GenDiS: Genomic Distribution of protein structural domain Superfamilies

Several proteins that have substantially diverged during evolution retain similar three-dimensional structures and biological function inspite of poor sequence identity. The database on Genomic Distribution of protein structural domain Superfamilies (GenDiS) provides record for the distribution of 4001 protein domains organized as 1194 structural superfamilies across 18 997 genomes at various levels of hierarchy in taxonomy. GenDiS database provides a survey of protein domains enlisted in sequence databases employing a 3-fold sequence search approach. Lineage-specific literature is obtained from the taxonomy database for individual protein members to provide a platform for performing genomic and phyletic studies across organisms. The database documents residual properties and provides alignments for the various superfamily members in genomes, offering insights into the rational design of experiments and for the better understanding of a superfamily. GenDiS database can be accessed at http://www.ncbs.res.in/~faculty/mini/gendis/home.html

PuLSE:Quality control and quantification of peptide sequences explored by phage display libraries

The design of highly diverse phage display libraries is based on assumption that DNA bases are incorporated at similar rates within the randomized sequence. As library complexity increases and expected copy numbers of unique sequences decrease, the exploration of library space becomes sparser and the presence of truly random sequences becomes critical. We present the program PuLSE (Phage Library Sequence Evaluation) as a tool for assessing randomness and therefore diversity of phage display libraries. PuLSE runs on a collection of sequence reads in the fastq file format and generates tables profiling the library in terms of unique DNA sequence counts and positions, translated peptide sequences, and normalized 'expected' occurrences from base to residue codon frequencies. The output allows at-a-glance quantitative quality control of a phage library in terms of sequence coverage both at the DNA base and translated protein residue level, which has been missing from toolsets and literature. The open source program PuLSE is available in two formats, a C++ source code package for compilation and integration into existing bioinformatics pipelines and precompiled binaries for ease of use

Beyond the natural proteome:nondegenerate saturation mutagenesis - methodologies and advantages

Beyond the natural proteome, high-throughput mutagenesis offers the protein engineer an opportunity to “tweak” the wild-type activity of a protein to create a recombinant protein with required attributes. Of the various approaches available, saturation mutagenesis is one of the core techniques employed by protein engineers and in recent times, nondegenerate saturation mutagenesis is emerging as the approach of choice. This review compares the current methodologies available for conducting nondegenerate saturation mutagenesis with traditional, degenerate saturation and briefly outlines the options available for screening the resulting libraries, to discover a novel protein with the required activity and/or specificity

Interrogating and Predicting Tolerated Sequence Diversity in Protein Folds: Application to E. elaterium Trypsin Inhibitor-II Cystine-Knot Miniprotein

Cystine-knot miniproteins (knottins) are promising molecular scaffolds for protein engineering applications. Members of the knottin family have multiple loops capable of displaying conformationally constrained polypeptides for molecular recognition. While previous studies have illustrated the potential of engineering knottins with modified loop sequences, a thorough exploration into the tolerated loop lengths and sequence space of a knottin scaffold has not been performed. In this work, we used the Ecballium elaterium trypsin inhibitor II (EETI) as a model member of the knottin family and constructed libraries of EETI loop-substituted variants with diversity in both amino acid sequence and loop length. Using yeast surface display, we isolated properly folded EETI loop-substituted clones and applied sequence analysis tools to assess the tolerated diversity of both amino acid sequence and loop length. In addition, we used covariance analysis to study the relationships between individual positions in the substituted loops, based on the expectation that correlated amino acid substitutions will occur between interacting residue pairs. We then used the results of our sequence and covariance analyses to successfully predict loop sequences that facilitated proper folding of the knottin when substituted into EETI loop 3. The sequence trends we observed in properly folded EETI loop-substituted clones will be useful for guiding future protein engineering efforts with this knottin scaffold. Furthermore, our findings demonstrate that the combination of directed evolution with sequence and covariance analyses can be a powerful tool for rational protein engineering

Prospective identification of parasitic sequences in phage display screens

Phage display empowered the development of proteins with new function and ligands for clinically relevant targets. In this report, we use next-generation sequencing to analyze phage-displayed libraries and uncover a strong bias induced by amplification preferences of phage in bacteria. This bias favors fast-growing sequences that collectively constitute <0.01% of the available diversity. Specifically, a library of 10[superscript 9] random 7-mer peptides (Ph.D.-7) includes a few thousand sequences that grow quickly (the ‘parasites’), which are the sequences that are typically identified in phage display screens published to date. A similar collapse was observed in other libraries. Using Illumina and Ion Torrent sequencing and multiple biological replicates of amplification of Ph.D.-7 library, we identified a focused population of 770 ‘parasites’. In all, 197 sequences from this population have been identified in literature reports that used Ph.D.-7 library. Many of these enriched sequences have confirmed function (e.g. target binding capacity). The bias in the literature, thus, can be viewed as a selection with two different selection pressures: (i) target-binding selection, and (ii) amplification-induced selection. Enrichment of parasitic sequences could be minimized if amplification bias is removed. Here, we demonstrate that emulsion amplification in libraries of ~10[superscript 6] diverse clones prevents the biased selection of parasitic clones

Development of a phage-based diagnostic sensor for active Tuberculosis

2016 Fall.Includes bibliographical references.Antibodies, the quintessential biological recognition molecules, are not ideal for many applications because of their large size, complex modifications, and thermal and chemical instability. Identifying alternative scaffolds that can be evolved into tight, specific binding molecules with improved physical properties is of increasing interest, particularly for biomedical applications in resource-limited environments. Hyperthermophilic organisms, such as Sulfolobus solfataricus, are an attractive source of highly stable proteins as starting points for alternative molecular recognition scaffolds. We describe the first application of phage display to identify binding proteins based on the Sulfolobus solfataricus protein Sso7d scaffold. Sso7d is a small (approximately 7 kDa, 63 amino acids), cysteine free DNA-binding protein with a melting temperature of nearly 100 °C. Tight binding Sso7d variants were selected for a diverse set of protein targets from a 1010 member library, demonstrating the versatility of the scaffold. These Sso7d variants are able to discriminate among closely-related human, bovine, and rabbit serum albumins. Equilibrium dissociation constants in the nanomolar to low micromolar range were measured via competitive ELISA. Importantly, the Sso7d variants continue to bind their targets in the absence of the phage context. Furthermore, phage-displayed Sso7d variants retain their binding affinity after exposure to temperatures up to 70 °C. Taken together, our results suggest that the Sso7d scaffold will be a complementary addition to the range of non-antibody scaffold proteins that can be utilized in phage display. Variants of hyperthermostable binding proteins have potential applications in diagnostics and therapeutics for environments with extreme conditions of storage and deployment. One application for utilizing Sso7d evolved binding molecules is development of Tuberculosis (TB) diagnostic tests. TB is the leading cause of death from infectious disease worldwide. The low sensitivity, extended processing time and high expense of diagnostics are major challenges to the detection and treatment of TB. Mycobacterium tuberculosis ornithine transcarbamylase (Mtb OTC, Rv1656) has been identified in the urine of patients with active TB infection, making Mtb OTC a promising target for point-of-care diagnostics in resource-limited settings. We are motivated to engineer phage-based diagnostic systems that feature improved physical stability, cost of production and sensitivity relative to traditional antibody-based reagents. Specific binding proteins with low nanomolar affinities for Mtb OTC were selected from the naïve Sso7d phage library. Phage particles displaying Sso7d variants along with a monoclonal antibody (mAb) generated by hybridoma technology were utilized to generate a capture ELISA-based assay for Mtb OTC. The ELISA assay signal is linear over the target concentration range of 2.0-125.0 ng/mL with limit of detection 0.4 ng/mL (12 pM), which is comparable to commercial available antibody-based assays. Importantly, this assay maintains functionality at both neutral and basic pH in presence of salt and urea over the range of concentrations typical for human urine. Furthermore, towards our phage-based diagnostic test development goal, a test with a pair of phage displaying 2 different Sso7d variants was established with a limit of detection 4.5 ng/mL (130 pM). Stability of TB diagnostic test is improved at acidic conditions in presence of salt and urea in the typical concentration range of human urine, which may due to the replacement of mAb with phage particles. This result demonstrates that phage particles replacing antibodies in the diagnostic test has the potential to improve stability at harsh conditions

The integration of ProxiMAX randomisation with CIS display for the production of novel peptides

Saturation mutagenesis is a powerful tool in modern protein engineering, which permits key residues within a protein to be targeted in order to potentially enhance specific functionalities. However, the creation of large libraries using conventional saturation mutagenesis with degenerate codons (NNN or NNK/S) has inherent redundancy and consequent disparities in codon representation. Therefore, both chemical (trinucleotide phosphoramidites) and biological methods (sequential, enzymatic single codon additions) of non-degenerate saturation mutagenesis have been developed in order to combat these issues and so improve library quality. Large libraries with multiple saturated positions can be limited by the method used to screen them. Although the traditional screening method of choice, cell-dependent methods, such as phage display, are limited by the need for transformation. A number of cell-free screening methods, such as CIS display, which link the screened phenotype with the encoded genotype, have the capability of screening libraries with up to 1014 members. This thesis describes the further development of ProxiMAX technology to reduce library codon bias and its integration with CIS display to screen the resulting library. Synthetic MAX oligonucleotides are ligated to an acceptor base sequence, amplified, and digested, subsequently adding a randomised codon to the acceptor, which forms an iterative cycle using the digested product of the previous cycle as the base sequence for the next. Initial use of ProxiMAX highlighted areas of the process where changes could be implemented in order to improve the codon representation in the final library. The refined process was used to construct a monomeric anti-NGF peptide library, based on two proprietary dimeric peptides (Isogenica) that bind NGF. The resulting library showed greatly improved codon representation that equated to a theoretical diversity of ~69%. The library was subsequently screened using CIS display and the discovered peptides assessed for NGF-TrkA inhibition by ELISA. Despite binding to TrkA, these peptides showed lower levels of inhibition of the NGF-TrkA interaction than the parental dimeric peptides, highlighting the importance of dimerization for inhibition of NGF-TrkA binding

Engineered Bacteriophage Enabled Nanoprobes for SKBR-3 Cancer Cell Specific Imaging and Therapy

With the recent progress in nanoscience and great deal of understanding in molecular biology, it is now possible to combine genetic tools with synthetic nano- constructs for improved biotechnology applications. Viruses with its inherent nanosize architecture, genetic flexibility, stability to harsh conditions, circulatory behavior and targeting ability, in combination with nano science, are currently an excellent source for designing nano based therapeutics for cancer diagnosis and treatment.Here, we integrate phage display technology (PDT) with nanotechnology to synthesize novel nano-conjguates for potential biomedical applications.The first part of this dissertation is focused on the identification and characterization of novel SKBR-3 breast cancer cell targeting/internalizing ligands using landscape phage libraries. We used several computational methods and biochemical approaches to characterize the specificity, affinity and selectivity of the screened bacteriophage against target SKBR-3 breast cancer cells. In order to understand the mechanism of entry, we investigated the actin dynamics by using live cell and fluorescence imaging during selected phage internalization into target SKBR-3 cells. In conclusion, we demonstrate that phage harboring VSSTQDFP and DGSIPWST peptides could selectively internalize into SKBR-3 cells with high affinity and show rapid involvement of membrane ruffling and rearrangements of actin cytoskeleton during phage entry.The second part of this dissertation is focused on the isolation of major coat proteins, pVIII from screened bacteriophage, its conjugation on functionalized gold nanorod using appropriate chemistry and its multipurpose applications. The successful conjugation of coat proteins on functionalized gold nanorods was verified by using spectroscopic and microscopic techniques. In conclusion, we demonstrate that the resulting protein/peptide- nanoconjugates can be used for imaging and selective photo thermal destruction of SKBR-3 breast cancer cells upon exposure to near-infrared (NIR) light. In order, to gain insight into the mechanism and understand the key cellular processes involved following the treatment of these nanoconjugates, we used illumina microarray technique to explore the molecular interactions with in our model SKBR-3 breast cancer cells. We identified 76 genes to be up regulated and 26 genes are down regulated following the treatment of protein nanoconjugates. Our recent preliminary animal studies in SKBR-3 tumor model (nude mice) shows that these protein-nanoconjugates are feasible for in vivo applications. However, more in vivo experiments are under investigations before its clinical significance is realized.The third part of this dissertation is focused on the assembly of coat proteins on functionalized carbon nanotubes and other biomedical applications of engineered bacteriophage in nanoscience. Using various spectroscopic and microscopic studies, we demonstrate phage proteins assembled on carbon nanotubes can be used for imaging purpose, and SKBR-3 specific bacteriophage can be used as a template for conjugation of photosensitizer, pyropheophorbid-a for targeted photo dynamic therapy. We also demonstrate filamentous bacteriophage displayed with eight glutamic acid residues [E8] on the N-terminus of major coat protein using phage display can be used as a template to assemble liposomes and form phage-liposome complex for targeted drug delivery

Filamentous Biological Macromolecules Based Nanostructures and Their Applications

In nanoscience, one promising strategy for achieving precise placements of nanomaterials and specific recognitions between individual build blocks is to use self-ordered templates to arrange them into designed pattern. Refined bio-molecules from nature, such as nucleic acids, proteins and viruses, have beautiful hierarchical nanostructures and precise molecular recognition capabilities, which make them ideal templates for fabricating hierarchical nanostructures. One branch of such biological templates is filamentous biological macromolecules like spider silks, M13 phages, tobacco mosaic virus, etc. The beauty of filamentous biological templates is that they can assemble functional nanomaterials into one-dimensional, two-dimensional or three-dimensional organizations with controlled size, shape, alignment and orientation.This thesis presents the synthesis and assembly of nanomaterials on individual or self-assembled filamentous biological templates including spider dragline silks, bacteriophages and bacterial pili. Specifically, we found: (1) Spider dragline silks could induce the nucleation of hydroxyapatite (HAP) crystals with preferred orientation; (2) The interactions between microtubule-associated proteins (MAPs) and microtubules were studied by biopanning of a phage displayed random peptide library against purified tubulins; (3) HAP-binding phages had an ability to attract and assemble HAP nanorods into a HAP-phage hybrid for bone regeneration; (4) Films made from bacteriophages could serve as a scaffold for the controlled growth and differentiation of resident mesenchymal stem (MSC) cells; (5) Rodlike bacterial pili particles could be induced to self-assemble into a novel colloidal crystal for nanosynthesis