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Tamamis P, Floudas CA. Elucidating a key component of cancer metastasis: CXCL12 (SDF-1α) binding to CXCR4. J Chem Inf Model 2014; 54:1174-88. [PMID: 24660779 PMCID: PMC4004218 DOI: 10.1021/ci500069y] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
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The chemotactic signaling induced
by the binding of chemokine CXCL12
(SDF-1α) to chemokine receptor CXCR4 is of significant biological
importance and is a potential therapeutic axis against HIV-1. However,
as CXCR4 is overexpressed in certain cancer cells, the CXCL12:CXCR4
signaling is involved in tumor metastasis, progression, angiogenesis,
and survival. Motivated by the pivotal role of the CXCL12:CXCR4 axis
in cancer, we employed a comprehensive set of computational tools,
predominantly based on free energy calculations and molecular dynamics
simulations, to obtain insights into the molecular recognition of
CXCR4 by CXCL12. We report, what is to our knowledge, the first computationally
derived CXCL12:CXCR4 complex structure which is in remarkable agreement
with experimental findings and sheds light into the functional role
of CXCL12 and CXCR4 residues which are associated with binding and
signaling. Our results reveal that the CXCL12 N-terminal domain is
firmly bound within the CXCR4 transmembrane domain, and the central
24–50 residue domain of CXCL12 interacts with the upper N-terminal
domain of CXCR4. The stability of the CXCL12:CXCR4 complex structure
is attributed to an abundance of nonpolar and polar intermolecular
interactions, including salt bridges formed between positively charged
CXCL12 residues and negatively charged CXCR4 residues. The success
of the computational protocol can mainly be attributed to the nearly
exhaustive docking conformational search, as well as the heterogeneous
dielectric implicit water-membrane-water model used to simulate and
select the optimum conformations. We also recently utilized this protocol
to elucidate the binding of an HIV-1 gp120 V3 loop in complex with
CXCR4, and a comparison between the molecular recognition of CXCR4
by CXCL12 and the HIV-1 gp120 V3 loop shows that both CXCL12 and the
HIV-1 gp120 V3 loop share the same CXCR4 binding pocket, as they mostly
interact with the same CXCR4 residues.
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First EL, Hasan MMF, Floudas CA. Discovery of novel zeolites for natural gas purification through combined material screening and process optimization. AIChE J 2014. [DOI: 10.1002/aic.14441] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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53
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Hasan MMF, Boukouvala F, First EL, Floudas CA. Nationwide, Regional, and Statewide CO2 Capture, Utilization, and Sequestration Supply Chain Network Optimization. Ind Eng Chem Res 2014. [DOI: 10.1021/ie402931c] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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54
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Smadbeck J, Peterson MB, Zee BM, Garapaty S, Mago A, Lee C, Giannis A, Trojer P, Garcia BA, Floudas CA. De novo peptide design and experimental validation of histone methyltransferase inhibitors. PLoS One 2014; 9:e90095. [PMID: 24587223 PMCID: PMC3938834 DOI: 10.1371/journal.pone.0090095] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Accepted: 01/30/2014] [Indexed: 11/18/2022] Open
Abstract
Histones are small proteins critical to the efficient packaging of DNA in the nucleus. DNA–protein complexes, known as nucleosomes, are formed when the DNA winds itself around the surface of the histones. The methylation of histone residues by enhancer of zeste homolog 2 (EZH2) maintains gene repression over successive cell generations. Overexpression of EZH2 can silence important tumor suppressor genes leading to increased invasiveness of many types of cancers. This makes the inhibition of EZH2 an important target in the development of cancer therapeutics. We employed a three-stage computational de novo peptide design method to design inhibitory peptides of EZH2. The method consists of a sequence selection stage and two validation stages for fold specificity and approximate binding affinity. The sequence selection stage consists of an integer linear optimization model that was solved to produce a rank-ordered list of amino acid sequences with increased stability in the bound peptide-EZH2 structure. These sequences were validated through the calculation of the fold specificity and approximate binding affinity of the designed peptides. Here we report the discovery of novel EZH2 inhibitory peptides using the de novo peptide design method. The computationally discovered peptides were experimentally validated in vitro using dose titrations and mechanism of action enzymatic assays. The peptide with the highest in vitro response, SQ037, was validated in nucleo using quantitative mass spectrometry-based proteomics. This peptide had an IC50 of 13.5 M, demonstrated greater potency as an inhibitor when compared to the native and K27A mutant control peptides, and demonstrated competitive inhibition versus the peptide substrate. Additionally, this peptide demonstrated high specificity to the EZH2 target in comparison to other histone methyltransferases. The validated peptides are the first computationally designed peptides that directly inhibit EZH2. These inhibitors should prove useful for further chromatin biology investigations.
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Niziolek AM, Onel O, Elia JA, Floudas CA, Xiao X. Production of Liquid Transportation Fuels From Coal and Duckweed Biomass. PROCEEDINGS OF THE 8TH INTERNATIONAL CONFERENCE ON FOUNDATIONS OF COMPUTER-AIDED PROCESS DESIGN 2014. [DOI: 10.1016/b978-0-444-63433-7.50080-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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56
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Khoury GA, Thompson JP, Smadbeck J, Kieslich CA, Floudas CA. Forcefield_PTM: Ab Initio Charge and AMBER Forcefield Parameters for Frequently Occurring Post-Translational Modifications. J Chem Theory Comput 2013; 9:5653-5674. [PMID: 24489522 PMCID: PMC3904396 DOI: 10.1021/ct400556v] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
In this work, we introduce Forcefield_PTM, a set of AMBER forcefield parameters consistent with ff03 for 32 common post-translational modifications. Partial charges were calculated through ab initio calculations and a two-stage RESP-fitting procedure in an ether-like implicit solvent environment. The charges were found to be generally consistent with others previously reported for phosphorylated amino acids, and trimethyllysine, using different parameterization methods. Pairs of modified and their corresponding unmodified structures were curated from the PDB for both single and multiple modifications. Background structural similarity was assessed in the context of secondary and tertiary structures from the global dataset. Next, the charges derived for Forcefield_PTM were tested on a macroscopic scale using unrestrained all-atom Langevin molecular dynamics simulations in AMBER for 34 (17 pairs of modified/unmodified) systems in implicit solvent. Assessment was performed in the context of secondary structure preservation, stability in energies, and correlations between the modified and unmodified structure trajectories on the aggregate. As an illustration of their utility, the parameters were used to compare the structural stability of the phosphorylated and dephosphorylated forms of OdhI. Microscopic comparisons between quantum and AMBER single point energies along key χ torsions on several PTMs were performed and corrections to improve their agreement in terms of mean squared errors and squared correlation coefficients were parameterized. This forcefield for post-translational modifications in condensed-phase simulations can be applied to a number of biologically relevant and timely applications including protein structure prediction, protein and peptide design, docking, and to study the effect of PTMs on folding and dynamics. We make the derived parameters and an associated interactive webtool capable of performing post-translational modifications on proteins using Forcefield_PTM available at http://selene.princeton.edu/FFPTM.
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Guzman YA, Sakellari D, Arsenakis M, Floudas CA. Proteomics for the discovery of biomarkers and diagnosis of periodontitis: a critical review. Expert Rev Proteomics 2013; 11:31-41. [PMID: 24308552 DOI: 10.1586/14789450.2014.864953] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Periodontitis is a common chronic and destructive disease whose pathogenetic mechanisms remain unclear. Due to their sensitivity and global scale, proteomics studies offer the opportunity to uncover critical host and pathogen activity indicators and can elucidate clinically applicable biomarkers for improved diagnosis and treatment of the disease. This review summarizes the literature of proteomics studies on periodontitis and comprehensively discusses commonly found candidate biomarkers. Key considerations in the design of an experimental proteomics platform are also outlined. The applicability of protein biomarkers across the progression of periodontitis and unexplored areas of research are highlighted.
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Khoury GA, Tamamis P, Pinnaduwage N, Smadbeck J, Kieslich CA, Floudas CA. Princeton_TIGRESS: protein geometry refinement using simulations and support vector machines. Proteins 2013; 82:794-814. [PMID: 24174311 DOI: 10.1002/prot.24459] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Revised: 10/18/2013] [Accepted: 10/22/2013] [Indexed: 12/30/2022]
Abstract
Protein structure refinement aims to perform a set of operations given a predicted structure to improve model quality and accuracy with respect to the native in a blind fashion. Despite the numerous computational approaches to the protein refinement problem reported in the previous three CASPs, an overwhelming majority of methods degrade models rather than improve them. We initially developed a method tested using blind predictions during CASP10 which was officially ranked in 5th place among all methods in the refinement category. Here, we present Princeton_TIGRESS, which when benchmarked on all CASP 7,8,9, and 10 refinement targets, simultaneously increased GDT_TS 76% of the time with an average improvement of 0.83 GDT_TS points per structure. The method was additionally benchmarked on models produced by top performing three-dimensional structure prediction servers during CASP10. The robustness of the Princeton_TIGRESS protocol was also tested for different random seeds. We make the Princeton_TIGRESS refinement protocol freely available as a web server at http://atlas.princeton.edu/refinement. Using this protocol, one can consistently refine a prediction to help bridge the gap between a predicted structure and the actual native structure.
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Khoury GA, Smadbeck J, Kieslich CA, Floudas CA. Protein folding and de novo protein design for biotechnological applications. Trends Biotechnol 2013; 32:99-109. [PMID: 24268901 DOI: 10.1016/j.tibtech.2013.10.008] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 10/10/2013] [Accepted: 10/18/2013] [Indexed: 11/19/2022]
Abstract
In the postgenomic era, the medical/biological fields are advancing faster than ever. However, before the power of full-genome sequencing can be fully realized, the connection between amino acid sequence and protein structure, known as the protein folding problem, needs to be elucidated. The protein folding problem remains elusive, with significant difficulties still arising when modeling amino acid sequences lacking an identifiable template. Understanding protein folding will allow for unforeseen advances in protein design; often referred to as the inverse protein folding problem. Despite challenges in protein folding, de novo protein design has recently demonstrated significant success via computational techniques. We review advances and challenges in protein structure prediction and de novo protein design, and highlight their interplay in successful biotechnological applications.
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60
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Gounaris CE, First EL, Floudas CA. Estimation of diffusion anisotropy in microporous crystalline materials and optimization of crystal orientation in membranes. J Chem Phys 2013; 139:124703. [DOI: 10.1063/1.4821583] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
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61
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Elia JA, Baliban RC, Floudas CA. Nationwide, Regional, and Statewide Energy Supply Chain Optimization for Natural Gas to Liquid Transportation Fuel (GTL) Systems. Ind Eng Chem Res 2013. [DOI: 10.1021/ie401378r] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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62
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Gorham RD, Forest DL, Tamamis P, López de Victoria A, Kraszni M, Kieslich CA, Banna CD, Bellows-Peterson ML, Larive CK, Floudas CA, Archontis G, Johnson LV, Morikis D. Novel compstatin family peptides inhibit complement activation by drusen-like deposits in human retinal pigmented epithelial cell cultures. Exp Eye Res 2013; 116:96-108. [PMID: 23954241 DOI: 10.1016/j.exer.2013.07.023] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 07/06/2013] [Accepted: 07/20/2013] [Indexed: 11/19/2022]
Abstract
We have used a novel human retinal pigmented epithelial (RPE) cell-based model that mimics drusen biogenesis and the pathobiology of age-related macular degeneration to evaluate the efficacy of newly designed peptide inhibitors of the complement system. The peptides belong to the compstatin family and, compared to existing compstatin analogs, have been optimized to promote binding to their target, complement protein C3, and to enhance solubility by improving their polarity/hydrophobicity ratios. Based on analysis of molecular dynamics simulation data of peptide-C3 complexes, novel binding features were designed by introducing intermolecular salt bridge-forming arginines at the N-terminus and at position -1 of N-terminal dipeptide extensions. Our study demonstrates that the RPE cell assay has discriminatory capability for measuring the efficacy and potency of inhibitory peptides in a macular disease environment.
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63
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Smadbeck J, Peterson MB, Khoury GA, Taylor MS, Floudas CA. Protein WISDOM: a workbench for in silico de novo design of biomolecules. J Vis Exp 2013. [PMID: 23912941 DOI: 10.3791/50476] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
The aim of de novo protein design is to find the amino acid sequences that will fold into a desired 3-dimensional structure with improvements in specific properties, such as binding affinity, agonist or antagonist behavior, or stability, relative to the native sequence. Protein design lies at the center of current advances drug design and discovery. Not only does protein design provide predictions for potentially useful drug targets, but it also enhances our understanding of the protein folding process and protein-protein interactions. Experimental methods such as directed evolution have shown success in protein design. However, such methods are restricted by the limited sequence space that can be searched tractably. In contrast, computational design strategies allow for the screening of a much larger set of sequences covering a wide variety of properties and functionality. We have developed a range of computational de novo protein design methods capable of tackling several important areas of protein design. These include the design of monomeric proteins for increased stability and complexes for increased binding affinity. To disseminate these methods for broader use we present Protein WISDOM (http://www.proteinwisdom.org), a tool that provides automated methods for a variety of protein design problems. Structural templates are submitted to initialize the design process. The first stage of design is an optimization sequence selection stage that aims at improving stability through minimization of potential energy in the sequence space. Selected sequences are then run through a fold specificity stage and a binding affinity stage. A rank-ordered list of the sequences for each step of the process, along with relevant designed structures, provides the user with a comprehensive quantitative assessment of the design. Here we provide the details of each design method, as well as several notable experimental successes attained through the use of the methods.
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64
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First EL, Gounaris CE, Floudas CA. Predictive framework for shape-selective separations in three-dimensional zeolites and metal-organic frameworks. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:5599-5608. [PMID: 23617929 DOI: 10.1021/la400547a] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
With the growing number of zeolites and metal-organic frameworks (MOFs) available, computational methods are needed to screen databases of structures to identify those most suitable for applications of interest. We have developed novel methods based on mathematical optimization to predict the shape selectivity of zeolites and MOFs in three dimensions by considering the energy costs of transport through possible pathways. Our approach is applied to databases of over 1800 microporous materials including zeolites, MOFs, zeolitic imidazolate frameworks, and hypothetical MOFs. New materials are identified for applications in gas separations (CO2/N2, CO2/CH4, and CO2/H2), air separation (O2/N2), and chemicals (propane/propylene, ethane/ethylene, styrene/ethylbenzene, and xylenes).
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65
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Baliban RC, Elia JA, Floudas CA, Xiao X, Zhang Z, Li J, Cao H, Ma J, Qiao Y, Hu X. Thermochemical Conversion of Duckweed Biomass to Gasoline, Diesel, and Jet Fuel: Process Synthesis and Global Optimization. Ind Eng Chem Res 2013. [DOI: 10.1021/ie3034703] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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66
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Baliban RC, Elia JA, Floudas CA. Biomass and Natural Gas to Liquid Transportation Fuels: Process Synthesis, Global Optimization, and Topology Analysis. Ind Eng Chem Res 2013. [DOI: 10.1021/ie3024643] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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67
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Li Z, Floudas CA. A Comparative Theoretical and Computational Study on Robust Counterpart Optimization: II. Probabilistic Guarantees on Constraint Satisfaction. Ind Eng Chem Res 2013; 51:6769-6788. [PMID: 23329868 DOI: 10.1021/ie201651s] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Probabilistic guarantees on constraint satisfaction for robust counterpart optimization are studied in this paper. The robust counterpart optimization formulations studied are derived from box, ellipsoidal, polyhedral, "interval+ellipsoidal" and "interval+polyhedral" uncertainty sets (Li, Z., Ding, R., and Floudas, C.A., A Comparative Theoretical and Computational Study on Robust Counterpart Optimization: I. Robust Linear and Robust Mixed Integer Linear Optimization, Ind. Eng. Chem. Res, 2011, 50, 10567). For those robust counterpart optimization formulations, their corresponding probability bounds on constraint satisfaction are derived for different types of uncertainty characteristic (i.e., bounded or unbounded uncertainty, with or without detailed probability distribution information). The findings of this work extend the results in the literature and provide greater flexibility for robust optimization practitioners in choosing tighter probability bounds so as to find less conservative robust solutions. Extensive numerical studies are performed to compare the tightness of the different probability bounds and the conservatism of different robust counterpart optimization formulations. Guiding rules for the selection of robust counterpart optimization models and for the determination of the size of the uncertainty set are discussed. Applications in production planning and process scheduling problems are presented.
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68
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Baliban RC, Elia JA, Floudas CA. Novel Natural Gas to Liquids Processes: Process Synthesis and Global Optimization Strategies. AIChE J 2013. [DOI: 10.1002/aic.13996] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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69
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Hasan MMF, First EL, Floudas CA. Cost-effective CO2 capture based on in silico screening of zeolites and process optimization. Phys Chem Chem Phys 2013; 15:17601-18. [DOI: 10.1039/c3cp53627k] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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70
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Baliban RC, Sakellari D, Li Z, Guzman YA, Garcia BA, Floudas CA. Discovery of biomarker combinations that predict periodontal health or disease with high accuracy from GCF samples based on high-throughput proteomic analysis and mixed-integer linear optimization. J Clin Periodontol 2012. [PMID: 23190455 DOI: 10.1111/jcpe.12037] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
AIM To identify optimal combination(s) of proteomic based biomarkers in gingival crevicular fluid (GCF) samples from chronic periodontitis (CP) and periodontally healthy individuals and validate the predictions through known and blind test sets. MATERIALS AND METHODS GCF samples were collected from 96 CP and periodontally healthy subjects and analysed using high-performance liquid chromatography, tandem mass spectrometry and the PILOT_PROTEIN algorithm. A mixed-integer linear optimization (MILP) model was then developed to identify the optimal combination of biomarkers which could clearly distinguish a blind subject sample as healthy or diseased. RESULTS A thorough cross-validation of the MILP model capability was performed on a training set of 55 samples and greater than 99% accuracy was consistently achieved when annotating the testing set samples as healthy or diseased. The model was then trained on all 55 samples and tested on two different blind test sets, and using an optimal combination of 7 human proteins and 3 bacterial proteins, the model was able to correctly predict 40 out of 41 healthy and diseased samples. CONCLUSIONS The proposed large-scale proteomic analysis and MILP model led to the identification of novel combinations of biomarkers for consistent diagnosis of periodontal status with greater than 95% predictive accuracy.
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Hasan MMF, Baliban RC, Elia JA, Floudas CA. Modeling, Simulation, and Optimization of Postcombustion CO2 Capture for Variable Feed Concentration and Flow Rate. 2. Pressure Swing Adsorption and Vacuum Swing Adsorption Processes. Ind Eng Chem Res 2012. [DOI: 10.1021/ie301572n] [Citation(s) in RCA: 138] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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72
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Hasan MMF, Baliban RC, Elia JA, Floudas CA. Modeling, Simulation, and Optimization of Postcombustion CO2 Capture for Variable Feed Concentration and Flow Rate. 1. Chemical Absorption and Membrane Processes. Ind Eng Chem Res 2012. [DOI: 10.1021/ie301571d] [Citation(s) in RCA: 135] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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73
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Monk PN, Bellows-Peterson ML, Smadbeck J, Floudas CA, Kieslich CA, Morikis D, Woodruff TM. De novo protein design of agonists and antagonists of C5a receptors. Immunobiology 2012. [DOI: 10.1016/j.imbio.2012.08.097] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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74
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Baliban RC, Dimaggio PA, Plazas-Mayorca MD, Garcia BA, Floudas CA. PILOT_PROTEIN: identification of unmodified and modified proteins via high-resolution mass spectrometry and mixed-integer linear optimization. J Proteome Res 2012; 11:4615-29. [PMID: 22788846 DOI: 10.1021/pr300418j] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
A novel protein identification framework, PILOT_PROTEIN, has been developed to construct a comprehensive list of all unmodified proteins that are present in a living sample. It uses the peptide identification results from the PILOT_SEQUEL algorithm to initially determine all unmodified proteins within the sample. Using a rigorous biclustering approach that groups incorrect peptide sequences with other homologous sequences, the number of false positives reported is minimized. A sequence tag procedure is then incorporated along with the untargeted PTM identification algorithm, PILOT_PTM, to determine a list of all modification types and sites for each protein. The unmodified protein identification algorithm, PILOT_PROTEIN, is compared to the methods SEQUEST, InsPecT, X!Tandem, VEMS, and ProteinProspector using both prepared protein samples and a more complex chromatin digest. The algorithm demonstrates superior protein identification accuracy with a lower false positive rate. All materials are freely available to the scientific community at http://pumpd.princeton.edu.
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Baliban RC, Elia JA, Misener R, Floudas CA. Global optimization of a MINLP process synthesis model for thermochemical based conversion of hybrid coal, biomass, and natural gas to liquid fuels. Comput Chem Eng 2012. [DOI: 10.1016/j.compchemeng.2012.03.008] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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