressed from SFV vectors, will further provide new methods and technologies for expression, solubilization, purification and crystallization of GPCRs.     

High-throughput docking as a source of novel drug leads

Receptor-based virtual screening has become a viable source of novel leads in the pharmaceutical industry. The rapidly growing availability of structural information across protein families, the accessibility to increased computational power at affordable cost, as well as an improved understanding on how to effectively apply virtual screening technologies has contributed to their emergence. Nonetheless, continued improvement in the accuracy of scoring functions and a greater understanding of protein mobility is critical to advance the technology further.     

Structural proteomics: a tool for genome annotation

In any newly sequenced genome, 30% to 50% of genes encode proteins with unknown molecular or cellular function. Fortunately, structural genomics is emerging as a powerful approach of functional annotation. Because of recent developments in high-throughput technologies, ongoing structural genomics projects are generating new structures at an unprecedented rate. In the past year, structural studies have identified many new structural motifs involved in enzymatic catalysis or in binding ligands or other macromolecules (DNA, RNA, protein). The efficiency by which function is deduced from structure can be further improved by the integration of structure with bioinformatics and other experimental approaches, such as screening for enzymatic activity or ligand binding.     

Managing and mining protein crystallization data

The crystallization of macromolecules remains a major bottleneck in structural biology. The routine screening of more than one thousand crystallization conditions and subsequent optimization by fine screening presents a challenge to conventional laboratory notebook keeping. In addition, the development of high-throughput robotic crystallization and imaging systems presents a pressing need for low-cost laboratory information management system (LIMS). Here we describe CLIMS2, a crystallization LIMS that features a simple, user-friendly graphical interface, allowing the storage, management, retrieval and mining of crystallization data. The CLIMS2 executable and documentation is freely available at http://clims.med.monash.edu.au.     

A SNP chip to detect introgression in wildcats allows accurate genotyping of single hairs

Genotyping non-invasively collected samples is challenging. Nevertheless, genetic monitoring of elusive species like the European wildcat (Felis silvestris silvestris) mainly relies on such samples. Wildcats are likely threatened through introgression with domestic cats (F. silvestris catus). To determine introgression based on single cat hairs, we developed a 96.96 Fluidigm single nucleotide polymorphism (SNP) genotyping array chip. To estimate the accuracy of this method, we compared genotypes of 17 cats called with both Sanger sequencing and Fluidigm. When Sanger sequencing genotypes were considered as a reference, the genotyping error rate with Fluidigm was 0.9 %. We subsequently compared 16 hair samples to tissue samples of the same individual. When the tissue samples were used as a reference, the genotyping error rate in hair samples was 1.6 %. This low error rate allowed reliable recognition of individuals and correct assessment of introgression levels. Thus, the genotyping method presented in this paper is suitable for non-invasively collected samples. It will help conservationists to monitor the introgression rate in wildcat populations based on non-invasive hair sampling and subsequently to conduct effective conservation measures.     

Derivation of chondrocyte and osteoblast reporter mouse embryonic stem cell lines

With the establishment of methods that provide evidence for the generation of chondrocyte and osteoblast cell types from ESCs, there is a need for reagents that will enable their further characterization. Here we report on the derivation of chondrocyte and osteoblast reporter ESCs from previously generated and characterized transgenic mouse lines, Collagen type 2 alpha 1(Col2a1)‐ECFP, Bone Sialoprotein (BSP)‐Topaz, and BSP‐Topaz/Dentin Matrix Protein 1 (DMP1)‐Cherry dual reporter mice. Col2a1‐ECFP is highly expressed in chondrocytes, while BSP‐Topaz and DMP1‐Cherry are highly expressed in osteoblasts and osteocytes, respectively. These new skeletal reporter mouse ESC lines will serve as valuable reagents to investigate the functionality of ESC derived chondrocyte and osteoblast cell types. genesis 53:294–298, 2015. © 2015 Wiley Periodicals, Inc.     

Thermofluor-based optimization strategy for the stabilization and crystallization of Campylobacter jejuni desulforubrerythrin

Desulforubrerythrin from Campylobacter jejuni has recently been biochemical and spectroscopically characterized. It is a member of the rubrerythrin family, and it is composed of three structural domains: the N-terminal desulforedoxin domain with a non-heme iron center, followed by a four-helix bundle domain harboring a binuclear iron center and finally a C-terminal rubredoxin domain. To date, this is the first example of a protein presenting this kind of structural domain organization, and therefore the determination of its crystal structure may unveil unexpected structural features. Several attempts were made in order to obtain protein crystals, but always without success. As part of our strategy the thermofluor method was used to increase protein stability and its propensity to crystallize. This approach has been recently used to optimize protein buffer formulation, thus yielding more stable and homogenous protein samples. Thermofluor has also been used to identify cofactors/ligands or small molecules that may help stabilize native protein states. A successful thermofluor approach was used to select a pH buffer condition that allowed the crystallization of Campylobacter jejuni desulforubrerythrin, by screening both buffer pH and salt concentration. A buffer formulation was obtained which increased the protein melting temperature by 7°C relatively to the initial purification buffer. Desulforubrerythrin was seen to be stabilized by lower pH and high salt concentration, and was dialyzed into the new selected buffer, 100mM MES pH 6.2, 500mM NaCl. This stability study was complemented with a second thermofluor assay in which different additives were screened. A crystallization screening was carried out and protein crystals were rapidly obtained in one condition. Protein crystal optimization was done using the same additive screening. Interestingly, a correlation between the stability studies and crystallization experiments using the additive screening could be established. The work presented here shows an elegant example where thermofluor was shown to be a key biophysical method that allowed the identification of an improved buffer formulation and the applicability of this technique to increase the propensity of a protein to crystallize is discussed.     

Depauperate genetic variability detected in the American and European bison using genomic techniques

 

A total of 929 polymorphic SNPs in EB (out of 54, 000 SNPs screened using a BovineSNP50 Illumina Genotyping BeadChip), and 1, 524 and 1, 403 polymorphic SNPs in WB and PB, respectively, were analysed. EB, WB and PB have all undergone recent drastic reductions in population size. Accordingly, they exhibited extremely depauperate genomes, deviations from genetic equilibrium and a genome organization consisting of a mosaic of haplotype blocks: regions with low haplotype diversity and high levels of linkage disequilibrium. No evidence for positive or stabilizing selection was found in EB, WB and PB, likely reflecting drift overwhelming selection. We suggest that utilization of genome-wide screening technologies, followed by utilization of less expensive techniques (e.g. VeraCode and Fluidigm EP1), holds large potential for genetic monitoring of populations. Additionally, these techniques will allow radical improvements of breeding practices in captive or managed populations, otherwise hampered by the limited availability of polymorphic markers. This result in improved possibilities for 1) estimating genetic relationships among individuals and 2) designing breeding strategies which attempt to preserve or reduce polymorphism in ecologically relevant genes and/or entire blocks.

Reviewers

This article was reviewed by: Fyodor Kondrashov and Shamil Sunyaev     

Efficient protein crystallization

High-throughput molecular biology and crystallography advances have placed an increasing demand on crystallization, the one remaining bottleneck in macromolecular crystallography. This paper describes three experimental approaches, an incomplete factorial crystallization screen, a high-throughput nanoliter crystallization system, and the use of a neural net to predict crystallization conditions via a small sample (approximately 0.1%) of screening results. The use of these technologies has the potential to reduce time and sample requirements. Initial experimental results indicate that the incomplete factorial design detects initial crystallization conditions not previously discovered using commercial screens. This may be due to the ability of the incomplete factorial screen to sample a broader portion of "crystallization space," using a multidimensional set of components, concentrations, and physical conditions. The incomplete factorial screen is complemented by a neural network program used to model crystallization. This capability is used to help predict new crystallization conditions. An automated, nanoliter crystallization system, with a throughput of up to 400 conditions/h in 40-nl droplets (total volume), accommodates microbatch or traditional "sitting-drop" vapor diffusion experiments. The goal of this research is to develop a fully-automated high-throughput crystallization system that integrates incomplete factorial screen and neural net capabilities.     

Protein crystallization in the structural genomics era

There are five broad areas where noteworthy advances have occurred in the field of macromolecular crystallization in the past 10 years, though some areas have seen the major part of those advances in only the last two years. This is largely a consequence of the international structural genomics initiative and its early results. The five areas are: (1) Physical studies and characterization of the protein crystallization process; (2) Development of new practical approaches and procedures; (3) The implementation of protein engineering by genetic means to enhance both purification and crystallization; (4) The creation of new screening conditions based on information and databases emerging from structural genomics; and (5) Development and implementation of automation, robotics, and mass screening of crystallization conditions using very small amounts of protein. A brief summary is provided here of the progress in the past few years and the influence of the structural genomics project.     

The promise of macromolecular crystallization in microfluidic chips

Microfluidics, or lab-on-a-chip technology, is proving to be a powerful, rapid, and efficient approach to a wide variety of bioanalytical and microscale biopreparative needs. The low materials consumption, combined with the potential for packing a large number of experiments in a few cubic centimeters, makes it an attractive technique for both initial screening and subsequent optimization of macromolecular crystallization conditions. Screening operations, which require a macromolecule solution with a standard set of premixed solutions, are relatively straightforward and have been successfully demonstrated in a microfluidics platform. Optimization methods, in which crystallization solutions are independently formulated from a range of stock solutions, are considerably more complex and have yet to be demonstrated. To be competitive with either approach, a microfluidics system must offer ease of operation, be able to maintain a sealed environment over several weeks to months, and give ready access for the observation and harvesting of crystals as they are grown.     

Prospective study of PAPNET: review of 25656 Pap smears negative on manual screening and rapid rescreening

In this prospective study, 27,014 Pap smears were selected for PAPNET review on the request of the referring practitioner or patient. Smears that were negative on routine manual screening were submitted for rapid rescreening. Smears considered normal after these two manual screens (n = 25,656) were reviewed using the PAPNET testing system. Routine manual screening identified 1340 (4.96%) of the smears as abnormal, and a further 18 (0.07%) abnormalities were detected by rapid rescreening. PAPNET review identified an additional 102 (0.4%) abnormal smears, including 10 histologically confirmed high grade lesions. The use of PAPNET testing following routine manual screening and rapid rescreening in tandem, enables cytologists to detect additional diagnostically significant abnormalities and reduce the rate of false-negative smears.     

Biomarkers in molecular medicine: cancer detection and diagnosis

In spite of advances in diagnostics and therapeutics, cancer remains the second leading cause of death in the U.S. Successful cancer treatment depends not only on better therapies but also on improved methods to assess an individual's risk of developing cancer and to detect cancers at early stages when they can be more effectively treated. Current cancer diagnostic imaging methods are labor-intensive and expensive, especially for screening large asymptomatic populations. Effective screening strategies depend on methods that are noninvasive and detect cancers in their early stages of development. There is increasing interest and enthusiasm in molecular markers as tools for cancer detection and prognosis. It is hoped that newly discovered cancer biomarkers and advances in high-throughput technologies would revolutionize cancer therapies by improving cancer risk assessment, early detection, diagnosis, prognosis, and monitoring therapeutic response. These biomarkers will be used either as stand-alone tests or to complement existing imaging methods.     

Optimizing non-natural protein function with directed evolution

Developing technologies such as unnatural amino acid mutagenesis, non-natural cofactor engineering, and computational design are generating proteins with novel functions; these proteins, however, often do not reach performance targets and would benefit from further optimization. Evolutionary methods can complement these approaches: recent work combining unnatural amino acid mutagenesis and phage selection has created useful proteins of novel composition. Weak initial activity in a computationally designed enzyme has been improved by iterative rounds of mutagenesis and screening. A marriage of ingenuity and evolution will expand the scope of protein function well beyond Mother Nature's designs.     

Cervical cancer screening, screening errors and reporting

Screening for cervical carcinoma by cervicovaginal cytology has led to a marked reduction in the incidence of and mortality from this tumor over the last 50 years in essentially all countries with a functioning screening program. It is the most successful cancer prevention program of all times. Consequently, approximately 80% of the current incidence of and mortality from this disease occurs in geographic areas of underserved and underscreened women. Essential components of a successful program are a high coverage rate of the female population, screening at regular intervals, well-trained clinical and laboratory staff, and an efficient follow-up and treatment system. Deficiencies in any of these areas may lead to a failing screening system. Thus, the most important reason for the remaining mortality from cervical carcinoma in developed countries is lack of complete coverage. It is questionable if new and more expensive technologies will be able to renmedy the remaining failures of the system if no improvement in the coverage rate is achieved. Screening errors do occur but represent only a small fraction of screening failures. Currently, there are a number of terminology systems around the world; thus, a unified terminology is currently not a realistic goal.     

Rapid detection of antigen binding by antibody fragments expressed in the periplasm of Escherichia coli.

Bacterial expression systems can greatly facilitate protein engineering of antibodies. We have developed a system for high-level expression of antibodies, antibody fragments, or hybrid antibodies with novel effector functions in the periplasm of Escherichia coli. From 5 ml of cells, a simple extraction yields sufficient material for SDS-gel electrophoresis, detection and characterization of hapten binding. To demonstrate our system, heavy-chain variable regions and lambda 1 light chains of a mouse anti-NP antibody were synthesized as hybrid proteins with a bacterial signal peptide (Omp F). Each chain is secreted into the periplasm where processing (cleavage of the signal peptide), folding and heterodimer association take place. Periplasmic proteins are released by cold osmotic shock, and hapten-binding activity is easily detected without further manipulation. The ease of genetic engineering in this system will facilitate the production of immunoglobulin derivatives designed for specific applications, and expression of these molecules in a native state will allow the rapid screening of combinatorial libraries and the results of mutagenesis.     

Laboratory scale structural genomics

At Lawrence Livermore National Laboratory, the development of the TB structural genomics consortium crystallization facility has paralleled several local proteomics research efforts that have grown out of gene expression microarray and comparative genomics studies. Collective experience gathered from TB consortium labs and other centers involved in the NIH-NIGMS protein structure initiative allows us to explore the possibilities and challenges of pursuing structural genomics on an academic laboratory scale. We discuss our procedures and protocols for genomic targeting approaches, primer design, cloning, small scale expression screening, scale-up and purification, through to automated crystallization screening and data collection. The procedures are carried out by a small group using a combination of traditional approaches, innovative molecular biochemistry approaches, software automation, and a modest investment in robotic equipment.     

Analysis and statistics of crystallisation success increase by composition modification of protein and precipitant mixing ratio

The nucleation zone has to be reached for any crystal to grow, and the search for crystallization conditions of new proteins is a trial and error process. Here a convenient screening strategy is studied in detail that varies the volume ratio of protein sample to the reservoir solution in the drop to initiate crystallization that is named "composition modification". It is applied after the first screen and has been studied with twelve proteins. Statistical analysis shows a significant improvement in screening using this strategy. The average improvement of "hits" at different temperatures is between 32 and 42%, for examples, 41.8% ± 14.0% and 35.7% ± 12.4% (± standard deviation) at 288 K and 300 K, respectively. Remarkably, some new crystals were found by composition modification which increased the probability of reaching the nucleation zone to initiate crystallization. This was confirmed by a phase diagram study. It is also demonstrated that composition modification can further increase crystallisation success significantly (1.3 times) after the improvement of "hits" by temperature screening. The trajectories of different composition modifications during vapour diffusion were plotted, further demonstrating that protein crystallizability can be increased by hitting more parts of the nucleation zone. It was also found to facilitate the finding of initial crystals for proteins of low solubility. These proteins gradually become more concentrated during the vapour diffusion process starting from a larger protein solution ratio in the initial mixture.