2016
Synthesis and in Vitro and in Vivo Evaluation of MMP-12 Selective Optical Probes
Bordenave T, Helle M, Beau F, Georgiadis D, Tepshi L, Bernes M, Ye Y, Levenez L, Poquet E, Nozach H, Razavian M, Toczek J, Stura EA, Dive V, Sadeghi MM, Devel L. Synthesis and in Vitro and in Vivo Evaluation of MMP-12 Selective Optical Probes. Bioconjugate Chemistry 2016, 27: 2407-2417. PMID: 27564088, PMCID: PMC5100701, DOI: 10.1021/acs.bioconjchem.6b00377.Peer-Reviewed Original ResearchConceptsDye moietyLinker lengthSelective optical probeVivo performanceDye structureFirst crystal structureCyanine dyesHydrophilic characterSeries of tracersSelective probeReporter groupCrystal structureNovel seriesBlood clearance rateFluorescent probePseudopeptide inhibitorsWhole conjugateNet chargeMoietyCrystallographic structureSelectivity profileSmall peptidesOptical probeVivo behaviorVivo evaluation
2013
DNA-dependent protein kinase and its inhibition in support of radiotherapy
Novotná E, Tichý A, Pejchal J, Lukášová E, Šalovská B, Vávrová J. DNA-dependent protein kinase and its inhibition in support of radiotherapy. International Journal Of Radiation Biology 2013, 89: 416-423. PMID: 23362996, DOI: 10.3109/09553002.2013.767993.Peer-Reviewed Original ResearchConceptsDNA-dependent protein kinaseRadiation-induced double strand break repairProtein kinaseDouble-strand break repairDNA repair proteinsDNA-PK inhibitionDNA-PK inhibitorKey DNA repair enzymeDNA repair enzymeBreak repairRepair proteinsPersonalized anti-cancer therapyRepair enzymesMolecular approachesMolecular mechanismsAnti-cancer therapyRecent discoveryCancer cellsKinaseRecent knowledgeRNASmall peptidesPivotal roleRecent studiesCancer therapy
2002
Using PC clusters to evaluate the transferability of molecular mechanics force fields for proteins
Okur A, Strockbine B, Hornak V, Simmerling C. Using PC clusters to evaluate the transferability of molecular mechanics force fields for proteins. Journal Of Computational Chemistry 2002, 24: 21-31. PMID: 12483672, DOI: 10.1002/jcc.10184.Peer-Reviewed Original ResearchConceptsForce fieldMolecular mechanics force fieldMolecular mechanics parametersMechanics force fieldForce field transferabilityModified force fieldFf99 force fieldMolecular dynamics simulationsSmall model systemsMolecular dynamicsAMBER packageModel peptidesDynamics simulationsAlpha-helical conformationConformationFf99Beta-hairpinStructural dataStructural behaviorSample structureSmall peptidesFf94TransferExperimental dataModel system
1991
Variations in the cytoplasmic region account for the heterogeneity of the chicken MHC class I (B-F) molecules
Møller L, Kaufman J, Verland S, Salomonsen J, Avila D, Lambris J, Skjødt K. Variations in the cytoplasmic region account for the heterogeneity of the chicken MHC class I (B-F) molecules. Immunogenetics 1991, 34: 110-120. PMID: 1869304, DOI: 10.1007/bf00211423.Peer-Reviewed Original ResearchConceptsN-terminal amino acid sequenceChicken MHC class IMolecular mass variantsTwo-dimensional gel electrophoresisAmino acid sequenceC-terminal partC-terminal variationsAcid sequenceMolecular variationProteolytic removalIsolated variantsGel electrophoresisCytoplasmic regionParent proteinPeptide mappingProtein poolEnzymatic deglycosylationProteolytic digestionMass variantsSmall peptidesVariantsFragmentsChickenPeptideMHC class I
1990
Metalloproteases of infective Ancylostoma hookworm larvae and their possible functions in tissue invasion and ecdysis
Hotez P, Haggerty J, Hawdon J, Milstone L, Gamble H, Schad G, Richards F. Metalloproteases of infective Ancylostoma hookworm larvae and their possible functions in tissue invasion and ecdysis. Infection And Immunity 1990, 58: 3883-3892. PMID: 2254016, PMCID: PMC313750, DOI: 10.1128/iai.58.12.3883-3892.1990.Peer-Reviewed Original ResearchConceptsProtease activitySodium dodecyl sulfate-polyacrylamide gel electrophoresisDodecyl sulfate-polyacrylamide gel electrophoresisProtein substratesSulfate-polyacrylamide gel electrophoresisMr polypeptideNematode Strongyloides stercoralisBovine elastinPossible functionsBiochemical similaritiesAlkaline pH optimumLarvaeConnective tissue macromoleculesHuman hookworms Ancylostoma duodenaleInvasion propertiesGel electrophoresisEnzyme activityAncylostoma speciesBiochemical differencesA. caninum larvaeMinor bandsProtease compositionSmall peptidesHuman fibronectinMajor band
1987
Photoaffinity labeling of the thymidine triphosphate binding domain in Escherichia coli DNA polymerase I: identification of histidine-881 as the site of cross-linking.
Pandey V, Williams K, Stone K, Modak M. Photoaffinity labeling of the thymidine triphosphate binding domain in Escherichia coli DNA polymerase I: identification of histidine-881 as the site of cross-linking. Biochemistry 1987, 26: 7744-8. PMID: 3322406, DOI: 10.1021/bi00398a031.Peer-Reviewed Original ResearchConceptsCross-linking reactionReversed-phase high-performance liquid chromatographyHigh-performance liquid chromatographyCross-linking sitesEscherichia coli DNA polymerase IPeptide lossKlenow fragmentChelate formLiquid chromatographyAmino acid analysisE. coli DNA Pol ISmall peptidesTryptic digestionSubstrate deoxynucleoside triphosphateHistidine residuesTryptic peptidesAmino acidsSingle peptideOptimal conditionsPeptide mappingDNA Pol IStaphylococcus aureus V8 protease digestionDNA polymerase IAcceptor sitesPeptides
1982
A structural model of human erythrocyte spectrin. Alignment of chemical and functional domains.
Speicher D, Morrow J, Knowles W, Marchesi V. A structural model of human erythrocyte spectrin. Alignment of chemical and functional domains. Journal Of Biological Chemistry 1982, 257: 9093-9101. PMID: 7096353, DOI: 10.1016/s0021-9258(18)34247-9.Peer-Reviewed Original ResearchConceptsNumerous small peptidesPeptide mapping techniquesChemical domainsPeptide segmentsMolecular weightChemical cleavageSized peptidesTwo-dimensional peptide mapping techniquesSmall peptidesIntact moleculeUnique peptidesPhosphorylated amino acidsFurther proteolytic cleavageOverlap peptidesPolypeptide segmentsIntermediate-sized peptidesMoleculesMild trypsin digestionTrypsin digestionTwo-dimensional peptide mapsPeptidesStructural modelSpectrin subunitsCleavagePeptide maps
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