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Items: 50

1.

On the relationship between docking scores and protein conformational changes in HIV-1 protease.

Mobaraki N, Hemmateenejad B, Weikl TR, Sakhteman A.

J Mol Graph Model. 2019 Sep;91:186-193. doi: 10.1016/j.jmgm.2019.06.011. Epub 2019 Jun 15.

PMID:
31261024
2.

Membrane Morphologies Induced by Arc-Shaped Scaffolds Are Determined by Arc Angle and Coverage.

Bonazzi F, Weikl TR.

Biophys J. 2019 Apr 2;116(7):1239-1247. doi: 10.1016/j.bpj.2019.02.017. Epub 2019 Feb 26.

PMID:
30902368
3.

The 2018 biomembrane curvature and remodeling roadmap.

Bassereau P, Jin R, Baumgart T, Deserno M, Dimova R, Frolov VA, Bashkirov PV, Grubmüller H, Jahn R, Risselada HJ, Johannes L, Kozlov MM, Lipowsky R, Pucadyil TJ, Zeno WF, Stachowiak JC, Stamou D, Breuer A, Lauritsen L, Simon C, Sykes C, Voth GA, Weikl TR.

J Phys D Appl Phys. 2018 Aug;51(34). pii: 343001. doi: 10.1088/1361-6463/aacb98. Epub 2018 Jul 20.

4.

Membrane fluctuations and acidosis regulate cooperative binding of 'marker of self' protein CD47 with the macrophage checkpoint receptor SIRPα.

Steinkühler J, Różycki B, Alvey C, Lipowsky R, Weikl TR, Dimova R, Discher DE.

J Cell Sci. 2018 Jul 16;132(4). pii: jcs216770. doi: 10.1242/jcs.216770.

5.

Author Correction: Protein-peptide association kinetics beyond the seconds timescale from atomistic simulations.

Paul F, Wehmeyer C, Abualrous ET, Wu H, Crabtree MD, Schöneberg J, Clarke J, Freund C, Weikl TR, Noé F.

Nat Commun. 2018 Mar 9;9(1):1073. doi: 10.1038/s41467-018-03452-0.

6.

Identifying Conformational-Selection and Induced-Fit Aspects in the Binding-Induced Folding of PMI from Markov State Modeling of Atomistic Simulations.

Paul F, Noé F, Weikl TR.

J Phys Chem B. 2018 May 31;122(21):5649-5656. doi: 10.1021/acs.jpcb.7b12146. Epub 2018 Mar 27.

PMID:
29522679
7.

Membrane-Mediated Cooperativity of Proteins.

Weikl TR.

Annu Rev Phys Chem. 2018 Apr 20;69:521-539. doi: 10.1146/annurev-physchem-052516-050637. Epub 2018 Feb 28.

PMID:
29490203
8.

Particle-based membrane model for mesoscopic simulation of cellular dynamics.

Sadeghi M, Weikl TR, Noé F.

J Chem Phys. 2018 Jan 28;148(4):044901. doi: 10.1063/1.5009107.

PMID:
29390800
9.

Curvature-Mediated Assembly of Janus Nanoparticles on Membrane Vesicles.

Bahrami AH, Weikl TR.

Nano Lett. 2018 Feb 14;18(2):1259-1263. doi: 10.1021/acs.nanolett.7b04855. Epub 2018 Jan 8.

PMID:
29281291
10.

Protein-peptide association kinetics beyond the seconds timescale from atomistic simulations.

Paul F, Wehmeyer C, Abualrous ET, Wu H, Crabtree MD, Schöneberg J, Clarke J, Freund C, Weikl TR, Noé F.

Nat Commun. 2017 Oct 23;8(1):1095. doi: 10.1038/s41467-017-01163-6. Erratum in: Nat Commun. 2018 Mar 9;9(1):1073.

11.

How to Distinguish Conformational Selection and Induced Fit Based on Chemical Relaxation Rates.

Paul F, Weikl TR.

PLoS Comput Biol. 2016 Sep 16;12(9):e1005067. doi: 10.1371/journal.pcbi.1005067. eCollection 2016 Sep.

12.
13.

Binding kinetics of membrane-anchored receptors and ligands: Molecular dynamics simulations and theory.

Hu J, Xu GK, Lipowsky R, Weikl TR.

J Chem Phys. 2015 Dec 28;143(24):243137. doi: 10.1063/1.4936135.

PMID:
26723622
14.

Binding constants of membrane-anchored receptors and ligands: A general theory corroborated by Monte Carlo simulations.

Xu GK, Hu J, Lipowsky R, Weikl TR.

J Chem Phys. 2015 Dec 28;143(24):243136. doi: 10.1063/1.4936134.

PMID:
26723621
15.

The role of membrane curvature for the wrapping of nanoparticles.

Bahrami AH, Lipowsky R, Weikl TR.

Soft Matter. 2016 Jan 14;12(2):581-7. doi: 10.1039/c5sm01793a. Epub 2015 Oct 27.

PMID:
26506073
16.

Modeling nanoparticle wrapping or translocation in bilayer membranes.

Curtis EM, Bahrami AH, Weikl TR, Hall CK.

Nanoscale. 2015 Sep 14;7(34):14505-14. doi: 10.1039/c5nr02255j.

17.

Conformational selection in protein binding and function.

Weikl TR, Paul F.

Protein Sci. 2014 Nov;23(11):1508-18. doi: 10.1002/pro.2539. Epub 2014 Sep 6. Review.

18.

Wrapping of nanoparticles by membranes.

Bahrami AH, Raatz M, Agudo-Canalejo J, Michel R, Curtis EM, Hall CK, Gradzielski M, Lipowsky R, Weikl TR.

Adv Colloid Interface Sci. 2014 Jun;208:214-24. doi: 10.1016/j.cis.2014.02.012. Epub 2014 Mar 12. Review.

PMID:
24703299
19.

Cooperative wrapping of nanoparticles by membrane tubes.

Raatz M, Lipowsky R, Weikl TR.

Soft Matter. 2014 May 28;10(20):3570-7. doi: 10.1039/c3sm52498a. Epub 2014 Mar 24.

PMID:
24658648
20.

Binding constants of membrane-anchored receptors and ligands depend strongly on the nanoscale roughness of membranes.

Hu J, Lipowsky R, Weikl TR.

Proc Natl Acad Sci U S A. 2013 Sep 17;110(38):15283-8. doi: 10.1073/pnas.1305766110. Epub 2013 Sep 4.

21.

How conformational changes can affect catalysis, inhibition and drug resistance of enzymes with induced-fit binding mechanism such as the HIV-1 protease.

Weikl TR, Hemmateenejad B.

Biochim Biophys Acta. 2013 May;1834(5):867-73. doi: 10.1016/j.bbapap.2013.01.027. Epub 2013 Feb 1.

PMID:
23376188
22.

Adhesion-induced phase behavior of two-component membranes and vesicles.

Rouhiparkouhi T, Weikl TR, Discher DE, Lipowsky R.

Int J Mol Sci. 2013 Jan 22;14(1):2203-29. doi: 10.3390/ijms14012203.

23.

Tubulation and aggregation of spherical nanoparticles adsorbed on vesicles.

Bahrami AH, Lipowsky R, Weikl TR.

Phys Rev Lett. 2012 Nov 2;109(18):188102. Epub 2012 Oct 31.

PMID:
23215335
24.

Conformational selection and induced changes along the catalytic cycle of Escherichia coli dihydrofolate reductase.

Weikl TR, Boehr DD.

Proteins. 2012 Oct;80(10):2369-83. doi: 10.1002/prot.24123. Epub 2012 Jul 3.

PMID:
22641560
25.

Line tension and stability of domains in cell-adhesion zones mediated by long and short receptor-ligand complexes.

Krobath H, Różycki B, Lipowsky R, Weikl TR.

PLoS One. 2011;6(8):e23284. doi: 10.1371/journal.pone.0023284. Epub 2011 Aug 17.

26.

Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations.

Noé F, Schütte C, Vanden-Eijnden E, Reich L, Weikl TR.

Proc Natl Acad Sci U S A. 2009 Nov 10;106(45):19011-6. doi: 10.1073/pnas.0905466106. Epub 2009 Nov 3.

27.

Invivo folding efficiencies for mutants of the P22 tailspike beta-helix protein correlate with predicted stability changes.

Reich L, Becker M, Seckler R, Weikl TR.

Biophys Chem. 2009 May;141(2-3):186-92. doi: 10.1016/j.bpc.2009.01.015. Epub 2009 Feb 12.

PMID:
19254821
28.

Selected-fit versus induced-fit protein binding: kinetic differences and mutational analysis.

Weikl TR, von Deuster C.

Proteins. 2009 Apr;75(1):104-10. doi: 10.1002/prot.22223.

PMID:
18798570
29.

The protein folding problem.

Dill KA, Ozkan SB, Shell MS, Weikl TR.

Annu Rev Biophys. 2008;37:289-316. doi: 10.1146/annurev.biophys.37.092707.153558. Review.

30.

Stable patterns of membrane domains at corrugated substrates.

Rózycki B, Weikl TR, Lipowsky R.

Phys Rev Lett. 2008 Mar 7;100(9):098103. Epub 2008 Mar 7.

PMID:
18352753
31.
32.

Loop-closure principles in protein folding.

Weikl TR.

Arch Biochem Biophys. 2008 Jan 1;469(1):67-75. Epub 2007 Jun 29. Review.

PMID:
17662688
33.

The protein folding problem: when will it be solved?

Dill KA, Ozkan SB, Weikl TR, Chodera JD, Voelz VA.

Curr Opin Struct Biol. 2007 Jun;17(3):342-6. Epub 2007 Jun 14. Review.

PMID:
17572080
34.

Stochastic resonance for adhesion of membranes with active stickers.

Rózycki B, Weikl TR, Lipowsky R.

Eur Phys J E Soft Matter. 2007 Jan;22(1):97-106. Epub 2007 Feb 21.

PMID:
17318287
35.

Transition-states in protein folding kinetics: the structural interpretation of Phi values.

Weikl TR, Dill KA.

J Mol Biol. 2007 Feb 2;365(5):1578-86. Epub 2006 Oct 28.

PMID:
17141267
36.

Adhesion of membranes via switchable molecules.

Rózycki B, Weikl TR, Lipowsky R.

Phys Rev E Stat Nonlin Soft Matter Phys. 2006 Jun;73(6 Pt 1):061908. Epub 2006 Jun 16.

PMID:
16906865
38.
39.

Adhesion of membranes with active stickers.

Rózycki B, Lipowsky R, Weikl TR.

Phys Rev Lett. 2006 Feb 3;96(4):048101. Epub 2006 Jan 31. Erratum in: Phys Rev Lett. 2006 Feb 10;96(5):059904.

PMID:
16486897
40.
41.

Phi values in protein-folding kinetics have energetic and structural components.

Merlo C, Dill KA, Weikl TR.

Proc Natl Acad Sci U S A. 2005 Jul 19;102(29):10171-5. Epub 2005 Jul 11.

42.

Pattern formation during T-cell adhesion.

Weikl TR, Lipowsky R.

Biophys J. 2004 Dec;87(6):3665-78. Epub 2004 Sep 17.

43.

Adhesion of membranes with competing specific and generic interactions.

Weikl TR, Andelman D, Komura S, Lipowsky R.

Eur Phys J E Soft Matter. 2002 May;8(1):59-66.

PMID:
15010982
44.

Indirect interactions of membrane-adsorbed cylinders.

Weikl TR.

Eur Phys J E Soft Matter. 2003 Oct;12(2):265-273. doi: 10.1140/epje/i2003-10058-x.

PMID:
15007662
45.

Cooperativity in two-state protein folding kinetics.

Weikl TR, Palassini M, Dill KA.

Protein Sci. 2004 Mar;13(3):822-9.

46.
47.

Folding rates and low-entropy-loss routes of two-state proteins.

Weikl TR, Dill KA.

J Mol Biol. 2003 Jun 6;329(3):585-98.

PMID:
12767836
48.

Dynamic phase separation of fluid membranes with rigid inclusions.

Weikl TR.

Phys Rev E Stat Nonlin Soft Matter Phys. 2002 Dec;66(6 Pt 1):061915. Epub 2002 Dec 30.

PMID:
12513325
49.

Adhesion-induced phase behavior of multicomponent membranes.

Weikl TR, Lipowsky R.

Phys Rev E Stat Nonlin Soft Matter Phys. 2001 Jul;64(1 Pt 1):011903. Epub 2001 Jun 13.

PMID:
11461284
50.

Unbinding transitions and phase separation of multicomponent membranes.

Weikl TR, Netz RR, Lipowsky R.

Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 2000 Jul;62(1 Pt A):R45-8.

PMID:
11088521

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