A spider toxin binding protein from bovine brain: its purification and N-terminal amino acid sequence determination.

A 60kDa spider toxin binding protein from bovine brain was solubilized with digitonin and purified up to 5800-folds over starting crude homogenate. The purification procedure entailed DEAE-cellulose, concanavalin-A affinity, 1-naphthylacetyl spermine affinity and high performance liquid chromatography. The purified protein owned a very high affinity for ligand 125I-JSTX-3 binding Kd 15.6nM and Bmax 6.5nM. The amino acid composition of the protein was determined. The N-terminal amino acid sequence analysis yielded a unique sequence: NH2-X-Pro-X-Val-Tyr-Phe-Lys-Glu-Gln-Phe-Leu-Asp-Gly-Asp-X.     

Evaluation of protein quantification using standard peptides containing single conservative amino acid replacements

Structural analogs are evaluated as peptide internal standards for protein quantification with liquid chromatography‐multiple reaction monitoring mass spectrometry (LC‐MRM); specifically, single conservative amino acid replacements (SCAR) are performed to create tagged standards that differ by the addition or subtraction of a single methylene group in one amino acid side chain. Because the performance of stable isotope‐labeled standards (SIS) has been shown to be superior to structural analogs, differences in both development and quantitative performance between assays based on SIS and SCAR peptides are explored. To establish an assay using the structural analogs, analysis of endogenous, SCAR and SIS peptides was performed to examine their ion signal, fragmentation patterns and response in LC‐MRM. Performance of SCAR and SIS peptides was compared for quantification of epidermal growth factor receptor from lung cancer cell lysates and immunoglobulin M in the serum of multiple myeloma patients. Copyright © 2012 John Wiley & Sons, Ltd.     

In silico prediction of deleterious single amino acid polymorphisms from amino acid sequence

Molecular cause of human disease retains as one of the most attractive scientific research targets for decades. An effective approach toward this topic is analysis and identification of disease-related amino acid polymorphisms. In this work, we developed a concise and promising deleterious amino acid polymorphism identification method SeqSubPred based on 44 features solely extracted from protein sequence. SeqSubPred achieved surprisingly good predictive ability with accuracy (0.88) and area under receiver operating characteristic (0.94) without resorting to homology or evolution information, which is frequently used in similar methods and usually more complex and time-consuming. SeqSubPred also identified several critical sequence features obtained from random forests model, and these features brought some interesting insights into the factors affecting human disease-related amino acid substitutions. The online version of SeqSubPred method is available at montana.informatics.indiana.edu/cgi-bin/seqmut/seqsubpred.cgi     

Computational design of a single amino acid sequence that can switch between two distinct protein folds

The functions of many proteins are mediated by specific conformational changes, and therefore the ability to design primary sequences capable of secondary and tertiary changes is an important step toward the creation of novel functional proteins. To this end, we have developed an algorithm that can optimize a single amino acid sequence for multiple target structures. The algorithm consists of an outer loop, in which sequence space is sampled by a Monte Carlo search with simulated annealing, and an inner loop, in which the effect of a given mutation is evaluated on the various target structures by using the rotamer packing routine and composite energy function of the protein design software, RosettaDesign. We have experimentally tested the method by designing a peptide, Sw2, which can be switched from a 2Cys-2His zinc finger-like fold to a trimeric coiled-coil fold, depending upon the pH or the presence of transition metals. Physical characterization of Sw2 confirms that it is able to reversibly adopt each intended target fold.     

Angle-dependent terahertz time-domain spectroscopy of amino acid single crystals

The measurement of absorption spectra using angle-dependent terahertz (THz) time-domain spectroscopy for amino acid single crystals of l-cysteine and l-histidine is reported for the first time. Linearly polarized THz radiation enables us to observe angle-dependent far-infrared absorption spectra of amino acid single crystals and determine the direction of the oscillating dipole of the molecules in the 20-100 cm(-1) range. By comparing the THz spectra of a single crystal and powder, we found that there was a clear hydrogen-bond peak in the crystal spectrum as a result of the larger hydrogen-bond network. The low-temperature THz spectra of amino acid microcrystals showed more intermolecular vibrational modes than those measured at room temperature. An ab initio frequency calculation of a single amino acid molecule was used to predict the intramolecular vibrational modes. The validity of the calculation models was confirmed by comparing the results with experimentally obtained data in the Raman spectral region.     

Engineering protein kinases with distinct nucleotide specificities and inhibitor sensitivities by mutation of a single amino acid

A major goal of signal transduction research is to identify the substrates and roles of the many protein kinases. The task might be simplified by the discovery that the mutation of a single amino acid dramatically alters the nucleotide specificity of protein kinases and their inhibition by a particular class of anti-inflammatory drug.     

A statistical method for predicting protein unfolding rates from amino acid sequence

The prediction of protein unfolding rates from amino acid sequences is one of the most important challenges in computational biology and chemistry. The analysis on the relationship between protein unfolding rates and physical-chemical, energetic, and conformational properties of amino acid residues provides valuable information to understand and predict the unfolding rates of two- and three-state proteins. We found that the classification of proteins into different structural classes shows an excellent correlation between amino acid properties and unfolding rates of two- and three-state proteins, indicating the importance of native-state topology in determining the protein unfolding rates. We have formulated three independent linear regression equations to different structural classes of proteins for predicting their unfolding rates from amino acid sequences and obtained an excellent agreement between predicted and experimentally observed unfolding rates of proteins; the correlation coefficients are 0.999, 0.990, and 0.992, respectively, for all-alpha, all-beta, and mixed-class proteins. Further, we have derived a general equation applicable to all structural classes of proteins, which can be used for predicting the unfolding rates for proteins of an unknown structural class. We observed a correlation of 0.987 and 0.930, respectively, for back-check and jack-knife tests. These accuracy levels are better than those of other methods in the literature.     

Unnatural amino acid mutagenesis of green fluorescent protein

Unnatural amino acid mutagenesis has been used to selectively substitute tyrosine 66 of green fluorescent protein (GFP) with five novel amino acids: p-amino-L-phenylalanine, p-methoxy-L-phenylalanine, p-iodo-L-phenylalanine, p-bromo-L-phenylalanine, and L-3-(2-naphthyl)alanine. The absorbance and emission maxima of the resulting mutant GFPs span the range from 375 to 435 nm and 428 to 498 nm, respectively. The spectral properties of the mutant GFPs, including the absorbance and fluorescence maxima and quantum yields, correlate with the structural and electronic properties of the substituents on the amino acids.     

Nonnatural amino acid ligands in heme protein design

The de novo design, synthesis, and characterization of a four-alpha-helix bundle scaffold containing heme ligated by 4-beta-(pyridyl)-l-alanine (Pal) is presented. The protein scaffold is highly helical, stable, and conformationally specific in the apo-state. Incorporation of heme using the designed bis-Pal axial ligation is shown using UV-visible and EPR spectroscopies. The observed heme midpoint reduction potential, +58 mV versus SHE, is 287 mV (6.8 kcal/mol) higher than the analogous bis-histidine-ligated heme protein.     

AbSep--an amino acid based pseudobioaffinity adsorbent for the purification of immunoglobulin G

The present work deals with the development and characterization of a tryptophan based pseudobioaffinity adsorbent for the purification of monoclonal and polyclonal antibodies. Tryptophan as a ligand was selected based on molecular docking and experimental screening studies of the amino acids involved in IgG-Protein A interaction. The ligand was coupled to a polymethacrylate based rigid, porous SEPABEADS beaded matrix to obtain the desired affinity adsorbent, which was named AbSep. Characterization studies with regards to the effect of matrix properties (pore size, particle size, nature of matrix, spacer arm) and the medium properties (pH, conductivity, additives) were performed to elucidate the nature of IgG-AbSep interactions and to determine the optimal conditions for obtaining high binding and purity of IgG. The equilibrium binding capacity of AbSep and dissociation constant was found to be 78 mg/ml and 5.31×10(-6)M respectively. AbSep was able to successfully purify polyclonal human IgG from plasma and monoclonal antibody (chimeric IgG1) from CHO cell culture supernatant. Both binding and elution steps were performed at near neutral pH resulting in a purity and recovery of more than 90% and 85% respectively. Additionally, AbSep was shown to be stable to 0.5M NaOH solutions, the preferred agent for cleaning and sanitization of chromatographic media.     

Hierarchically porous polymers with ultra-high affinity for bisphenol A enables high efficient water purification

The widespread use of bisphenol A(BPA) poses a serious threat to the environment and human health. However, efficient removal of BPA in water is incredibly challenging, owing to the inert chemical nature and electrical neutrality of BPA. In order to solve this problem, for the first time, we propose that a strategy of designing conjugated porous polymers with the pore size matching the size of BPA can greatly enhance the binding force of BPA. On this basis, we developed a novel conjugated poly1,3,5-tri[4-(diphenylamino)phenyl]benzene(MPDPB) with intrinsic pore matching the size of BPA and multi-stage porous structure by editing polymerization with nitrobenzene. The binding energy of MPDPB to BPA is the highest at present(37.84 kcal/mol), which is 2.3 times that of the most powerful adsorbent previously reported and five times that of the conventional adsorbent. These advantages make MPDPB have super-high adsorption performance towards BPA and high absorbing stability under extreme environments. Impressively, MPDPB could be easily loaded on a non-woven fabric to generate point-of-use devices, which could eliminate more than 99.8% of BPA, making it the best BPA candidate adsorbent material. We believe that the proposed material design derived from the specific structure of the contaminant molecule can be extended to exploring further innovative adsorbents.     

A new bicyclic proline-mimetic amino acid

A new constrained bicyclic α-amino acid proline-mimetic was developed. The synthesis was achieved starting from derivatives of the chiral pool, thus allowing to prepare analogues of either l- or d-proline by choosing appropriate stereoisomers of serine and α,β-isopropylidene-glycerol derivatives. The scaffolds were prepared as N-Fmoc-amino acid suitable for solid-phase peptide synthesis.     

A genetically encoded fluorescent amino acid

The fluorescent amino acid l-(7-hydroxycoumarin-4-yl) ethylglycine 1 has been genetically encoded in E. coli in response to the amber TAG codon. Because of its high fluorescence quantum yield, relatively large Stoke's shift, and sensitivity to both pH and polarity, this amino acid should provide a useful probe of protein localization and trafficking, protein conformation changes, and protein-protein interactions.     

A genetically encoded photocaged amino acid

We have developed a second orthogonal tRNA/synthetase pair for use in yeast based on the Escherichia coli tRNALeu/leucyl tRNA-synthetase pair. Using a novel genetic selection, we have identified a series of synthetase mutants that selectively charge the amber suppresor tRNA with the C8 amino acid, alpha-aminocaprylic acid, and the photocaged amino acid, o-nitrobenzyl cysteine, allowing them to be inserted into proteins in yeast in response to the amber nonsense codon, TAG.