Positive aspects of negative design: simultaneous selection of specificity and interaction stability

The energetic determinants that drive specific protein-protein interactions are not entirely understood. We describe simultaneous in vivo selection of specific and stable interactions using homologous peptides which compete with protein libraries for an interaction with a target molecule. Library members binding to their target, and promoting cell growth, must outcompete competitor interactions with the target (i.e., competition) and evade binding to the competitors (i.e., negative design). We term this a competitive and negative design initiative (CANDI). We combined CANDI with a protein-fragment complementation assay (PCA) and observed major specificity improvements, by driving selection of winning library members that bind their target with maximum efficacy, ensuring that otherwise energetically accessible alternatives are inaccessible. CANDI-PCA has been used with libraries targeted at coiled coil regions of oncogenic AP-1 components cJun and cFos. We demonstrate that comparable hydrophobic and electrostatic contributions in desired species are compromised in nondesired species when CANDI is executed, demonstrating that both core and electrostatic residues are required to direct specific interactions. Major energetic differences (>or=5.6 kcal/mol) are observed between desired and nondesired interaction stabilities for a CANDI-PCA derived peptide relative to a conventional PCA derived helix, with significantly more stability (3.2 kcal/mol) than the wild-type cJun-cFos complex. As a negative control, a library lacking a residue repertoire able to generate a specific and stable helix was tested. Negative protein design has broad implications in generating specific and therapeutically relevant peptide-based drugs, proteins able to act with minimal cross-talk to homologues or analogues, and in nanobiotechnological design.

[Sarcoidosis as a mimicry of haemangiotic carcinomatosis]

The radiologic work-up of a 67-year-old female patient for dyspnea revealed micronodular infiltrates in both lungs, which in combination with enlarged mediastinal and abdominal lymph-nodes were highly suspicious of sarcoidosis stage II. A bronchoscopic examination including transbronchial biopsy in another hospital was not diagnostic, so the patient was referred to us for surgical lung biopsy. A specimen from the right middle lobe showed massive haemangiotic carcinomatosis of a clear-cell carcinoma. The pathologist--without knowing the history of the patient--discussed a renal-cell carcinoma as potential primary malignancy, which could easily be confirmed as the patient had a tumor-nephrectomy two years ago.

Versatile DNA fragmentation and directed evolution with nucleotide exchange and excision technology

Mimicking natural evolution by DNA shuffling is a commonly used method for the optimization of DNA and protein properties. Here, we present an advancement of this approach whereby a gene library is amplified using a standard polymerase chain reaction (PCR), but incorporates dUTP as a fragmentation-defining exchange nucleotide, together with the four standard dNTPs. Incorporated uracil bases are excised using uracil-DNA-glycosylase, and the DNA backbone subsequently is cleaved with piperidine. This oligonucleotide pool is then reassembled with an internal primer extension procedure using a proofreading polymerase to increase yield, and, finally, is amplified by PCR. Denaturing polyacrylamide urea gels demonstrate this method to produce adjustable fragmentation size ranges dependent on the dUTP:dTTP ratios. Using the model protein, chloramphenicol acetyltransferase I, the sequencing of shuffled gene libraries based on a PCR containing 33% dUTP revealed a low mutation rate, of approx 0.1%, with an average parental fragments size of 86 bases, even without the use of a fragment-size separation. Nucleotide exchange and excision technology (NExT) DNA shuffling is, thus, reproducible and easily executed, making it superior to competing techniques. Additionally, NExT fragmentation outcome can be predicted using the computer software, NExTProg.

Considerations in the design and optimization of coiled coil structures

Coiled coil motifs are, despite their apparent simplicity, highly specific, and play a significant role in the understanding of tertiary structure and its formation. The most commonly observed of the coiled coils, the parallel dimeric, is yet to be fully characterized for this structural class in general. Nonetheless, strict rules have emerged for the necessity of specific types of amino acids at specific positions. In this chapter, we discuss this system in light of existing coiled coil structures and in applying rules to coiled coils that are to be designed or optimized. Understanding and expanding on these rules is crucial in using these motifs, which play key roles in virtually every cellular process, to act as drug-delivery agents by sequestering other proteins that are not behaving natively or that have been upregulated (for example, by binding to coiled coil domains implicated in oncogenesis). The roles of the a and d "hydrophobic" core positions and the e and g "electrostatic" edge positions in directing oligomerization and pairing specificity are discussed. Also discussed is the role of these positions in concert with the b, c, and f positions in maintaining alpha-helical propensity, helix solubility, and dimer stability.

A general method of terminal truncation, evolution, and re-elongation to generate enzymes of enhanced stability

Improving enzyme stability is a highly desirable design step in generating enzymes able to function under extreme conditions, such as elevated temperatures, while having the additional benefit of being less susceptible to cleavage by proteases. For these reasons, many different approaches and techniques have been devised in constructing such proteins, but the results to date have been of mixed success. Here, we present a robust method involving the terminal truncation, random mutagenesis and fragmentation, recombination, elongation, and finally, selection at physiological temperatures, to generate an enzyme with improved stability. Three cycles of directed evolution comprising of random mutagenesis, DNA shuffling, and selection at 37 degrees C were used, using the bacterial enzyme TEM-1 beta-lactamase as a model protein to yield deletion mutants with in vivo ampicillin resistance levels comparable to wild-type (wt) enzyme. Kinetic studies demonstrate the selected mutant to have a significantly improved thermostability relative to its wt counterpart. Elongation of this mutant to the full-length gene resulted in a beta-lactamase variant with dramatically increased thermostability. This technique was so fruitful that the evolved enzyme retained its maximum catalytic activity even 20 degrees C above its wt parent protein optimum. Thus, structural perturbation by terminal truncation and subsequent compensation by directed evolution at physiological temperatures is a fast, efficient, and highly effective way to improve the thermostability of proteins without the need for selecting at elevated temperatures.

Semirational design of Jun-Fos coiled coils with increased affinity: Universal implications for leucine zipper prediction and design

Activator protein-1 (AP-1) is a crucial transcription factor implicated in numerous cancers. For this reason, nine homologues of the AP-1 leucine zipper region have been characterized: Fos (c-Fos, FosB, Fra1, and Fra2), Jun (c-Jun, JunB, and JunD), and semirational library-designed winning peptides FosW and JunW. The latter two were designed to specifically target c-Fos or c-Jun. They have been identified by using protein-fragment complementation assays combined with growth competition. This assay removes nonspecific, unstable, and protease susceptible library members from the pool, leaving winners with excellent drug potential. Thermal melts of all 45 possible dimeric interactions have been surveyed, with the FosW-c-Jun complex displaying a melting temperature (T(m)) of 63 degrees C, compared to only 16 degrees C for wild-type c-Fos-c-Jun interaction. This impressive 70,000-fold K(D) decrease is largely due to optimized core packing, alpha-helical propensity, and electrostatics. Contrastingly, due to a poor c-Fos core, c-Fos-JunW dimerizes with lower affinity. However the T(m) far exceeds wild-type c-Fos-c-Jun and averaged JunW and c-Fos, indicating a preference over either homodimer. Finally, and with wider implications, we have compiled a method for predicting interaction of parallel, dimeric coiled coils, using our T(m) data as a training set, and applying it to 59 bZIP proteins previously reported. Our algorithm, unlike others to date, accounts for helix propensity, which is found to be integral in coiled coil stability. Indeed, in applying the algorithm to these 59(2) bZIP interactions, we were able to correctly identify 92% of all strong interactions and 92% of all noninteracting pairs.

[Diffuse smooth muscle proliferation of the lung and severe pulmonary hypertension]

A 50-year old female forest worker presented with the complaints of progressive exercise induced dyspnea and the history of a recent syncope. Right heart catheterisation revealed the diagnosis of severe precapillary pulmonary hypertension. Ventilation perfusion lung scan indicated the existence of multiple pulmonary emboli with high probability. However, pulmonary angiography did not confirm this finding. Computed tomography of the lung demonstrated a slight mosaic pattern of diffuse ground glass opacities. After video assisted thoracoscopy, the histological diagnosis of diffuse smooth muscle proliferation of the lung could be concluded from the removed lung tissue. Diffuse smooth muscle proliferation of the lung is a rarely diagnosed disease, however it should be considered in patients with suspected pulmonary embolism by ventilation perfusion scan but a normal finding in pulmonary angiography, who are suffering from otherwise not explained pulmonary hypertension.

Structural perturbation and compensation by directed evolution at physiological temperature leads to thermostabilization of beta-lactamase

The choice of protein for use in technical and medical applications is limited by stability issues, making understanding and engineering of stability key. Here, enzyme destabilization by truncation was combined with directed evolution to create stable variants of TEM-1 beta-lactamase. This enzyme was chosen because of its implication in prodrug activation therapy, pathogen resistance to lactam antibiotics, and reporter enzyme bioassays. Removal of five N-terminal residues generated a mutant which did not confer antibiotic resistance at 37 degrees C. Accordingly, the half-life time in vitro was only 7 s at 40 degrees C. However, three cycles comprising random mutagenesis, DNA shuffling, and metabolic selection at 37 degrees C yielded mutants providing resistance levels significantly higher than that of the wild type. These mutants demonstrated increased thermoactivity and thermostability in time-resolved kinetics at various temperatures. Chemical denaturation revealed improved thermodynamic stabilities of a three-state unfolding pathway exceeding wild-type construct stability. Elongation of one optimized deletion mutant to full length increased its stability even further. Compared to that of the wild type, the temperature optimum was shifted from 35 to 50 degrees C, and the beginning of heat inactivation increased by 20 degrees C while full activity at low temperatures was maintained. We attribute these effects mainly to two independently acting boundary interface residue exchanges (M182T and A224V). Structural perturbation by terminal truncation, evolutionary compensation at physiological temperatures, and elongation is an efficient way to analyze and improve thermostability without the need for high-temperature selection, structural information, or homologous proteins.

Nucleotide exchange and excision technology (NExT) DNA shuffling: a robust method for DNA fragmentation and directed evolution

DNA shuffling is widely used for optimizing complex properties contained within DNA and proteins. Demonstrated here is the amplification of a gene library by PCR using uridine triphosphate (dUTP) as a fragmentation defining exchange nucleotide with thymidine, together with the three other nucleotides. The incorporated uracil bases were excised using uracil-DNA-glycosylase and the DNA backbone subsequently cleaved with piperidine. These end-point reactions required no adjustments. Polyacrylamide urea gels demonstrated adjustable fragmentation size over a wide range. The oligonucleotide pool was reassembled by internal primer extension to full length with a proofreading polymerase to improve yield over Taq. We present a computer program that accurately predicts the fragmentation pattern and yields all possible fragment sequences with their respective likelihood of occurrence, taking the guesswork out of the fragmentation. The technique has been demonstrated by shuffling chloramphenicol acetyltransferase gene libraries. A 33% dUTP PCR resulted in shuffled clones with an average parental fragment size of 86 bases even without employment of a fragment size separation, and revealed a low mutation rate (0.1%). NExT DNA fragmentation is rational, easily executed and reproducible, making it superior to other techniques. Additionally, NExT could feasibly be applied to several other nucleotide analogs.

[Imaging techniques for showing the morphology and surface structure of extracranial internal carotid artery plaques]

Methods of determining plaques in the extracranial internal carotid artery are ultrasound, computed tomography (CT) and magnetic resonance imaging (MRI). The goal of this overview is to introduce these methods and discuss their diagnostic and clinical significance. Ultrasound has the capability of showing the echogenity of the plaques. This method seems to demonstrate a relationship with the incidence of hemispheric symptoms. A histological association could only rarely be seen. The surface structure can only be clearly and correctly evaluated in individual cases under optimal circumstances. Computed tomography is capable of showing the calcium content and specific site of the plaques. However, lipid content and fibrous tissue cannot be deduced reliably. The currently available image resolutions limit a detailed imaging of surface characteristics. Magnetic resonance imaging provides, in vitro, a correct rendering of plaque composition and endoluminal surface structure. In vivo it is possible to recognize both the fibrous cap and necrotic core as well as intraplaque hemorrhage. Because of certain artefacts more detailed images are difficult to interpret. In conclusion, further clinical trials should reveal, whether these methods can be set in clinical routine to detect plaque surface and morphology for stratifying patients at risk of hemispheric symptoms during the spontaneous course as well as during carotid interventions.

Interstitial lung disease in a baby with a de novo mutation in the SFTPC gene

Mutations in the surfactant protein C gene (SFTPC) were recently reported in patients with interstitial lung disease. In a 13-month-old infant with severe respiratory insufficiency, a lung biopsy elicited combined histological patterns of nonspecific interstitial pneumonia and pulmonary alveolar proteinosis. Immunohistochemical and biochemical analyses showed an intra-alveolar accumulation of surfactant protein (SP)-A, precursors of SP-B, mature SP-B, aberrantly processed proSP-C, as well as mono- and dimeric SP-C. Sequencing of genomic DNA detected a de novo heterozygous missense mutation of the SFTPC gene (g.1286T>C) resulting in a substitution of threonine for isoleucine (173T) in the C-terminal propeptide. At the ultrastructural level, abnormal transport vesicles were detected in type-II pneumocytes. Fusion proteins, consisting of enhanced green fluorescent protein and wild-type or mutant proSP-C, were used to evaluate protein trafficking in vitro. In contrast to wild-type proSP-C, mutant proSP-C was routed to early endosomes when transfected into A549 epithelial cells. In contrast to previously reported mutations, the 173T represents a new class of surfactant protein C gene mutations, which is marked by a distinct trafficking, processing, palmitoylation, and secretion of the mutant and wild-type surfactant protein C. This report heralds the emerging diversity of phenotypes associated with the expression of mutant surfactant C proteins.