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Items: 1 to 50 of 232

1.

Membrane perforation by the pore-forming toxin pneumolysin.

Vögele M, Bhaskara RM, Mulvihill E, van Pee K, Yildiz Ö, Kühlbrandt W, Müller DJ, Hummer G.

Proc Natl Acad Sci U S A. 2019 Jul 2;116(27):13352-13357. doi: 10.1073/pnas.1904304116. Epub 2019 Jun 17.

2.

Inward-facing conformation of a multidrug resistance MATE family transporter.

Zakrzewska S, Mehdipour AR, Malviya VN, Nonaka T, Koepke J, Muenke C, Hausner W, Hummer G, Safarian S, Michel H.

Proc Natl Acad Sci U S A. 2019 Jun 18;116(25):12275-12284. doi: 10.1073/pnas.1904210116. Epub 2019 Jun 3.

PMID:
31160466
3.

Curvature induction and membrane remodeling by FAM134B reticulon homology domain assist selective ER-phagy.

Bhaskara RM, Grumati P, Garcia-Pardo J, Kalayil S, Covarrubias-Pinto A, Chen W, Kudryashev M, Dikic I, Hummer G.

Nat Commun. 2019 May 30;10(1):2370. doi: 10.1038/s41467-019-10345-3.

4.

Finite-Size-Corrected Rotational Diffusion Coefficients of Membrane Proteins and Carbon Nanotubes from Molecular Dynamics Simulations.

Vögele M, Köfinger J, Hummer G.

J Phys Chem B. 2019 Jun 20;123(24):5099-5106. doi: 10.1021/acs.jpcb.9b01656. Epub 2019 Jun 10.

5.

Structural basis for functional interactions in dimers of SLC26 transporters.

Chang YN, Jaumann EA, Reichel K, Hartmann J, Oliver D, Hummer G, Joseph B, Geertsma ER.

Nat Commun. 2019 May 2;10(1):2032. doi: 10.1038/s41467-019-10001-w.

6.

Dynamic cluster formation determines viscosity and diffusion in dense protein solutions.

von Bülow S, Siggel M, Linke M, Hummer G.

Proc Natl Acad Sci U S A. 2019 May 14;116(20):9843-9852. doi: 10.1073/pnas.1817564116. Epub 2019 Apr 29.

7.

Mechanism of the electroneutral sodium/proton antiporter PaNhaP from transition-path shooting.

Okazaki KI, Wöhlert D, Warnau J, Jung H, Yildiz Ö, Kühlbrandt W, Hummer G.

Nat Commun. 2019 Apr 15;10(1):1742. doi: 10.1038/s41467-019-09739-0.

8.

Efficient Ensemble Refinement by Reweighting.

Köfinger J, Stelzl LS, Reuter K, Allande C, Reichel K, Hummer G.

J Chem Theory Comput. 2019 May 14;15(5):3390-3401. doi: 10.1021/acs.jctc.8b01231. Epub 2019 Apr 17.

PMID:
30939006
9.

Structure of Outward-Facing PglK and Molecular Dynamics of Lipid-Linked Oligosaccharide Recognition and Translocation.

Perez C, Mehdipour AR, Hummer G, Locher KP.

Structure. 2019 Apr 2;27(4):669-678.e5. doi: 10.1016/j.str.2019.01.013. Epub 2019 Feb 21.

PMID:
30799077
10.

Bidirectional Control of Autophagy by BECN1 BARA Domain Dynamics.

Chang C, Young LN, Morris KL, von Bülow S, Schöneberg J, Yamamoto-Imoto H, Oe Y, Yamamoto K, Nakamura S, Stjepanovic G, Hummer G, Yoshimori T, Hurley JH.

Mol Cell. 2019 Jan 17;73(2):339-353.e6. doi: 10.1016/j.molcel.2018.10.035. Epub 2018 Dec 20.

PMID:
30581147
11.

ATP-dependent force generation and membrane scission by ESCRT-III and Vps4.

Schöneberg J, Pavlin MR, Yan S, Righini M, Lee IH, Carlson LA, Bahrami AH, Goldman DH, Ren X, Hummer G, Bustamante C, Hurley JH.

Science. 2018 Dec 21;362(6421):1423-1428. doi: 10.1126/science.aat1839.

12.

Structural and functional insights into the interaction and targeting hub TMD0 of the polypeptide transporter TAPL.

Bock C, Löhr F, Tumulka F, Reichel K, Würz J, Hummer G, Schäfer L, Tampé R, Joseph B, Bernhard F, Dötsch V, Abele R.

Sci Rep. 2018 Oct 23;8(1):15662. doi: 10.1038/s41598-018-33841-w.

13.

Dispersion Correction Alleviates Dye Stacking of Single-Stranded DNA and RNA in Simulations of Single-Molecule Fluorescence Experiments.

Grotz KK, Nueesch MF, Holmstrom ED, Heinz M, Stelzl LS, Schuler B, Hummer G.

J Phys Chem B. 2018 Dec 13;122(49):11626-11639. doi: 10.1021/acs.jpcb.8b07537. Epub 2018 Oct 17.

PMID:
30285443
14.

Analysis and engineering of substrate shuttling by the acyl carrier protein (ACP) in fatty acid synthases (FASs).

Rossini E, Gajewski J, Klaus M, Hummer G, Grininger M.

Chem Commun (Camb). 2018 Oct 11;54(82):11606-11609. doi: 10.1039/c8cc06838k.

PMID:
30264077
15.

Biomimetic water channels: general discussion.

Baaden M, Barboiu M, Bill RM, Chen CL, Davis J, Di Vincenzo M, Freger V, Fröba M, Gale PA, Gong B, Hélix-Nielsen C, Hickey R, Hinds B, Hou JL, Hummer G, Kumar M, Legrand YM, Lokesh M, Mi B, Murail S, Pohl P, Sansom M, Song Q, Song W, Törnroth-Horsefield S, Vashisth H, Vögele M.

Faraday Discuss. 2018 Sep 28;209(0):205-229. doi: 10.1039/c8fd90020e. No abstract available.

PMID:
30225508
16.

Structure and function of natural proteins for water transport: general discussion.

Baaden M, Barboiu M, Bill RM, Casanova S, Chen CL, Conner M, Freger V, Gong B, Góra A, Hinds B, Horner A, Hummer G, Kumar M, Lokesh M, Mitra S, Noy A, Pohl P, Sadet A, Sansom M, Törnroth-Horsefield S, Vashisth H.

Faraday Discuss. 2018 Sep 28;209(0):83-95. doi: 10.1039/c8fd90019a. No abstract available.

PMID:
30215655
17.

The modelling and enhancement of water hydrodynamics: general discussion.

Baaden M, Borthakur MP, Casanova S, Coalson R, Freger V, Gonzalez M, Góra A, Hinds B, Hirunpinyopas W, Hummer G, Kumar M, Lynch C, Murail S, Noy A, Sansom M, Song Q, Vashisth H, Vögele M.

Faraday Discuss. 2018 Sep 28;209(0):273-285. doi: 10.1039/c8fd90021c. No abstract available.

PMID:
30215654
18.

Applications to water transport systems: general discussion.

Baaden M, Barboiu M, Borthakur MP, Chen CL, Coalson R, Davis J, Freger V, Gong B, Hélix-Nielsen C, Hickey R, Hinds B, Hirunpinyopas W, Horner A, Hou JL, Hummer G, Iamprasertkun P, Kazushi K, Kumar M, Legrand YM, Lokesh M, Mi B, Mitra S, Murail S, Noy A, Nunes S, Pohl P, Song Q, Song W, Tornroth-Horsefield S, Vashisth H.

Faraday Discuss. 2018 Sep 28;209(0):389-414. doi: 10.1039/c8fd90022a. No abstract available.

PMID:
30215649
19.

Precision DEER Distances from Spin-Label Ensemble Refinement.

Reichel K, Stelzl LS, Köfinger J, Hummer G.

J Phys Chem Lett. 2018 Oct 4;9(19):5748-5752. doi: 10.1021/acs.jpclett.8b02439. Epub 2018 Sep 19.

PMID:
30212206
20.

Optimal Destabilization of DNA Double Strands by Single-Nucleobase Caging.

Seyfried P, Heinz M, Pintér G, Klötzner DP, Becker Y, Bolte M, Jonker HRA, Stelzl LS, Hummer G, Schwalbe H, Heckel A.

Chemistry. 2018 Nov 27;24(66):17568-17576. doi: 10.1002/chem.201804040. Epub 2018 Nov 5.

PMID:
30199112
21.

Redox-coupled quinone dynamics in the respiratory complex I.

Warnau J, Sharma V, Gamiz-Hernandez AP, Di Luca A, Haapanen O, Vattulainen I, Wikström M, Hummer G, Kaila VRI.

Proc Natl Acad Sci U S A. 2018 Sep 4;115(36):E8413-E8420. doi: 10.1073/pnas.1805468115. Epub 2018 Aug 17.

22.

Integrated Functions of Membrane Property Sensors and a Hidden Side of the Unfolded Protein Response.

Covino R, Hummer G, Ernst R.

Mol Cell. 2018 Aug 2;71(3):458-467. doi: 10.1016/j.molcel.2018.07.019. Review.

PMID:
30075144
23.

Bayesian inference of rotor ring stoichiometry from electron microscopy images of archaeal ATP synthase.

Cossio P, Allegretti M, Mayer F, Müller V, Vonck J, Hummer G.

Microscopy (Oxf). 2018 Oct 1;67(5):266-273. doi: 10.1093/jmicro/dfy033.

PMID:
30032235
24.

Hydrodynamics of Diffusion in Lipid Membrane Simulations.

Vögele M, Köfinger J, Hummer G.

Phys Rev Lett. 2018 Jun 29;120(26):268104. doi: 10.1103/PhysRevLett.120.268104.

PMID:
30004782
25.

Molecular dynamics simulations of carbon nanotube porins in lipid bilayers.

Vögele M, Köfinger J, Hummer G.

Faraday Discuss. 2018 Sep 28;209(0):341-358. doi: 10.1039/c8fd00011e.

PMID:
29974904
26.

The molecular recognition of phosphatidic acid by an amphipathic helix in Opi1.

Hofbauer HF, Gecht M, Fischer SC, Seybert A, Frangakis AS, Stelzer EHK, Covino R, Hummer G, Ernst R.

J Cell Biol. 2018 Sep 3;217(9):3109-3126. doi: 10.1083/jcb.201802027. Epub 2018 Jun 25.

27.

Membrane Permeability: Characteristic Times and Lengths for Oxygen and a Simulation-Based Test of the Inhomogeneous Solubility-Diffusion Model.

De Vos O, Venable RM, Van Hecke T, Hummer G, Pastor RW, Ghysels A.

J Chem Theory Comput. 2018 Jul 10;14(7):3811-3824. doi: 10.1021/acs.jctc.8b00115. Epub 2018 Jun 28.

28.

Rotational Diffusion Depends on Box Size in Molecular Dynamics Simulations.

Linke M, Köfinger J, Hummer G.

J Phys Chem Lett. 2018 Jun 7;9(11):2874-2878. doi: 10.1021/acs.jpclett.8b01090. Epub 2018 May 17.

PMID:
29749735
29.

Transition paths in single-molecule force spectroscopy.

Cossio P, Hummer G, Szabo A.

J Chem Phys. 2018 Mar 28;148(12):123309. doi: 10.1063/1.5004767.

PMID:
29604884
30.

Likelihood-based structural analysis of electron microscopy images.

Cossio P, Hummer G.

Curr Opin Struct Biol. 2018 Apr;49:162-168. doi: 10.1016/j.sbi.2018.03.004. Epub 2018 Mar 24. Review.

PMID:
29579548
31.

Retinal isomerization and water-pore formation in channelrhodopsin-2.

Ardevol A, Hummer G.

Proc Natl Acad Sci U S A. 2018 Apr 3;115(14):3557-3562. doi: 10.1073/pnas.1700091115. Epub 2018 Mar 19.

32.

Structural basis of the molecular ruler mechanism of a bacterial glycosyltransferase.

Ramírez AS, Boilevin J, Mehdipour AR, Hummer G, Darbre T, Reymond JL, Locher KP.

Nat Commun. 2018 Jan 31;9(1):445. doi: 10.1038/s41467-018-02880-2.

33.

Fully Anisotropic Rotational Diffusion Tensor from Molecular Dynamics Simulations.

Linke M, Köfinger J, Hummer G.

J Phys Chem B. 2018 May 31;122(21):5630-5639. doi: 10.1021/acs.jpcb.7b11988. Epub 2018 Feb 20.

PMID:
29382197
34.

Cryo-EM structure of the bifunctional secretin complex of Thermus thermophilus.

D'Imprima E, Salzer R, Bhaskara RM, Sánchez R, Rose I, Kirchner L, Hummer G, Kühlbrandt W, Vonck J, Averhoff B.

Elife. 2017 Dec 27;6. pii: e30483. doi: 10.7554/eLife.30483.

35.

Classical Molecular Dynamics with Mobile Protons.

Lazaridis T, Hummer G.

J Chem Inf Model. 2017 Nov 27;57(11):2833-2845. doi: 10.1021/acs.jcim.7b00603. Epub 2017 Nov 14.

36.

Scaffolding the cup-shaped double membrane in autophagy.

Bahrami AH, Lin MG, Ren X, Hurley JH, Hummer G.

PLoS Comput Biol. 2017 Oct 24;13(10):e1005817. doi: 10.1371/journal.pcbi.1005817. eCollection 2017 Oct.

37.

Dynamic Histogram Analysis To Determine Free Energies and Rates from Biased Simulations.

Stelzl LS, Kells A, Rosta E, Hummer G.

J Chem Theory Comput. 2017 Dec 12;13(12):6328-6342. doi: 10.1021/acs.jctc.7b00373. Epub 2017 Nov 9.

PMID:
29059525
38.

Transition path sampling of rare events by shooting from the top.

Jung H, Okazaki KI, Hummer G.

J Chem Phys. 2017 Oct 21;147(15):152716. doi: 10.1063/1.4997378.

PMID:
29055335
39.

Peptide dimerization-dissociation rates from replica exchange molecular dynamics.

Leahy CT, Kells A, Hummer G, Buchete NV, Rosta E.

J Chem Phys. 2017 Oct 21;147(15):152725. doi: 10.1063/1.5004774.

PMID:
29055328
40.

Formation and Stability of Lipid Membrane Nanotubes.

Bahrami AH, Hummer G.

ACS Nano. 2017 Sep 26;11(9):9558-9565. doi: 10.1021/acsnano.7b05542. Epub 2017 Sep 8.

PMID:
28873296
41.

Resolving the Conformational Dynamics of DNA with Ångstrom Resolution by Pulsed Electron-Electron Double Resonance and Molecular Dynamics.

Stelzl LS, Erlenbach N, Heinz M, Prisner TF, Hummer G.

J Am Chem Soc. 2017 Aug 30;139(34):11674-11677. doi: 10.1021/jacs.7b05363. Epub 2017 Aug 17.

PMID:
28777549
42.

Activation of the Unfolded Protein Response by Lipid Bilayer Stress.

Halbleib K, Pesek K, Covino R, Hofbauer HF, Wunnicke D, Hänelt I, Hummer G, Ernst R.

Mol Cell. 2017 Aug 17;67(4):673-684.e8. doi: 10.1016/j.molcel.2017.06.012. Epub 2017 Jul 6.

43.

Kinetics from Replica Exchange Molecular Dynamics Simulations.

Stelzl LS, Hummer G.

J Chem Theory Comput. 2017 Aug 8;13(8):3927-3935. doi: 10.1021/acs.jctc.7b00372. Epub 2017 Jul 21.

PMID:
28657736
44.

Intrinsic map dynamics exploration for uncharted effective free-energy landscapes.

Chiavazzo E, Covino R, Coifman RR, Gear CW, Georgiou AS, Hummer G, Kevrekidis IG.

Proc Natl Acad Sci U S A. 2017 Jul 11;114(28):E5494-E5503. doi: 10.1073/pnas.1621481114. Epub 2017 Jun 20.

45.

Helical jackknives control the gates of the double-pore K+ uptake system KtrAB.

Diskowski M, Mehdipour AR, Wunnicke D, Mills DJ, Mikusevic V, Bärland N, Hoffmann J, Morgner N, Steinhoff HJ, Hummer G, Vonck J, Hänelt I.

Elife. 2017 May 16;6. pii: e24303. doi: 10.7554/eLife.24303.

46.

Modeling Hsp70/Hsp40 interaction by multi-scale molecular simulations and coevolutionary sequence analysis.

Malinverni D, Jost Lopez A, De Los Rios P, Hummer G, Barducci A.

Elife. 2017 May 12;6. pii: e23471. doi: 10.7554/eLife.23471.

47.

Position-Dependent Diffusion Tensors in Anisotropic Media from Simulation: Oxygen Transport in and through Membranes.

Ghysels A, Venable RM, Pastor RW, Hummer G.

J Chem Theory Comput. 2017 Jun 13;13(6):2962-2976. doi: 10.1021/acs.jctc.7b00039. Epub 2017 May 19.

48.

Molecule Counts in Localization Microscopy with Organic Fluorophores.

Karathanasis C, Fricke F, Hummer G, Heilemann M.

Chemphyschem. 2017 Apr 19;18(8):942-948. doi: 10.1002/cphc.201601425. Epub 2017 Feb 28.

PMID:
28196307
49.

Equivalence of M- and P-Summation in Calculations of Ionic Solvation Free Energies.

Simonson T, Hummer G, Roux B.

J Phys Chem A. 2017 Feb 23;121(7):1525-1530. doi: 10.1021/acs.jpca.6b12691. Epub 2017 Feb 13.

PMID:
28152306
50.

Carbon Nanotubes Mediate Fusion of Lipid Vesicles.

Bhaskara RM, Linker SM, Vögele M, Köfinger J, Hummer G.

ACS Nano. 2017 Feb 28;11(2):1273-1280. doi: 10.1021/acsnano.6b05434. Epub 2017 Jan 24.

PMID:
28103440

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