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Items: 1 to 50 of 162

1.

A Combined Linear Interaction Energy and Alchemical Solvation Free Energy Approach for Protein-Binding Affinity Computation.

Rifai EA, Ferrario V, Pleiss J, Geerke DP.

J Chem Theory Comput. 2020 Jan 2. doi: 10.1021/acs.jctc.9b00890. [Epub ahead of print]

PMID:
31894691
2.

The modular structure of α/β-hydrolases.

Bauer TL, Buchholz PCF, Pleiss J.

FEBS J. 2019 Sep 23. doi: 10.1111/febs.15071. [Epub ahead of print]

PMID:
31545554
3.

Modelling of substrate access and substrate binding to cephalosporin acylases.

Ferrario V, Fischer M, Zhu Y, Pleiss J.

Sci Rep. 2019 Aug 27;9(1):12402. doi: 10.1038/s41598-019-48849-z.

4.

Multiplexed primer extension sequencing: A targeted RNA-seq method that enables high-precision quantitation of mRNA splicing isoforms and rare pre-mRNA splicing intermediates.

Gildea MA, Dwyer ZW, Pleiss JA.

Methods. 2019 May 21. pii: S1046-2023(18)30383-9. doi: 10.1016/j.ymeth.2019.05.013. [Epub ahead of print]

PMID:
31121301
5.

Navigating within thiamine diphosphate-dependent decarboxylases: Sequences, structures, functional positions, and binding sites.

Buchholz PCF, Ferrario V, Pohl M, Gardossi L, Pleiss J.

Proteins. 2019 Sep;87(9):774-785. doi: 10.1002/prot.25706. Epub 2019 May 20.

PMID:
31070804
6.

The Structural Dynamics of Engineered β-Lactamases Vary Broadly on Three Timescales yet Sustain Native Function.

Gobeil SMC, Ebert MCCJC, Park J, Gagné D, Doucet N, Berghuis AM, Pleiss J, Pelletier JN.

Sci Rep. 2019 Apr 30;9(1):6656. doi: 10.1038/s41598-019-42866-8.

7.

Alteration of the Route to Menaquinone towards Isochorismate-Derived Metabolites.

Fries A, Mazzaferro LS, Grüning B, Bisel P, Stibal K, Buchholz PCF, Pleiss J, Sprenger GA, Müller M.

Chembiochem. 2019 Jul 1;20(13):1672-1677. doi: 10.1002/cbic.201900050. Epub 2019 May 24.

8.

Thermophysical properties of glyceline-water mixtures investigated by molecular modelling.

Baz J, Held C, Pleiss J, Hansen N.

Phys Chem Chem Phys. 2019 Mar 28;21(12):6467-6476. doi: 10.1039/c9cp00036d. Epub 2019 Mar 6.

PMID:
30840001
9.

The Short-chain Dehydrogenase/Reductase Engineering Database (SDRED): A classification and analysis system for a highly diverse enzyme family.

Gräff M, Buchholz PCF, Stockinger P, Bommarius B, Bommarius AS, Pleiss J.

Proteins. 2019 Jun;87(6):443-451. doi: 10.1002/prot.25666. Epub 2019 Feb 25.

PMID:
30714194
10.

Chorismatases - the family is growing.

Grüninger MJ, Buchholz PCF, Mordhorst S, Strack P, Müller M, Hubrich F, Pleiss J, Andexer JN.

Org Biomol Chem. 2019 Feb 20;17(8):2092-2098. doi: 10.1039/c8ob03038c.

PMID:
30706936
11.

Detection of splice isoforms and rare intermediates using multiplexed primer extension sequencing.

Xu H, Fair BJ, Dwyer ZW, Gildea M, Pleiss JA.

Nat Methods. 2019 Jan;16(1):55-58. doi: 10.1038/s41592-018-0258-x. Epub 2018 Dec 20.

12.

Asymmetric Enzymatic Hydration of Unactivated, Aliphatic Alkenes.

Demming RM, Hammer SC, Nestl BM, Gergel S, Fademrecht S, Pleiss J, Hauer B.

Angew Chem Int Ed Engl. 2019 Jan 2;58(1):173-177. doi: 10.1002/anie.201810005. Epub 2018 Nov 30.

13.

The scale-free nature of protein sequence space.

Buchholz PCF, Zeil C, Pleiss J.

PLoS One. 2018 Aug 1;13(8):e0200815. doi: 10.1371/journal.pone.0200815. eCollection 2018.

14.

Progress Curve Analysis Within BioCatNet: Comparing Kinetic Models for Enzyme-Catalyzed Self-Ligation.

Buchholz PCF, Ohs R, Spiess AC, Pleiss J.

Biotechnol J. 2019 Mar;14(3):e1800183. doi: 10.1002/biot.201800183. Epub 2018 Jul 26.

PMID:
29999245
15.

New imine-reducing enzymes from β-hydroxyacid dehydrogenases by single amino acid substitutions.

Lenz M, Fademrecht S, Sharma M, Pleiss J, Grogan G, Nestl BM.

Protein Eng Des Sel. 2018 Apr 1;31(4):109-120. doi: 10.1093/protein/gzy006.

PMID:
29733377
16.

Simulation of protein diffusion: a sensitive probe of protein-solvent interactions.

Ferrario V, Pleiss J.

J Biomol Struct Dyn. 2019 Apr;37(6):1534-1544. doi: 10.1080/07391102.2018.1461689. Epub 2018 Apr 24.

PMID:
29667536
17.

Interpretation of cytochrome P450 monooxygenase kinetics by modeling of thermodynamic activity.

Ferrario V, Hansen N, Pleiss J.

J Inorg Biochem. 2018 Jun;183:172-178. doi: 10.1016/j.jinorgbio.2018.02.016. Epub 2018 Mar 2.

PMID:
29530593
18.

Enzymatic Production of Biodiesel: Strategies to Overcome Methanol Inactivation.

Lotti M, Pleiss J, Valero F, Ferrer P.

Biotechnol J. 2018 May;13(5):e1700155. doi: 10.1002/biot.201700155. Epub 2018 Mar 6. Review.

PMID:
29461685
19.

The ω-transaminase engineering database (oTAED): A navigation tool in protein sequence and structure space.

Buß O, Buchholz PCF, Gräff M, Klausmann P, Rudat J, Pleiss J.

Proteins. 2018 May;86(5):566-580. doi: 10.1002/prot.25477. Epub 2018 Mar 5.

PMID:
29423963
20.

Percolation in protein sequence space.

Buchholz PCF, Fademrecht S, Pleiss J.

PLoS One. 2017 Dec 20;12(12):e0189646. doi: 10.1371/journal.pone.0189646. eCollection 2017.

21.

Determinants and Prediction of Esterase Substrate Promiscuity Patterns.

Martínez-Martínez M, Coscolín C, Santiago G, Chow J, Stogios PJ, Bargiela R, Gertler C, Navarro-Fernández J, Bollinger A, Thies S, Méndez-García C, Popovic A, Brown G, Chernikova TN, García-Moyano A, Bjerga GEK, Pérez-García P, Hai T, Del Pozo MV, Stokke R, Steen IH, Cui H, Xu X, Nocek BP, Alcaide M, Distaso M, Mesa V, Peláez AI, Sánchez J, Buchholz PCF, Pleiss J, Fernández-Guerra A, Glöckner FO, Golyshina OV, Yakimov MM, Savchenko A, Jaeger KE, Yakunin AF, Streit WR, Golyshin PN, Guallar V, Ferrer M, The Inmare Consortium.

ACS Chem Biol. 2018 Jan 19;13(1):225-234. doi: 10.1021/acschembio.7b00996. Epub 2017 Dec 20.

PMID:
29182315
22.

Thermodynamic Activity-Based Progress Curve Analysis in Enzyme Kinetics.

Pleiss J.

Trends Biotechnol. 2018 Mar;36(3):234-238. doi: 10.1016/j.tibtech.2017.10.004. Epub 2017 Nov 5.

PMID:
29107319
23.

Sde2 is an intron-specific pre-mRNA splicing regulator activated by ubiquitin-like processing.

Thakran P, Pandit PA, Datta S, Kolathur KK, Pleiss JA, Mishra SK.

EMBO J. 2018 Jan 4;37(1):89-101. doi: 10.15252/embj.201796751. Epub 2017 Sep 25.

24.

The conserved AU dinucleotide at the 5' end of nascent U1 snRNA is optimized for the interaction with nuclear cap-binding-complex.

Yeh CS, Chang SL, Chen JH, Wang HK, Chou YC, Wang CH, Huang SH, Larson A, Pleiss JA, Chang WH, Chang TH.

Nucleic Acids Res. 2017 Sep 19;45(16):9679-9693. doi: 10.1093/nar/gkx608.

25.

Terpene Cyclizations inside a Supramolecular Catalyst: Leaving-Group-Controlled Product Selectivity and Mechanistic Studies.

Zhang Q, Catti L, Pleiss J, Tiefenbacher K.

J Am Chem Soc. 2017 Aug 23;139(33):11482-11492. doi: 10.1021/jacs.7b04480. Epub 2017 Jun 23.

PMID:
28590723
26.

Structural toggle in the RNaseH domain of Prp8 helps balance splicing fidelity and catalytic efficiency.

Mayerle M, Raghavan M, Ledoux S, Price A, Stepankiw N, Hadjivassiliou H, Moehle EA, Mendoza SD, Pleiss JA, Guthrie C, Abelson J.

Proc Natl Acad Sci U S A. 2017 May 2;114(18):4739-4744. doi: 10.1073/pnas.1701462114. Epub 2017 Apr 17.

27.

Self-Assembly Nanostructures of Triglyceride-Water Interfaces Determine Functional Conformations of Candida antarctica Lipase B.

Benson SP, Pleiss J.

Langmuir. 2017 Mar 28;33(12):3151-3159. doi: 10.1021/acs.langmuir.6b04570. Epub 2017 Mar 17.

PMID:
28274117
28.

Thermodynamic Activity-Based Interpretation of Enzyme Kinetics.

Pleiss J.

Trends Biotechnol. 2017 May;35(5):379-382. doi: 10.1016/j.tibtech.2017.01.003. Epub 2017 Feb 9.

PMID:
28190624
29.

Reply to "The Curious Case of TEM-116".

Pleiss J, Zeil C.

Antimicrob Agents Chemother. 2016 Oct 21;60(11):7001. doi: 10.1128/AAC.01786-16. Print 2016 Nov. No abstract available.

30.

Molecular Surface Maps.

Krone M, Friess F, Scharnowski K, Reina G, Fademrecht S, Kulschewski T, Pleiss J, Ertl T.

IEEE Trans Vis Comput Graph. 2017 Jan;23(1):701-710.

PMID:
27875185
31.

BioCatNet: A Database System for the Integration of Enzyme Sequences and Biocatalytic Experiments.

Buchholz PC, Vogel C, Reusch W, Pohl M, Rother D, Spieß AC, Pleiss J.

Chembiochem. 2016 Nov 3;17(21):2093-2098. doi: 10.1002/cbic.201600462. Epub 2016 Sep 22.

PMID:
27562499
32.

Phospho-site mutants of the RNA Polymerase II C-terminal domain alter subtelomeric gene expression and chromatin modification state in fission yeast.

Inada M, Nichols RJ, Parsa JY, Homer CM, Benn RA, Hoxie RS, Madhani HD, Shuman S, Schwer B, Pleiss JA.

Nucleic Acids Res. 2016 Nov 2;44(19):9180-9189. Epub 2016 Jul 8.

33.

Structural basis of steroid binding and oxidation by the cytochrome P450 CYP109E1 from Bacillus megaterium.

Jóźwik IK, Kiss FM, Gricman Ł, Abdulmughni A, Brill E, Zapp J, Pleiss J, Bernhardt R, Thunnissen AW.

FEBS J. 2016 Nov;283(22):4128-4148. doi: 10.1111/febs.13911. Epub 2016 Oct 17.

34.

The power of fission: yeast as a tool for understanding complex splicing.

Fair BJ, Pleiss JA.

Curr Genet. 2017 Jun;63(3):375-380. doi: 10.1007/s00294-016-0647-6. Epub 2016 Sep 14. Review.

35.

Binding of Solvent Molecules to a Protein Surface in Binary Mixtures Follows a Competitive Langmuir Model.

Kulschewski T, Pleiss J.

Langmuir. 2016 Sep 6;32(35):8960-8. doi: 10.1021/acs.langmuir.6b02546. Epub 2016 Aug 24.

PMID:
27523916
36.

Semirational Protein Engineering of CYP153AM.aq. -CPRBM3 for Efficient Terminal Hydroxylation of Short- to Long-Chain Fatty Acids.

Notonier S, Gricman Ł, Pleiss J, Hauer B.

Chembiochem. 2016 Aug 17;17(16):1550-7. doi: 10.1002/cbic.201600207. Epub 2016 Jul 1.

PMID:
27251775
37.
38.

Mating-Induced Transcriptome Changes in the Reproductive Tract of Female Aedes aegypti.

Alfonso-Parra C, Ahmed-Braimah YH, Degner EC, Avila FW, Villarreal SM, Pleiss JA, Wolfner MF, Harrington LC.

PLoS Negl Trop Dis. 2016 Feb 22;10(2):e0004451. doi: 10.1371/journal.pntd.0004451. eCollection 2016 Feb.

39.

Network Analysis of Sequence-Function Relationships and Exploration of Sequence Space of TEM β-Lactamases.

Zeil C, Widmann M, Fademrecht S, Vogel C, Pleiss J.

Antimicrob Agents Chemother. 2016 Apr 22;60(5):2709-17. doi: 10.1128/AAC.02930-15. Print 2016 May.

40.

Identification of imine reductase-specific sequence motifs.

Fademrecht S, Scheller PN, Nestl BM, Hauer B, Pleiss J.

Proteins. 2016 May;84(5):600-10. doi: 10.1002/prot.25008. Epub 2016 Mar 6.

PMID:
26857686
41.

A Proteome-wide Fission Yeast Interactome Reveals Network Evolution Principles from Yeasts to Human.

Vo TV, Das J, Meyer MJ, Cordero NA, Akturk N, Wei X, Fair BJ, Degatano AG, Fragoza R, Liu LG, Matsuyama A, Trickey M, Horibata S, Grimson A, Yamano H, Yoshida M, Roth FP, Pleiss JA, Xia Y, Yu H.

Cell. 2016 Jan 14;164(1-2):310-323. doi: 10.1016/j.cell.2015.11.037.

42.

Enantioselective Benzylic Hydroxylation Catalysed by P450 Monooxygenases: Characterisation of a P450cam Mutant Library and Molecular Modelling.

Eichler A, Gricman Ł, Herter S, Kelly PP, Turner NJ, Pleiss J, Flitsch SL.

Chembiochem. 2016 Mar 2;17(5):426-32. doi: 10.1002/cbic.201500536. Epub 2016 Feb 16.

PMID:
26698167
43.

Solvent Flux Method (SFM): A Case Study of Water Access to Candida antarctica Lipase B.

Benson SP, Pleiss J.

J Chem Theory Comput. 2014 Nov 11;10(11):5206-14. doi: 10.1021/ct500791e.

PMID:
26584392
44.

The effect of thermodynamic properties of solvent mixtures explains the difference between methanol and ethanol in C.antarctica lipase B catalyzed alcoholysis.

Sasso F, Kulschewski T, Secundo F, Lotti M, Pleiss J.

J Biotechnol. 2015 Nov 20;214:1-8. doi: 10.1016/j.jbiotec.2015.08.023. Epub 2015 Sep 12.

PMID:
26325200
45.

Mdm1/Snx13 is a novel ER-endolysosomal interorganelle tethering protein.

Henne WM, Zhu L, Balogi Z, Stefan C, Pleiss JA, Emr SD.

J Cell Biol. 2015 Aug 17;210(4):541-51. doi: 10.1083/jcb.201503088.

46.

Widespread alternative and aberrant splicing revealed by lariat sequencing.

Stepankiw N, Raghavan M, Fogarty EA, Grimson A, Pleiss JA.

Nucleic Acids Res. 2015 Sep 30;43(17):8488-501. doi: 10.1093/nar/gkv763. Epub 2015 Aug 10.

47.

Identification of universal selectivity-determining positions in cytochrome P450 monooxygenases by systematic sequence-based literature mining.

Gricman Ł, Vogel C, Pleiss J.

Proteins. 2015 Sep;83(9):1593-603. doi: 10.1002/prot.24840. Epub 2015 Aug 1.

PMID:
26033392
48.

Simulation of protein association: Kinetic pathways towards crystal contacts.

Taudt A, Arnold A, Pleiss J.

Phys Rev E Stat Nonlin Soft Matter Phys. 2015 Mar;91(3):033311. Epub 2015 Mar 30.

PMID:
25871250
49.

The effect of mutations near the T1 copper site on the biochemical characteristics of the small laccase from Streptomyces coelicolor A3(2).

Prins A, Kleinsmidt L, Khan N, Kirby B, Kudanga T, Vollmer J, Pleiss J, Burton S, Le Roes-Hill M.

Enzyme Microb Technol. 2015 Jan;68:23-32. doi: 10.1016/j.enzmictec.2014.10.003. Epub 2014 Oct 23.

PMID:
25435502
50.

Enzyme toolbox: novel enantiocomplementary imine reductases.

Scheller PN, Fademrecht S, Hofelzer S, Pleiss J, Leipold F, Turner NJ, Nestl BM, Hauer B.

Chembiochem. 2014 Oct 13;15(15):2201-4. doi: 10.1002/cbic.201402213. Epub 2014 Aug 27.

PMID:
25163890

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