A proteome database of human primary T helper cells

We have established the first public database of human primary T helper cell proteome using two-dimensional electrophoresis (2-DE) and matrix assisted laser desorption/ionization-time of flight-mass spectrometry. For the database, CD4+ human T cells were activated with anti-CD3+anti-CD28 antibodies and metabolically labeled with [35S]methionine for 24 h. Cells were lysed and proteins were separated by 2-DE. About 1500 protein spots were detected in the resulting 2-DE gels with silver staining, and 2000 spots with autoradiography. We have identified 91 proteins from the 2-DE gels using peptide mass fingerprinting, and annotated them to our database. The identified proteins are also linked to SWISS-PROTand NCBI protein databases. Our database is available via the Internet at http://www3.btk.utu.fi:8080/Genomics/Proteomics/Database.     

Proteome database of unsensitized CD4 positive T lymphocytes in T cell receptor transgenic mice

We established a two-dimensional electrophoresis (2-DE) mapping database of splenic CD4 T cells prepared from I-A(d)-restricted ovalbumin (OVA)(323-339) specific T cell receptor (TCR) transgenic mice (OVA23-3). First we examined the purification of CD4 T cells and found that the high purity of cells produced more accurate protein maps. The first dimension utilized narrow-range immobilized pH gradients (IPGs), pH 4.0-5.0, pH 4.5-5.5, pH 5.0-6.0, and pH 5.5-6.7. Approximately 1300 spots were detected by silver staining. Detection was performed by in-gel tryptic digestion of the spots, matrix assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF-MS) technology and database searches via the world wide web (WWW). We have so far identified 255 proteins on 2-DE gels of whole cell lysates. This is the first construction of a proteome database for murine unsensitized CD4 T lymphocytes. To examine this further, 2-DE mapping was utilized for splenic CD4 T cells from another TCR transgenic mouse strain (DO11.10 TCR transgenic mice). Mapping patterns were found to be almost identical to those from CD4 T cells from OVA23-3 mice. These results indicated that the 2-DE maps in this study could be used for mouse CD4 T cells to examine protein changes in cells given certain stimuli.     

Computationally identified novel diphenyl- and phenylpyridine androgen receptor antagonist structures

We have identified and profiled a set of androgen receptor (AR) binding compounds representing two nonsteroidal scaffolds from a public chemical database supplied by Asinex with virtual screening procedure incorporating our recently published 3D QSAR model of AR ligands. The diphenyl- and phenylpyridine-based compounds act as antagonists in wild-type AR in CV1 cells and also retain this antagonistic character in CV1 cells expressing T877A mutant receptor. This mutation is frequently associated with prostate cancer. Two of the compounds repress the androgen-dependent cell growth of LNCaP prostate cancer cells expressing the T877A AR mutant. Molecular modeling of the observed in vitro antagonism with induced fit docking suggests that W741 and M895 could be mechanistically involved in the initiation of the antagonism. The results indicate finding of nonsteroidal AR antagonist compounds from a public chemical database with computational methods. Compounds could serve as a novel platform to develop more potent AR antagonists with inhibitory activity in both wild-type and T877A mutant AR.     

A comparative analysis of alterations in protein expression after activation or human immunodeficiency virus, type 1 infection of human CD4+ T cells

We have previously described an in vitro model for studying human immunodeficiency virus, type 1 (HIV-1) infection in CD4+ T cells [1]. This model employs the WE17/10 cell line, which loses expression of its T cell receptor/CD3 (TCR/CD3) after several months of productive infection. We have used this model to analyze the synthesis and posttranslational modification of viral and cellular proteins after HIV-1 infection and to determine the relationship of these changes to TCR/CD3 expression. Mainly we observe positive changes in protein expression after infection. A phosphoprotein, referred to as WH:1, appears in infected cells that still express their TCR/CD3 complex, and its persistence is linked to the presence of the complex. We examined whether loss of the TCR/CD3 complex could be associated with alterations in the T cell activation pathway as a result of infection. We used T cell activators and inhibitors to determine whether there were common elements between the two events. Quantitative enhancement in one spot, Cs:1, occurred after both Cyclosporin A treatment of uninfected cells and HIV-1 infection of untreated cells. Taken altogether, these data suggest that a correlation exists between negative regulation of late events in the T cell activation pathway and down regulation of the TCR/CD3 complex after HIV-1 infection.     

Topological shape and size of peptides: identification of potential allele specific helper T cell antigenic sites

A database of primary sequences of 28 immunogenic peptides, known to elicit T cell response, derived from five different haplotypes was compiled to identify allele specific helper T cell antigenic sites using a rule based graph-theoretical method. The prediction was based on the identification of allele specific patterns in the form of "topological shape and size" present in the peptides. Indices computed from weighted connected graph models of amino acid side chains and peptides were used in this purpose. The system was trained by 10 Ad and 10 non-Ad restricted peptide sequences, assigned actives and inactives, respectively, chosen randomly from the database, and four Ad and four non-Ad restricted sequences were kept as test peptides. This allowed the system to learn about "topological shape and size" specific for Ad restricted peptides from the differences, if any, they had with the inactive peptides in that respect. The system made 100% correct prediction for the training set peptides and misclassified only one inactive peptide of the test set. The system also identified crucial residues for lambda repressor 12-24 and insulin A-chains. This identification also shows that activity related/crucial residues could be located at varying distances from the peptide terminals. To our knowledge, the method is unique of its kind in the literature and may find application in the rational design of synthetic vaccines and other peptides of immunological importance.     

Predicting aqueous free energies of solvation as functions of temperature

This work introduces a model, solvation model 6 with temperature dependence (SM6T), to predict the temperature dependence of aqueous free energies of solvation for compounds containing H, C, and O in the range 273-373 K. In particular, we extend solvation model 6 (SM6), which was previously developed (Kelly, C. P.; Cramer, C. J.; Truhlar, D. G. J. Chem. Theory Comput. 2005, 1, 1133) for predicting aqueous free energies of solvation at 298 K, to predict the variation of the free energy of solvation relative to 298 K. Also, we describe the database of experimental aqueous free energies of solvation for compounds containing H, C, and O that was used to parametrize and test the new model. SM6T partitions the temperature dependence of the free energy of solvation into two components: the temperature dependence of the bulk electrostatic contribution to the free energy of solvation, which is computed using the generalized Born equation, and the temperature dependence of first-solvation-shell effects which is modeled using a parametrized solvent-exposed surface-area-dependent term. We found that SM6T predicts the temperature dependence of aqueous free energies of solvation with a mean unsigned error of 0.08 kcal/mol over our entire database, whereas using the experimental value at 298 K produces a mean unsigned error of 0.53 kcal/mol.     

Analysis of cancer cell lipids using matrix‐assisted laser desorption/ionization 15‐T Fourier transform ion cyclotron resonance mass spectrometry

A combination of methodologies using the extremely high mass accuracy and resolution of 15‐T Fourier transform ion cyclotron resonance (FT‐ICR) mass spectrometry (MS) was introduced for the identification of intact cancer cell phospholipids. Lipids from a malignant glioma cell line were initially analyzed at a resolution of >200 000 and identified by setting the mass tolerance to ±1 mDa using matrix‐assisted laser desorption/ionization (MALDI) 15‐T FT‐ICR MS in positive ion mode. In most cases, a database search of potential lipid candidates using the exact masses of the lipids yielded only one possible chemical composition. Extremely high mass accuracy (<0.1 ppm) was then attained by using previously identified lipids as internal standards. This, combined with an extremely high resolution (>800 000), yielded well‐resolved isotopic fine structures allowing for the identification of lipids by MALDI 15‐T FT‐ICR MS without using tandem mass spectrometric (MS/MS) analysis. Using this method, a total of 38 unique lipids were successfully identified. Copyright © 2012 John Wiley & Sons, Ltd.     

Extension of a temperature-dependent aqueous solvation model to compounds containing nitrogen, fluorine, chlorine, bromine, and sulfur

Most methods for predicting free energies of solvation have been developed or validated exclusively for room temperature. Recently, we developed a model called SM6T for predicting aqueous solvation free energies as a function of temperature for solutes composed of C, H, or O, and here we present solvation model 8 with temperature dependence (SM8T) for predicting the temperature dependence of aqueous free energies of solvation for compounds containing H, C, N, O, F, S, Cl, and Br in the range 273-373 K. We also describe the database of experimental aqueous free energies of solvation used to parametrize the model. SM8T partitions the temperature dependence of the free energy of solvation into two components: the temperature dependence of the bulk electrostatic contribution to the free energy of solvation, which is computed using the generalized Born equation, and the temperature dependence of first-solvation-shell effects, which is modeled by terms proportional to the solvent-exposed surface areas of atoms in functional groups determined entirely by geometry. SM8T predicts the temperature dependence of aqueous free energies of solvation with a mean unsigned error of 0.08 kcal/mol over a database of 4403 measurements on 348 compounds at various temperatures. We also discuss the accuracy of SM8T for predicting the temperature dependence of aqueous free energies of solvation for ions and present free energies of solvation as a function of temperature for two sample ions.     

Enabling the exploration of biochemical pathways

The Biochemical Pathways Wall Chart (http://www.expasy.org/tools/pathways/ref.1) has been converted into a molecule and reaction database. Major features of this database are that each molecule is represented by lists of all atoms and bonds (as connection tables), and in the reactions the reaction centre, the atoms and bonds directly involved in the bond rearrangement process, are marked. The information in the database has been enriched by a set of diverse 3D structure conformations generated by the programs CORINA and ROTATE. The web-based structure and reaction retrieval system C@ROL provides a wide range of search methods to mine this rich database. The database is accessible at http://www2.chemie.uni-erlangen.de/services/biopath/index.html and http://www.mol-net.de/databases/biopath.html .     

'Information-Based-Acquisition' (IBA) technique with an ion-trap/time-of-flight mass spectrometer for high-throughput and reliable protein profiling

Highly complex protein mixtures can be analyzed after proteolysis using liquid chromatography/mass spectrometry (LC/MS). In an LC/MS run, intense peptide ions originating from high-abundance proteins are preferentially analyzed using tandem mass spectrometry (MS(2)), so obtaining the MS(2) spectra of peptide ions from low-abundance proteins is difficult even if such ions are detected. Furthermore, the MS(2) spectra may produce insufficient information to identify the peptides or proteins. To solve these problems, we have developed a real-time optimization technique for MS(2), called the Information-Based-Acquisition (IBA) system. In a preliminary LC/MS run, a few of the most intense ions detected in every MS spectrum are selected as precursors for MS(2) and their masses, charge states and retention times are automatically registered in an internal database. In the next run, a sample similar to that used in the first run is analyzed using database searching. Then, the ions registered in the database are excluded from the precursor ion selection to avoid duplicate MS(2) analyses. Furthermore, real-time de novo sequencing is performed just after obtaining the MS(2) spectrum, and an MS(3) spectrum is obtained for accurate peptide identification when the number of interpreted amino acids in the MS(2) spectrum is less than five. We applied the IBA system to a yeast cell lysate which is a typical crude sample, using a nanoLC/ion-trap time-of flight (IT/TOF) mass spectrometer, repeating the same LC/MS run five times. The obtained MS(2) and MS(3) spectra were analyzed by applying the Mascot (Matrix Science, Boston, MA, USA) search engine to identify proteins from the sequence database. The total number of identified proteins in five LC/MS runs was three times higher than that in the first run and the ion scores for peptide identification also significantly increased, by about 70%, when the MS(3) spectra were used, combined with the MS(2) spectra, before being subjected to Mascot analysis.     

Spleen SORT LNP Generated in situ CAR T Cells Extend Survival in a Mouse Model of Lymphoreplete B Cell Lymphoma

Chimeric Antigen Receptor (CAR) T cell immunotherapy is revolutionizing treatment for patients suffering from B-cell lymphoma (BL). However, the current method of CAR T cell production is complicated and expensive, requiring collection of patient blood to enrich the T cell population, ex vivo engineering/activation, and quality assessment before the patient can receive the treatment. Herein we leverage Spleen Selective ORgan Targeted (SORT) Lipid Nanoparticles (LNPs) to produce CAR T cells in situ and bypass the extensive and laborious process currently used. Optimized Spleen SORT LNPs containing 10 % 18 : 1 PA transfected CD3+, CD8+, and CD4+ T cells in wild-type mice. Spleen SORT LNPs delivered Cre recombinase mRNA and CAR encoding mRNA to T cells in reporter mice and in a lymphoreplete B cell lymphoma model (respectively) after intravenous injection without the need for active targeting ligands. Moreover, in situ CAR T cells increased the overall survival of mice with a less aggressive form of B cell lymphoma. In addition, in situ transfected CAR T cells reduced tumor metastasis to the liver by increasing tumor infiltrating lymphocytes. Overall, these results offer a promising alternative method for CAR T cell production with pre-clinical potential to treat hematological malignancies.     

Validation of electronic structure methods for isomerization reactions of large organic molecules

In this work the ISOL24 database of isomerization energies of large organic molecules presented by Huenerbein et al. [Phys. Chem. Chem. Phys., 2010, 12, 6940] is updated, resulting in the new benchmark database called ISOL24/11, and this database is used to test 50 electronic model chemistries. To accomplish the update, the very expensive and highly accurate CCSD(T)-F12a/aug-cc-pVDZ method is first exploited to investigate a six-reaction subset of the 24 reactions, and by comparison of various methods with the benchmark, MCQCISD-MPW is confirmed to be of high accuracy. The final ISOL24/11 database is composed of six reaction energies calculated by CCSD(T)-F12a/aug-cc-pVDZ and 18 calculated by MCQCISD-MPW. We then tested 40 single-component density functionals (both local and hybrid), eight doubly hybrid functionals, and two other methods against ISOL24/11. It is found that the SCS-MP3/CBS method, which is used as benchmark for the original ISOL24, has an MUE of 1.68 kcal mol(-1), which is close to or larger than some of the best tested DFT methods. Using the new benchmark, we find ωB97X-D and MC3MPWB to be the best single-component and doubly hybrid functionals respectively, with PBE0-D3 and MC3MPW performing almost as well. The best single-component density functionals without molecular mechanics dispersion-like terms are M08-SO, M08-HX, M05-2X, and M06-2X. The best single-component density functionals without Hartree-Fock exchange are M06-L-D3 when MM terms are included and M06-L when they are not.     

A database of new zeolite-like materials

We here describe a database of computationally predicted zeolite-like materials. These crystals were discovered by a Monte Carlo search for zeolite-like materials. Positions of Si atoms as well as unit cell, space group, density, and number of crystallographically unique atoms were explored in the construction of this database. The database contains over 2.6 M unique structures. Roughly 15% of these are within +30 kJ mol(-1) Si of α-quartz, the band in which most of the known zeolites lie. These structures have topological, geometrical, and diffraction characteristics that are similar to those of known zeolites. The database is the result of refinement by two interatomic potentials that both satisfy the Pauli exclusion principle. The database has been deposited in the publicly available PCOD database and in www.hypotheticalzeolites.net/database/deem/.     

"Affinity-proteomics": direct protein identification from biological material using mass spectrometric epitope mapping

We describe here a new approach for the identification of affinity-bound proteins by proteolytic generation and mass spectrometric analysis of their antibody bound epitope peptides (epitope excision). The cardiac muscle protein troponin T was chosen as a protein antigen because of its diagnostic importance in myocardial infarct, and its previously characterised epitope structure. Two monoclonal antibodies (IgG1-1B10 and IgG1-11.7) raised against intact human troponin T were found to be completely cross reactive with bovine heart troponin T. A combination of immuno-affinity isolation, partial proteolytic degradation (epitope excision), mass spectrometric peptide mapping, and database analysis was used for the direct identification of Tn T from bovine heart cell lysate. Selective binding of the protein was achieved by addition of bovine heart cell lysate to the Sepharose-immobilised monoclonal antibodies, followed by removal of supernatant material containing unbound protein. While still bound to the affinity matrix the protein was partially degraded thereby generating a set of affinity-bound, overlapping peptide fragments comprising the epitope. Following dissociation from the antibody the epitope peptides were analysed by matrix assisted laser desorption-ionisation (MALDI) and electrospray-ionisation (ESI) mass spectrometry. The peptide masses identified by mass spectrometry were used to perform an automated database search, combined with a search for a common "epitope motif". This procedure resulted in the unequivocal identification of the protein from biological material with only a minimum number of peptide masses, and requiring only limited mass-determination accuracy. The dramatic increase of selectivity for identification of the protein by combining the antigen-antibody specificity with the redundancy of peptide sequences renders this "affinity-proteomics" approach a powerful tool for mass spectrometric identification of proteins from biological material.     

Interferon gamma regulates a unique set of proteins in fresh human bladder transitional cell carcinomas

Poly(A) mRNA was isolated from human placental trophoblast cells stimulated with 100 U/mL of interleukin-2 and 5 microg/mL of phytohemagglutinin and reverse-transcribed. The cDNA coding for the mature interferon-gamma (IFN-gamma) protein was amplified using specific primers, cloned into the pGEX-4T2 vector, and expressed in Escherichia coli. Treatment of four fresh bladder transitional cell carcinoma (TCC) biopsies (TCCs 845-1, grade II, Ta; TCC 925-1, grade II, Ta; TCC 919-1, grade III, T1; TCC 950-1, grade III, T1) with the purified recombinant trophoblast IFN-gamma (50 U/mL, 20 h), followed by proteome analysis using two-dimensional gel electrophoresis, revealed several major proteins whose level of expression were affected by this cytokine. Of these, five (tryptophanyl-tRNA synthetase, the interferon gamma-inducible protein gamma3, mangase superoxide dismutase, and two unknown proteins of apparent molecular masses of 35.8 and 11.2 kDa, respectively) were upregulated in at least 75% of the tumors analyzed while one was downregulated (aldose reductase). Proteins were identified using a combination of techniques that included microsequencing, two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) immunoblotting and comparison with the transitional cell carcinoma isoelectric focusing (IEF) database (http://biobase.dk/cgi-bin/celis). Proteome profile analysis of primary cultures from a low-grade lesion (TCC 846-1, Grade II, Ta) labeled in the presence and absence of IFN-gamma showed that all of the proteins disregulated in vivo were also affected in the cultures. The cultured cells, on the other hand, exhibited additional changes that were not detected in vivo and that may reflect adaptation to the culturing conditions. Taken together, the results provide a first glance at the effect of IFN-gamma on the protein expression profiles of TCCs, and in due course may form the basis for more comprehensive studies aimed at evaluating the usefulness of this cytokine in bladder cancer management.     

Vibrational Energy Transfer in CO+N2 Collisions: A Database for V–V and V–T/R Quantum-Classical Rate Coefficients

Knowledge of energy exchange rate constants in inelastic collisions is critically required for accurate characterization and simulation of several processes in gaseous environments, including planetary atmospheres, plasma, combustion, etc. Determination of these rate constants requires accurate potential energy surfaces (PESs) that describe in detail the full interaction region space and the use of collision dynamics methods capable of including the most relevant quantum effects. In this work, we produce an extensive collection of vibration-to-vibration (V–V) and vibration-to-translation/rotation (V–T/R) energy transfer rate coefficients for collisions between CO and N2 molecules using a mixed quantum-classical method and a recently introduced (A. Lombardi, F. Pirani, M. Bartolomei, C. Coletti, and A. Laganà, Frontiers in chemistry, 7, 309 (2019)) analytical PES, critically revised to improve its performance against ab initio and experimental data of different sources. The present database gives a good agreement with available experimental values of V–V rate coefficients and covers an unprecedented number of transitions and a wide range of temperatures. Furthermore, this is the first database of V–T/R rate coefficients for the title collisions. These processes are shown to often be the most probable ones at high temperatures and/or for highly excited molecules, such conditions being relevant in the modeling of hypersonic flows, plasma, and aerospace applications.     

Monitoring of protein profiles for the optimization of recombinant fermentation processes using public domain databases

The expression of human superoxide dismutase in fed-batch fermentation of E. coli HMS174(DE3)(pET3ahSOD) was studied as model system. Due to the frequently used strong T7 promoter system a high metabolic load is exerted, which triggers stress response mechanisms and finally leads to the differentiation of the host cell. As a consequence, host cell metabolism is partly shifted from growth to survival accompanied by significant alterations of the protein pattern. In terms of process optimization two-dimensional electrophoresis deserves as a powerful tool to monitor these changes on protein level. For the analysis of samples derived from different states of recombinant protein production wide-range Immobiline Dry Strips pH 3-10 were used. In order to establish an efficient procedure for accelerated process optimization and to avoid costly and time-consuming analysis like mass spectrometry (MS), a database approach for the identification of significant changes of the protein pattern was evaluated. On average, 935 spots per gel were detected, whereby 50 are presumably stress-relevant. Out of these, 24 proteins could be identified by using the SWISS-2DPAGE database (www.expasy.ch/ch2d/). The identified proteins are involved in regulatory networks, energy metabolism, purine and pyrimidine nucleotide synthesis and translation. By this database approach, significant fluctuations of individual proteins in relation to recombinant protein production could be identified. Seven proteins show strong alterations (>100%) directly after induction and can therefore be stated as reliable marker proteins for the assessment of stress response. For distinctive interpretation of this highly specific information, a bioinformatic and statistic tool would be essential in order to perceive the role and contribution of individual proteins in stress response.     

FreeSolv: a database of experimental and calculated hydration free energies,with input files

This work provides a curated database of experimental and calculated hydration free energies for small neutral molecules in water, along with molecular structures, input files, references, and annotations. We call this the Free Solvation Database, or FreeSolv. Experimental values were taken from prior literature and will continue to be curated, with updated experimental references and data added as they become available. Calculated values are based on alchemical free energy calculations using molecular dynamics simulations. These used the GAFF small molecule force field in TIP3P water with AM1-BCC charges. Values were calculated with the GROMACS simulation package, with full details given in references cited within the database itself. This database builds in part on a previous, 504-molecule database containing similar information. However, additional curation of both experimental data and calculated values has been done here, and the total number of molecules is now up to 643. Additional information is now included in the database, such as SMILES strings, PubChem compound IDs, accurate reference DOIs, and others. One version of the database is provided in the Supporting Information of this article, but as ongoing updates are envisioned, the database is now versioned and hosted online. In addition to providing the database, this work describes its construction process. The database is available free-of-charge via http://www.escholarship.org/uc/item/6sd403pz.     

Rapid determination of amino acid incorporation by stable isotope labeling with amino acids in cell culture (SILAC)

Stable isotope labeling with amino acids in cell culture (SILAC) has evolved to be a major technique for quantitative proteomics using cell cultures. We developed a rapid method to follow and determine the incorporation of arginine and lysine. Analysis of the heavy state is required to avoid quantification errors. Moreover, the mixture of light and heavy states can be exploited to normalize the protein amount for subsequent relative quantification experiments. Therefore, peptides from different cell lines were extracted with 0.1% trifluoroacetic acid and analyzed by matrix-assisted laser desorption/ionization tandem time-of-flight (MALDI-TOF/TOF) mass spectrometry (MS). This analysis was highly reproducible and was performed in less than 2 h, significantly faster than other methods for the same purpose. Similar peptide mass profiles were obtained for human EBV-transformed B, Jurkat T, and HeLa cells as well as for mouse embryonic fibroblasts. Proteolytic fragments of 27 human proteins were identified with 56 peptides by MALDI-MS/MS and can be used as a database for these kinds of experiments. Sequencing revealed that the peptides were predominantly amino- and carboxy-terminal protein fragments displaying a specificity characteristic of the acidic proteases cathepsin D and E. Many of the identified peptides contained arginine and/or lysine, allowing determination of the incorporation rate of these amino acids. Furthermore, the rate of conversion of arginine into proline could be monitored easily.