Personal tools
You are here: Home People Prof. Dr. Helms List of publications

List of publications

Publications in Refereed International Journals , Publications submitted, and views, Book Chapters, and other Publications

Publications in Refereed International Journals 

[1]           Olkhova, E., Hutter, M.C., Lill, M.A., Helms, V. and Michel, H. (2004) Dynamic Water Networks in Cytochrome c Oxidase from Paracoccus denitrificans Investigated by Molecular Dynamics Simulations. Biophysical Journal. In press.

[2]           De Groot, B.L., Frigato, T., Helms, V. and Grubmüller, H. (2003) Journal of Molecular Biology, 333, 279-293. The Mechanism of Proton Exclusion in the Aquaporin-1 Water Channel.

[3]           Hutter, M.C. and Helms, V. (2003) International Journal of Quantum Chemistry 95, 479-486. Mechanism of Phosphoryl Transfer in Kinases Investigated by Semiempirical Calculations.

[4]           Zachariae, U., Helms, V., and Engelhardt, H. (2003) Biophysical Journal 85, 954-962. Multistep Mechanism of Chloride Translocation in a Strongly Anion-Selective Porin Channel.

[5]           Gorba, C. and Helms, V. (2003) Soft Materials 1, 187-204. Diffusional Dynamics of Cytochrome c Molecules in the Presence of a Charged Surface.

[6]           Helms, V. (2002) EMBO Reports 3, 1133-1138. Attraction within the Membrane - Forces behind transmembrane protein folding and supramolecular complex assembly.

[7]           Hutter, M.C., Krebs, J., Meiler, J., Griesinger, C., Carafoli, E. and Helms, V. (2002) ChemBioChem, 3, 1200-1208. A Structural Model of the Complex between Phospholamban and the Calcium Pump of Sarcoplasmatic Reticulum obtained by Molecular Mechanics.

[8]           Deprez, E., Gill, E., Helms, V., Wade, R.C. and Hoa, G.H.H. (2002) Journal of Bioinorganic Chemistry, 91, 597-606, Specific and Non-specific Effects of Potassium Cations on Substrate-protein Interactions in Cytochromes P450cam and P450lin .

[9]           Hutter, M.C. and Helms, V. (2002) ChemBioChem, 3, 643-651. The Mechanism of Phosphorylation of Natural Nucleosides and Anti-HIV Analogs by Nucleoside Diphosphate Kinase is Independent of their Sugar Substituents .

[10]       Lill, M.A. and Helms, V. (2002) Proceedings of the National Academy of Sciences USA, 99, 2778-2781. Dynamic Simulations Identify Ultrafast Proton Relay in Green Fluorescent Protein.

[11]       Flöck, D. and Helms, V. (2002) PROTEINS: Structure, Function, and Genetics, 47, 75-85. Protein-Protein Docking of Electron Transfer Complexes – Cytochrome c Oxidase and Cytochrome c.

[12]       Kamberaj, H. and Helms, V. (2001) Computer Physics Communications, 141, 375-402. Monte Carlo simulation of biomolecular systems with BIOMCSIM.

[13]       Lill, M.A. and Helms, V. (2001) Journal of Chemical Physics, 115,  7993-8005. Molecular dynamics simulation of proton transport with quantum mechanically derived proton hopping rates (Q-HOP MD).

[14]       Lill, M.A. and Helms, V. (2001) Journal of Chemical Physics, 115, 7985-7992. Reaction Rates for Proton Transfer over Small Barriers and Connection to Transition State Theory.

[15]       Bartoschek, S., Buurman, G., Thauer, R.K., Geierstanger, B.H., Weyrauch, J.P., Griesinger, C., Nilges, M., Hutter, M.C. and Helms, V. (2001) ChemBioChem, 2, 530-541, Re-face stereospecificity of methylenetetrahydromethanopterin dehydrogenases and methylenetetrahydrofolate dehydrogenases is predetermined by intrinsic properties of the substrate.

[16]       Yoo, H.Y., Boatz, J.A., Helms, V., McCammon, J.A. and Langhoff, P.W. (2001) Journal of Physical Chemistry A, 105, 2850-2857. Chromophore Protonation States and the Proton Shuttle Mechanism in Green Fluorescent Protein: Inferences Drawn from Ab-Initio Theoretical Studies of Chemical Structures and Vibrational Spectra.

[17]       Lill, M.A. and Helms, V. (2001) Journal of Chemical Physics, 114, 1125-1132. Compact parameter set for fast estimation of proton transfer rates.

[18]       Hutter, M.C. and Helms, V. (2000) Protein Science, 9, 2225-2231. Phosphoryl transfer by a concerted reaction mechanism in UMP/CMP-kinase.

[19]       Lill, M.A., Hutter, M.C. and Helms, V. (2000) Journal of Physical Chemistry A, 104, 8283-8289. Accounting for Environmental Effects in Ab Initio Calculations of Proton Transfer Barriers.

[20]       Das, B., Helms, V., Lounnas, V. and Wade, R.C. (2000) Journal of Inorganic Biochemistry, 81, 121-131. Multicopy Molecular Dynamics Simulations Suggest How to Reconcile Crystallographic and Product Formation Data for Camphor Enantiomers Boand to Cytochrome P-450cam.

[21]       Helms, V., Winstead, C. and Langhoff, P.W. (2000) Journal of Molecular Structure (THEOCHEM), 506, 179-189. Low-lying electronic excitations of the Green Fluorescent Protein chromophore.

[22]       Hutter, M.C. and Helms, V. (1999) Protein Science, 8, 2728-2733. Influence of key residues on the reaction mechanism of the cAMP-dependent protein kinase.

[23]       Weber, W., Helms, V., McCammon, J.A. and Langhoff, P.W. (1999) Proceedings of the National Academy of Sciences USA, 96, 6177-6182. Shedding light on the dark and weakly fluorescent states of Green Fluorescent Proteins.

[24]       Baker, N.A., Helms, V. and McCammon, J.A. (1999) PROTEINS: Structure, Function, and Genetics, 36, 447-453. Dynamical Properties of Fasciculin-2.

[25]       Tara, S., Helms, V., Straatsma, T.P. and McCammon, J.A. (1999) Biopolymers, 50, 347-359. Molecular Dynamics of Mouse Acetylcholinesterase Complexed with Huperzine A.

[26]       Helms, V., Straatsma, T.P. and McCammon, J.A. (1999) Journal of Physical Chemistry B, 103, 3263-3269. Internal dynamics of green fluorescent protein.

[27]       Huenenberger, P., Helms, V., Narayana, N., Taylor, S.S. and McCammon, J.A. (1999) Biochemistry, 38, 2358-2366. Determinants of Ligand Binding to cAMP-dependent Protein Kinase.

[28]       Helms, V. and Wade, R.C. (1998) PROTEINS: Structure, Function, and Genetics, 32, 381-396. Hydration Energy Landscape of the Active Site Cavity in Cytochrome P450cam.

[29]       Helms, V. and Wade, R.C. (1998) Journal of the American Chemical Society, 120, 2710-2713. Computational Alchemy to Calculate Absolute Protein-Ligand Binding Free Energy.

[30]       Helms, V. and McCammon, J.A. (1997) Protein Science, 6, 2336-2343. Kinase conformations: A computational study of the effect of ligand binding.

[31]       Helms, V. and Wade, R.C. (1997) Journal of Computational Chemistry, 18, 449-462. Free energies of hydration from thermodynamic integration : A comparison of molecular mechanics force fields and evaluation of calculation accuracy.

[32]       Schulze, H., Hui Bon Hoa, G., Helms, V., Wade, R.C. and Jung, C. (1996), Biochemistry, 35, 14127-14138. Structural Changes in Cytochrome P450cam Effected by the Binding of the Enantiomers (1R)-Camphor and (1S)-Camphor.

[33]       Helms, V., Deprez, E., Gill, E., Barret, C., Hui Bon Hoa, G. and Wade, R.C. (1996) Biochemistry, 35, 1485-1499. Improved binding of cytochrome P450cam substrate analogues designed to fill extra space in the substrate binding pocket.

[34]       Helms, V. and Wade, R.C. (1995) Biophysical Journal, 69, 810-824. Thermodynamics of Water Mediating Protein-Ligand Interactions in Cytochrome P450cam: A Molecular Dynamics Study.

[35]       Koehler, J., Koehler, C., Helms, V. and Adelhard, K. (1991) Croatica Chemica Acta, 64, 561-575. Importance of atomic charge concepts in empirical force fields – the SCALCHA approach to obtaining atomic charges.

 

Publications submitted

[36]       Gu, W., Rahi, S.J. and Helms, V. Solvation Free Energies and Transfer Free Energies of Amino Acids from Hydrophobic Solution to Water Solution from a Very Simple Residue Model. Submitted.

[37]       Park, Y., Elsner, M., Staritzbichler, R. and Helms, V. A novel potential function for modeling structures of tightly packing transmembrane alpha-helices. Almost submitted.

[38]       Geyer, T., Gorba, C. and Helms, V. Interfacing Brownian dynamics simulations. Submitted.

[39]       Flöck, D. and Helms, V. A Brownian Dynamics Study: The Effect of a Membrane Environment on an Electron Transfer System. Submitted.

[40]       Gorba, C., Geyer, T. and Helms, V. Brownian Dynamics Simulations of Simplified Cytochrome c Molecules in the Presence of a Charged Surface. Submitted.

[41]       Chandran, V., Flöck, D., Axelrod, H. and Helms, V.  Critical Assessment of Protein-Protein Docking: The complex of reaction center from Rhodobacter sphaeroides with cytochrome c2. Submitted.

[42]       Frigato, T., Lill, M.A. and Helms, V. Effects of environmental dynamics on proton and deuterium transfer rates over small energy barriers. Submitted.

 

Reviews, Book Chapters, and other Publications (without abstracts)

[43]       Krebs, J., Helms, V., Griesinger, C., Carafoli, E. The Regulation of the Calcium Signal by Membrane Pumps. To appear in Helvetica Chimica Acta.

[44]       Helms, V. (2002) Current Opinion in Structural Biology, 12, 169-175. Electronic excitations of biomolecules studies by quantum chemistry.

[45]       Helms, V., Lill., M.A. and Gorba, C. (2002) Developments in Mathematical and Experimental Physics, Kluwer Academic Press, Computer Simulation Meets Molecular Biology.

[46]       Straatsma, T.P. and Helms, V. (2000) Molecular Dynamics on Parallel Computers, Proceedings des Workshops in Jülich Feb. 8-10, 1999, World Scientific. p. 70-82. Esser, R. Grassberger, P., Grotendorst, J. and Lewerenz, M., Editoren. The Molecular Dynamics Module of NWChem - Design and Application in Protein Simulations.

[47]       Helms, V., Hom, E.F.Y., Straatsma, T.P., McCammon, J.A. and Langhoff, P.W. (1998) ACS Symposium Series 712. p. 288-295. Exciting Green Fluorescent Protein.

[48]       Helms, V. and McCammon, J.A. (1998) "Computational Molecular Dynamics: Challenges, Methods, Ideas", Lecture Notes in Computational Science and Engineering, Springer. p. 66-77. Deuflhard, P., Hermans, J., Leimkuehler, B., Mark, A.E., Reich, S. and Skeel, R.D.,  Editoren. Conformational Transitions of Proteins from Atomistic Simulations.

[49]       Wade, R.C., Lounnas, V., Helms, V., Hui Bon Hoa, G., Di Primo, C., Deprez, E., Barret, C., Kozin, S., Jung, C., Schulze, H., Contzen, J., Mouro, C., Gill, E., Simonneaux, G., Bondon, A., Legrand, N. and Schlichting, I. (1996) Perspectives on Protein Engineering 5, Ed. M. Geisow. (1996). Fundamentals of Enzyme-Ligand Interactions in Cytochrome P450cam.

Document Actions
« October 2017 »
October
MoTuWeThFrSaSu
1
2345678
9101112131415
16171819202122
23242526272829
3031