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Publications
2011
Denning, E. J., Priyakumar, U. D., Nilsson, L., and Mackerell, A. D. (2011) Impact of 2'-hydroxyl sampling on the conformational properties of RNA: Update of the CHARMM all-atom additive force field for RNA, Journal of Computational Chemistry 32, 1929-1943.
Burendahl, S., and Nilsson, L. (2011) Computational studies of molecular interactions and communication between LXR cofactors and ligand binding, Proteins, in press.
Uyar, A., Kurkcuoglu, O., Nilsson, L., and Doruker, P. (2011) The elastic network model reveals a consistent picture on intrinsic functional dynamics of type II restriction endonucleases, Physical Biology 8(5).
Ito, M., Johansson, J., Stromberg, R., and Nilsson, L. (2011) Unfolding of the Amyloid b-Peptide Central Helix: Mechanistic Insights from Molecular Dynamics Simulations, PLoS ONE 6, e17587.
Karshikoff, A., and Nilsson, L. (2011) Multiple pH regime molecular dynamics simulation for pK calculations, PLoS One, in press.
Uchtenhagen, H., Friemann, R., Raszewski, G., Spetz, A.-L., Nilsson, L., and Achour, A. (2011) Crystal structure of the HIV-2 neutralizing Fab fragment 7C8 with high specificity to the V3 region of gp125, PloS One, in press.
Allner, O., and Nilsson, L. (2011) Nucleotide modifications and tRNA anticodon-mRNA codon interactions on the ribosome, RNA, in press.
2010
Juneja, A., Numata, J., Nilsson, L., and Knapp, E. W. (2010) Merging Implicit with Explicit Solvent Simulations: Polyethylene Glycol, Journal of Chemical Theory and Computation 6, 1871-1883.
Moutsatsou, P., Papoutsi, Z., Kassi, E., Heldring, N., Zhao, C., Tsiapara, A., Melliou, E., Chrousos, G. P., Chinou, I., Karshikoff, A., Nilsson, L., and Dahlman-Wright, K. (2010) Fatty Acids Derived from Royal Jelly Are Modulators of Estrogen Receptor Functions, PLoS ONE 5, e15594.
Siponen, M. I., Wisniewska, M., Lehtio, L., Johansson, I., Svensson, L., Raszewski, G., Nilsson, L., Sigvardsson, M., and Berglund, H. (2010) Structural Determination of Functional Domains in Early B-cell Factor (EBF) Family of Transcription Factors Reveals Similarities to Rel DNA-binding Proteins and a Novel Dimerization Motif, Journal of Biological Chemistry 285, 25875-25879.
Talukdar, A., Morgunova, E., Duan, J., Meining, W., Foloppe, N., Nilsson, L., Bacher, A., Illarionov, B., Fischer, M., Ladenstein, R., and Cushman, M. (2010) Virtual screening, selection and development of a benzindolone structural scaffold for inhibition of lumazine synthase, Bioorganic & Medicinal Chemistry 18, 3518-3534.
2009
Brooks, B. R., Brooks III, C. L., MacKerell Jr., A. D., Nilsson, L.,Roux, B., Won, Y., Archontis, G., Bartels, C., Boresch, S., Caflisch, A.,Caves, L., Cui, Q., Dinner, A. R., Fischer, S., Gao, J., Hodoscek, M., Kuczera, K., Lazaridis, T., Ma, J., Paci, E., Pastor, R. W., Petrella, R. J., Post, C. B., Schaefer, M., Tidor, B., Venable, R. M., Woodcock, H. L., Wu, X., York, D. M. and Karplus, M. (2009) CHARMM: The Biomolecular Simulation Program. J Comp Chem. 30, 1545-1614.
Burendahl, S., Danciulescu, C., and Nilsson, L. (2009) Ligand unbinding from the estrogen receptor: A computational study of pathways and ligand specificity, Proteins: Structure, Function, and Bioinformatics 77, 842-856.
Halle, B., and Nilsson, L. (2009) Does the Dynamic Stokes Shift Report on Slow Protein Hydration Dynamics?, The Journal of Physical Chemistry B 113, 8210-8213.
Nilsson, L. (2009) Efficient table lookup without inverse square roots for calculation of pair wise atomic interactions in classical simulations, Journal of Computational Chemistry 30, 1490-1498.
Roos, G., Foloppe, N., Van Laer, K., Wyns, L., Nilsson, L., Geerlings, P., and Messens, J. (2009) How Thioredoxin Dissociates Its Mixed Disulfide, PLoS Comput Biol 5, e1000461.
Holmlund, T., Farge, G., Pande, V., Korhonen, J., Nilsson, L. and Falkenberg, M. (2009) Structure-Function Defects Of The Twinkle Amino-Terminal Region In Progressive External Ophthalmoplegia. Biochimica et Biophysica Acta. 1792, 132-139.
2008
Burendahl S, Treuter E & Nilsson L (2008) Molecular Dynamics Simulations of Human LRH-1: The Impact of Ligand Binding in a Constitutively Active Nuclear Receptor. Biochemistry 47, 5205-5215.
Duchardt E, Nilsson L & Schleucher J (2008) Increased cytosine ribose flexibility in DNA: A combined NMR 13C spin relaxation and molecular dynamics simulation study. Nucl. Acids Res. 12:4211-4219.
Hart K & Nilsson L (2008) Investigation of transcription factor Ndt80 affinity differences for wild type and mutant DNA: a molecular dynamics study. Proteins, 73, 325-337.
Korhonen JA, Pande V, Holmiund T, Farge G, Pham XH, Nilsson L & Falkenberg M (2008) Structure-function defects of the TWINKLE linker region in progressive external ophthalmoplegia. Journal of Molecular Biology 377, 691-705.
MacKerell Jr AD & Nilsson L (2008) Molecular dynamics simulations of nucleic acid-protein complexes. Current Opinion in Structural Biology 18, 194-199.
Nilsson L (2008) Efficient table lookup without inverse square roots for calculation of pair wise atomic interactions in classical simulations. J. Comp. Chem.,DOI 10.1002/jcc.21169.
Nyström Macchion B, Strömberg R & Nilssson L (2008) Analysis of the stability and flexibility of RNA complexes containing bulge loops of different sizes. J Biomol Struct Dyn, 26, 163-173.
Pande, V., and Nilsson, L. (2008) Insights into structure, dynamics and hydration of locked nucleic acid (LNA) strand-based duplexes from molecular dynamics simulations. Nucl. Acids Res. 36, 1508-1516. .
2007
Danciulescu, C., Ladenstein, R. and Nilsson, L. (2007) Dynamic Arrangement of Ion Pairs and Individual Contributions to the Thermal Stability of the Cofactor-Binding Domain of Glutamate Dehydrogenase from Thermotoga maritima. Biochemistry 46, 8537-8549.
Foloppe, N. and Nilsson, L. (2007) Stabilization of the Catalytic Thiolate in a Mammalian Glutaredoxin: Structure, Dynamics and Electrostatics of Reduced Pig Glutaredoxin and its Mutants. J. Mol. Biol. 372, 798-816.
Lahiri, A., Sarzynska, J., Nilsson, L., and Kulinski, T. (2007). Molecular Dynamics Simulation of the Preferred Conformations of 2-Thiouridine in Aqueous Solution. Theor. Chem. Acc. 117, 267-273.
Mark, P. and Nilsson, L. (2007) A molecular dynamics study of Cyclophilin A free and in
complex with the Ala-Pro dipeptide. Eur. Biophys. J. 36, 213-224.
Nilsson, A., Duan, J., Mo-Boquist, L.L., Benedikz, E., and Sundstrom, E. (2007) Characterization of the human NMDA receptor subunit NR3A glycine binding site. Neuropharmacology 52, 1151-1159.
Nyström, B. and Nilsson, L. (2007) Molecular dynamics study of intrinsic stability in six RNA terminal loop motifs. J Biomol Struct Dyn 24, 525-536.
Porat, A., Lillig, C.H., Johansson, C., Fernandes, A.P., Nilsson, L., Holmgren, A. and Beckwith, J. (2007) The Reducing Activity of Glutaredoxin 3 Towards Cytoplasmic Substrate Proteins is Restricted by Methionine 43. Biochemistry 46, 3366-3377.
Tu, Y., Nilsson, L. and Laaksonen, A. (2007) In Gustavson, F. G., Dongarra, J., Kågström, B., Kressner, D., Sala, M., Cai, X., Gerndt, M., Morris, A., Mohr, B. and Maloney, A. D. (eds.), Applied Parallel Computing. State of the Art in Scientific Computing. Springer, Berlin/Heidelberg, Vol. 4699, pp. 100-108.
Watanabe, T., Inadomi, Y., Fukuzawa, K., Nakano, T., Tanaka, S., Nilsson, L. and Nagashima, U. (2007) DNA and Estrogen Receptor Interaction Revealed by Fragment Molecular Orbital Calculations. J. Phys. Chem. B 111, 9621-9627.
2006
Caballero-Herrera, A., and Nilsson, L. (2006). Urea Parametrization for
Molecular Dynamics Simulations. J Mol Struct THEOCHEM 758, Issues 2-3, 139-148 .
Carlsson, P., S. Burendahl, and Nilsson, L. (2006). Exploring the Unbinding of Retinoic Acid from the Retinoic Acid Receptor Using Random Expulsion Molecular Dynamics. Biophys. J. 91, 3151-3161.
Doruker, P., O. Kurkcuoglu, and Nilsson, L. (2006). Collective Dynamics of EcoRI-DNA Complex by Elastic Network Model and Molecular Dynamics Simulations. J. Biomol. Struct. Dyn. 24, 1-16.
Duan, J., and Nilsson, L. (2006). Effect of Zn2+ on DNA Recognition and Stability of the p53 DNA-Binding Domain. Biochemistry 45, 7483-7492.
Law, M. J., Linde, M. E., Chambers, E. J., Oubridge, C., Katsamba, P. S., Nilsson, L., Haworth, I. S., and Laird-Offringa, I. A. (2006). The role of positively charged amino acids and electrostatic interactions in the complex of U1A protein and U1 hairpin II RNA. Nucleic Acids Res 34, 275-285.
Bredenberg, J., Mark, P., and Nilsson, L. (2006). Solvent Effects on Biomolecular Dynamics Simulations: A Comparison between TIP3P, SPC and SPC/E acting on the Glucocorticoid Receptor DNA-binding Domain. In Modern methods for theoretical physical chemistry of biopolymers, E. Starikov, S. Tanaka, and J. P. Lewis, eds. (Elsevier), pp 123-135.
Goto, H., Obata, S., Kamakura, T., Nakayama, N., Sato, M., Nakajima, Y., Nagashima, U., Watanabe, T., Inadomi, Y., Ito, M., et al. (2006). Drug Discovery Using Grid Technology. In Modern methods for theoretical physical chemistry of biopolymers, E. Starikov, S. Tanaka, and J. P. Lewis, eds. (Elsevier), pp 227-248.
Elliott, J., Starikov, E., Crawshaw, J., Claiden, P., Nilsson, L., and Windle, A. (2006). Nucleation of polyglutamine amyloid fibres modelling using molecular dynamics. In Modern methods for theoretical physical chemistry of biopolymers, E. Starikov, S. Tanaka, and J. P. Lewis, eds. (Elsevier), pp 211-226.
MacKerell Jr, A. D., and Nilsson, L. (2006). Theoretical Studies of Nucleic Acids and Nucleic Acid-protein Complexes Using CHARMM. In DNA and RNA Computing, J. Sponer, ed. (Springer).
2005
Caballero-Herrera, A., Nordstrand, K., Berndt, K. D., and Nilsson, L.
(2005). Effect of Urea on Peptide Conformation in Water: Molecular Dynamics
and Experimental Characterization. Biophys J 89, 842-857.
Carlsson, P., Koehler, K. F., and Nilsson, L. (2005). Glucocorticoid
Receptor Point Mutation V571M Facilitates Coactivator and Ligand Binding by
Structural Rearrangement and Stabilization. Mol Endocrinol 19, 1960-1977.
Duan, J., and Nilsson, L. (2005). THERMAL UNFOLDING SIMULATIONS OF A
MULTIMERIC PROTEIN - transition state and unfolding pathways. Proteins 59,
170-182.
Foloppe, N., and Nilsson, L. (2005). Towards a full characterization of
nucleic acid components in aqueous solution: simulations of nucleosides. J
Phys Chem B 109, 9119-9131.
Hart, K., Nyström, B., Öhman, M., and Nilsson, L. (2005). Molecular dynamics
simulations and free energy calculations of base flipping in dsRNA. RNA 11,
609-618.
Nilsson, L., and Halle, B. (2005). Molecular origin of time-dependent
fluorescence shifts in proteins. Proc Natl Acad Sci USA 102, 13867-13872.
Norberg, J., Foloppe, N., and Nilsson, L. (2005). Intrinsic Relative
Stabilities of the Neutral Tautomers of Arginine Side-Chain Models. J Chem
Theor Comp 1, 986-993.
Bredenberg, J., Mark, P., and Nilsson, L. (2005). Solvent Effects on
Biomolecular Dynamics Simulations: A Comparison between TIP3P, SPC and SPC/E
acting on the Glucocorticoid Receptor DNA-binding Domain. In Modern methods
for theoretical physical chemistry of biopolymers, E. Starikov, S. Tanaka,
and J. P. Lewis, eds. (Elsevier).
Elliott, J., Starikov, E., Crawshaw, J., Claiden, P., Nilsson, L., and
Windle, A. (2005). Nucleation of polyglutamine amyloid fibres modelling
using molecular dynamics. In Modern methods for theoretical physical
chemistry of biopolymers, E. Starikov, S. Tanaka, and J. P. Lewis, eds.
(Elsevier).
MacKerell Jr, A. D., and Nilsson, L. (2005). Theoretical Studies of Nucleic
Acids and Nucleic Acid-protein Complexes Using CHARMM. In DNA and RNA
Computing, J. Sponer, ed. (Springer)
2004
Duan, J., Nilsson, L., and Lambert, B. (2004). Structural and functional
analysis of mutations at the human hypoxanthine guanine phosphoribosyl
transferase (HGPRT1) locus. Hum Mutat 23, 599-611.
Foloppe, N., and Nilsson, L. (2004). The Glutaredoxin -C-P-Y-C- Motif: Influence
of Peripheral Residues. Structure 12, 289-300.
Njålsson, R., Carlsson, K., Bhansali, V., Luo, J.-L., Nilsson, L., Ladenstein,
R., Anderson, M., Larsson, A., and Norgren, S. (2004). Human hereditary
glutathione synthetase deficiency: kinetic properties of mutant enzymes. Bioch J
381, 489-494.
Norberg, J., and Nilsson, L. (2004). Comment on "Free energy calculations for
DNA base stacking by replica-exchange umbrella sampling" by Katsumi Murata, Yuji
Sugita, Yuko Okamoto. Chem Phys Lett 393, 282-283.
Starikov EB. (2004). Importance Of Charge Transfer Excitations In DNA
Electron Spectrum: A Zindo Semiempirical Quantum-Chemical Study. Mod. Phys.
Lett. B 18(16):825-831.
Starikov EB. (2004). Why DNA Electrical Properties Change On Molecular
Oxygen Doping: A Quantum-Chemical Study. Mod. Phys. Lett. B 18(16):785-790.
Tanabe T, Noda K, Saito M, Starikov EB, Tateno M. (2004). Regular
threshold-energy increase with charge for neutral-particle emission in
collisions of electrons with oligonucleotide anions. Physical Review Letters
93(4): doi: 10.1103 /PhysRevLett93.043201
2003
Caballero-Herrera, A., and Nilsson, L. (2003). Molecular Dynamics Simulations
of the E1/E2 Transmembrane Domain of the Semliki Forest Virus. Biophys J 85,
3646-3658.
Carlsson, P., and Nilsson, L. (2003). Improved precision and efficiency of free
energy calculations for small systems using lambda-scaled atomic masses and
separating conformational and transformational sampling. J Comp Chem 24,
1383-1389.
Norberg, J., and Nilsson, L. (2003). Advances in Biomolecular Simulations:
Methodology and Recent Applications. Quart Rev Biophys 36, 257-306.
Sarzynska, J., Nilsson, L., and Kulinski, T. (2003). Effects of Base
Substitutions in an RNA Hairpin from Molecular Dynamics and Free Energy
Simulations. Biophys J 85, 3445-3459.
Kunz S, Sandoval R, Carlsson P, Carlstedt-Duke J, Bloom JW, Miesfeld RL.
2003. Identification of a Novel Glucocorticoid Receptor Mutation in
Budesonide-Resistant Human Bronchial Epithelial Cells, Mol Endo, in print
Lewis JP, Cheatham III TE, Starikov EB, Wang H, Sankey OF. (2003).
Dynamically Amorphous Character of Electronic States in Poly(dA)-Poly(dT)
DNA. J. Phys. Chem. B. 107(11):2581-2587.
Norberg J. (2003). Association of protein-DNA recognition complexes:
electrostatic and nonelectrostatic effects. Arch. Bioch. Bioph.
410(1):48-68.
Starikov EB. (2003). Role of electron correlations in deoxyribonucleic
acid duplexes: is an extended Hubbard Hamiltonian a good model in this case?
Phil. Mag. Lett. 83(11):699-708.
2002
Bredenberg, J., and Nilsson, L. (2002). Conformational States of the
Glucocorticoid Receptor DNA-Binding Domain from Molecular Dynamics Simulations.
PROTEINS 49, 24-36.
Duan, J., and Nilsson, L. (2002). The role of residue 50 and hydration water
molecules in homeodomain DNA recognition. Eur Biophys J 31, 306-316.
Foloppe, N., Hartmann, B., Nilsson, L., and MacKerell, A. D., Jr. (2002).
Intrinsic Conformational Energetics Associated with the Glycosyl Torsion in DNA:
A Quantum Mechanical Study. Biophys J 82, 1554-1569.
Foloppe, N., Nilsson, L., and MacKerell, A. D., Jr. (2002). Ab initio
conformational analysis of nucleic acid components: Intrinsic energetic
contributions to nucleic acid structure and dynamics. Biopolymers 61, 61-76.
Mark, P., and Nilsson, L. (2002). A Molecular Dynamics Study of Tryptophan in
Water. J Phys Chem B 106, 9440-9445.
Mark, P., and Nilsson, L. (2002). Structure and dynamics of liquid water with
different long-range interaction truncation and temperature control methods in
molecular dynamics simulations. J Comp Chem 23, 1211-1219.
Norberg, J., and Nilsson, L. (2002). Molecular dynamics applied to nucleic
acids. Accounts of Chemical Research 35, 465-472.
Starikov, E. B., and Nilsson, L. (2002). Structural basis of biotin-RNA aptamer
binding: a theoretical study. Chem Phys Lett 363, 39-44.
Lewis, JP, Pikus, J. Cheatham III, TE, Starikov, EB, Wang, H, Tomfohr, J,
Sankey, OF. (2002). A Comparison of Electronic States in Periodic and
Aperiodic Poly(dA)-Poly(dT) DNA, Phys. Stat. Sol. (b) 233: 90-100.
Starikov EB. (2002). Quantum chemistry of nucleic acids: how it could
help and when it is necessary. J. Photoch. Photobiol. C: Photoch. Rev.
3(2):147-164.
2001
Bredenberg, J., and Nilsson, L. (2001). Modeling zinc sulfhydryl interactions
in zinc fingers. Int J Quant Chem 83, 230-244.
Foloppe, N., Sagemark, J., Nordstrand, K., Berndt, K. D., and Nilsson, L.
(2001). Structure, Dynamics and Electrostatics of the Active Site of
Glutaredoxin 3 from Escherichia coli: Comparison with Functionally Related
Proteins. J Mol Biol 310, 449-470.
Lahiri, A., Nilsson, L., and Laaksonen, A. (2001). Exploring the Idea of
Self-guided Dynamics. Journal of Chemical Physics 114, 5993-5999.
MacKerell Jr., A. D., and Nilsson, L. (2001). Nucleic Acid Simulations. In
Computational Biochemistry and Biophysics, O. Becker, A. D. MacKerell Jr., B.
Roux, and M. Watanabe, eds. (New York, Marcel Dekker, Inc.), pp. 441-464.
Mark, P., and Nilsson, L. (2001). Molecular Dynamics of the Ala-Pro Dipetide in
Water. Conformational Dynamics of Cis- and Trans Isomers Using Different Water
Models. J Phys Chem B 105, 8028-8035.
Mark, P., and Nilsson, L. (2001). Structure and Dynamics of the TIP3P, SPC and
SPC/E Water Models at 298K. J Phys Chem A 105, 9954-9960.
Ruiz, M., Lind, U., Gåfvels, M., Eggertsen, G., Carlstedt-Duke, J., Nilsson, L.,
Holtmann, M., Stierna, P., Wikström, A.-C., and Werner, S. (2001).
Characterization of two novel mutations in the glucocorticoid receptor gene in
patients with primary cortisol resistance. Clin Endocrin 55, 363-371.
Sen, S., and Nilsson, L. (2001). MD Simulations of Homomorphous PNA, DNA and RNA
Single Strands: Characterization and Comparison of Conformations and Dynamics. J
Am Chem Soc 123, 7414-7422.
2000
Lahiri, A., and Nilsson, L. (2000). Molecular Dynamics of the Anticodon
Domain of Yeast tRNAPhe: Codon-anticodon Interaction. Biophysical Journal 79,
2276-2289.
Norberg, J., and Nilsson, L. (2000). On the Truncation of Long-Range
Electrostatic Interactions in DNA. Biophysical Journal 79, 1537-1553.
Sarzynska, J., Kulinski, T., and Nilsson, L. (2000). Conformational Dynamics of
a 5S rRNA Hairpin Domain Containing Loop D and a Single Nucleotide Bulge.
Biophysical Journal 79, 1213-1227.
Tomic, S., Nilsson, L., and Wade, R. C. (2000). Nuclear receptor-DNA binding
specificity: A COMBINE and Free- Wilson QSAR analysis. Journal of Medicinal
Chemistry 43, 1780-1792.
1999
Eriksson, M. A., and Nilsson, L. (1999). Structural and dynamic differences
of the estrogen receptor DNA-binding domain, binding as a dimer and as a monomer
to DNA: molecular dynamics simulation studies [published erratum appears in Eur
Biophys J 1999;28(4):356]. Eur Biophys J 28, 102-111.
Lahiri, A., and Nilsson, L. (1999). Examining the characteristics of chaos in
biomolecular dynamics: a random matrix approximation. Chem Phys Lett 311,
459-466.
Sen, S., and Nilsson, L. (1999). Free energy calculations and molecular dynamics
simulations of wild- type and variants of the DNA-EcoRI complex. Biophys J 77,
1801-1810.
Sen, S., and Nilsson, L. (1999). Some practical aspects of free energy
calculations from molecular dynamics simulation. Journal of Computational
Chemistry 20, 877-885.
Sen, S., and Nilsson, L. (1999). Structure, interaction, dynamics and solvent
effects on the DNA-EcoRI complex in aqueous solution from molecular dynamics
simulation. Biophys J 77, 1782-1800.
Tang, Y., and Nilsson, L. (1999). Effect of G40R mutation on the binding of
human SRY protein to DNA: A molecular dynamics view. Proteins-Structure Function
and Genetics 35, 101-113.
Tang, Y., and Nilsson, L. (1999). Molecular dynamics simulations of the complex
between human U1A protein and hairpin II of U1 small nuclear RNA and of free RNA
in solution. Biophys J 77, 1284-1305.
1998
Eriksson, M. A., and Nilsson, L. (1998). Structural and dynamic effects of
point mutations in the recognition helix of the glucocorticoid receptor
DNA-binding domain. Protein Eng 11, 589-600.
MacKerell Jr., A. D., Brooks, B. R., Brooks III, C. L., Nilsson, L., Roux, B.,
Won, Y., and Karplus, M. (1998). CHARMM: The Energy Function and Its
Parameterization with an Overview of the Program. In The Encyclopedia of
Computational Chemistry, N. L. A. P. v. R. Schleyer, T. Clark, J. Gasteiger, P.
A. Kollman, , and P. R. S. H. F. Schaefer III, eds. (Chichester, John Wiley &
Sons), pp. 271-277.
Nilsson, L. (1998). Protein Nucleic Acid Interactions. In Encyclopedia of
Computational Chemistry, P. von Ragué Schleyer, N. L. Allinger, T. Clark, J.
Gasteiger, P. A. Kollman, and H. F. Schaefer III, eds. (New York, John Wiley &
Sons), pp. 2220-2229.
Norberg, J., and Nilsson, L. (1998). Solvent Influence on Base Stacking. Biophys
J 74, 394-402.
Sen, S., and Nilsson, L. (1998). Molecular dynamics of duplex systems involving
PNA: Structural and dynamical consequences of the nucleic acid backbone. Journal
of the American Chemical Society 120, 619-631.
Tang, Y., and Nilsson, L. (1998). Interaction of human SRY protein with DNA: A
molecular dynamics study. Proteins-Structure Function and Genetics 31, 417-433.
1997
Eriksson, M. A. L., and
Nilsson, L. (1997). Computer Simulations of Protein:DNA Interactions. In
Theoretical and Computational Methods in Genome Research, S. Suhai, ed. (New
York, Plenum), pp. 279-286.
Lahiri, A., and Nilsson, L. (1997). Properties of dianionic oxyphosphorane
intermediates from hybrid QM/MM simulation: implications for ribozyme
reactions. Theochem-Journal of Molecular Structure 419, 51-55.
Lamminmäki, U., Villoutreix, B. O., Jauria, P., Saviranta, P., Vihinen, M.,
Nilsson, L., Teleman, O., and Lövgren, T. (1997). Structural analysis of an
anti-estradiol antibody. Molecular Immunology 34, 1215-1226.
1996
Elofsson, A., and Nilsson, L. (1996). A 1.2 ns Molecular Dynamics
Simulation of the Ribonuclease T-1-3'-Guanosine Monophosphate Complex. J
Phys Chem 100, 2480-2488.
Norberg, J., and Nilsson, L. (1996). Conformational Free Energy Landscape of
ApApA From Molecular Dynamics Simulations. J Phys Chem 100, 2550-2554.
Norberg, J., and Nilsson, L. (1996). Constant Pressure Molecular Dynamics
Simulations of the Dodecamers - d(GCGCGCGCGCGC)(2) and r(GCGCGCGCGCGC)(2). J
Chem Phys 104, 6052-6057.
Norberg, J., and Nilsson, L. (1996). Glass transition in DNA from molecular
dynamics simulations. Proceedings of the National Academy of Sciences of the
United States of America 93, 10173-10176.
Norberg, J., and Nilsson, L. (1996). Influence of adjacent bases on the
stacking-unstacking process of single-stranded oligonucleotides. Biopolymers
39, 765-768.
Norberg, J., and Nilsson, L. (1996). Internal Mobility of the
Oligonucleotide Duplexes d(TCGCG)2 and d(CGCGCG)2 in Aqueous Solution From
Molecular Dynamics Simulations. J Biomol NMR 7, 305-314.
Skoging, U., Vihinen, M., Nilsson, L., and Liljestrom, P. (1996). Aromatic
interactions define the binding of the alphavirus spike to its nucleocapsid.
Structure 4, 519-529.
1995
Eriksson, M. A. L., Hard, T., and Nilsson, L. (1995). Molecular Dynamics
Simulations of the Glucocorticoid Receptor DNA-Binding Domain in Complex
With DNA and Free in Solution. Biophysical Journal 68, 402-426.
Eriksson, M. A. L., Hard, T., and Nilsson, L. (1995). On the pH Dependence
of Amide Proton Exchange Rates in Proteins. Biophys J 69, 329-339.
Eriksson, M. A. L., and Nilsson, L. (1995). Structure, Thermodynamics and
Cooperativity of the Glucocorticoid Receptor DNA-Binding Domain in Complex
With Different Response Elements - Molecular Dynamics Simulation and Free
Energy Perturbation Studies. J Mol Biol 253, 453-472.
Maniar, H. S., Vihinen, M., Webster, A. D. B., Nilsson, L., and Smith, C. I.
E. (1995). Structural Basis For X-Linked Agammaglobulinemia (XLA) -
Mutations At Interacting Btk Residues R562, W563, and A582. Clinical
Immunology & Immunopathology 76, S 198-S 202.
Nilsson, L. (1995). Dynamics of Nucleic Acids and Nucleic Acid:Protein
Complexes. Springer Ser Synergetics 65, 156-164.
Norberg, J., and Nilsson, L. (1995). NMR Relaxation Times, Dynamics, and
Hydration of a Nucleic Acid Fragment From Molecular Dynamics Simulations. J
Phys Chem 99, 14876-14884.
Norberg, J., and Nilsson, L. (1995). Potential of Mean Force Calculations of
the Stacking Unstacking Process in Single-Stranded Deoxyribodinucleoside
Monophosphates. Biophys J 69, 2277-2285.
Norberg, J., and Nilsson, L. (1995). Stacking Free Energy Profiles For All
16 Natural Ribodinucleoside Monophosphates in Aqueous Solution. J Am Chem
Soc 117, 10832-10840.
Norberg, J., and Nilsson, L. (1995). Temperature Dependence of the Stacking
Propensity of Adenylyl-3',5'-Adenosine. J Phys Chem 99, 13056-13058.
Vihinen, M., Zvelebil, M., Zhu, Q. L., Brooimans, R. A., Ochs, H. D.,
Zegers, B. J. M., Nilsson, L., Waterfield, M. D., and Smith, C. I. E.
(1995). Structural Basis For Pleckstrin Homology Domain Mutations in
X-Linked Agammaglobulinemia. Biochemistry 34, 1475-1481.
Vorechovsky, I., Vihinen, M., Desaintbasile, G., Honsova, S., Hammarstrom,
L., Muller, S., Nilsson, L., Fischer, A., and Smith, C. I. E. (1995).
DNA-Based Mutation Analysis of Brutons Tyrosine Kinase Gene in Patients With
X-Linked Agammaglobulinaemia. Human Molecular Genetics 4, 51-58.
Zilliacus, J., Wright, A. P., Carlstedt-Duke, J., Nilsson, L., and
Gustafsson, J.-Å. (1995). Modulation of DNA-Binding Specificity Within the
Nuclear Receptor Family By Substitutions At a Single Amino Acid Position.
Proteins: Struct Funct Genet 21, 57-67.
1994
Eriksson, M., Härd, T., and Nilsson, L. (1994). Molecular Dynamics
Simulation of a DNA Binding Protein Free and in Complex With DNA. In
Computational Approaches to Supramolecular Chemistry, G. Wipff, ed.
(Dordrecht, Kluwer), pp. 441-456.
Norberg, J., and Nilsson, L. (1994). High-Pressure Molecular Dynamics of a
Nucleic Acid Fragment. Chem Phys Lett 224, 219-224.
Norberg, J., and Nilsson, L. (1994). Stacking-Unstacking of the Dinucleoside
Monophosphate Guanylyl-3',5'-Uridine Studied With Molecular Dynamics.
Biophys J 67, 812-824.
Vihinen, M., Nilsson, L., and Smith, C. I. E. (1994). Structural Basis of
Sh2 Domain Mutations in X-Linked Agammaglobulinemia. Biochemical &
Biophysical Research Communications 205, 1270-1277.
Vihinen, M., Nilsson, L., and Smith, C. I. E. (1994). Tec Homology (TH)
Adjacent to the PH Domain. FEBS Letters 350, 263-265.
Vihinen, M., Vetrie, D., Maniar, H. S., Ochs, H. D., Zhu, Q. L.,
Vorechovsky, I., Webster, A. D. B., Notarangelo, L. D., Nilsson, L.,
Sowadski, J. M., and Smith, C. I. E. (1994). Structural Basis For Chromosome
X-Linked Agammaglobulinemia - a Tyrosine Kinase Disease. Proceedings of the
National Academy of Sciences of the United States of America 91,
12803-12807.
Zhu, Q. L., Zhang, M., Rawlings, D. J., Vihinen, M., Hagemann, T., Saffran,
D. C., Kwan, S. P., Nilsson, L., Smith, C. I. E., Witte, O. N., et al.
(1994). Deletion Within the Src Homology Domain 3 of Brutons Tyrosine Kinase
Resulting in X-Linked Agammaglobulinemia (XLA). Journal of Experimental
Medicine 180, 461-470.
1993
Brooks, C. L., and Nilsson, L. (1993). Promotion of Helix Formation in
Peptides Dissolved in Alcohol and Water-Alcohol Mixtures. J Am Chem Soc 115,
11034-11035.
Carlstedt-Duke, J., Nilsson, L., and Norinder, U. (1993). Steroid Receptor
Models. In 3D QSAR in Drug Design - Theory, Methods and Applications, H.
Kubinyi, ed. (Leiden, ESCOM), pp. 373-385.
Elofsson, A., Kulinski, T., Rigler, R., and Nilsson, L. (1993).
Site-Specific Point Mutation Changes Specificity - a Molecular Modeling
Study By Free-Energy Simulations and Enzyme-Kinetics of the Thermodynamics
in Ribonuclease T1 Substrate Interactions. Proteins 17, 161-175.
Elofsson, A., and Nilsson, L. (1993). Free Energy Perturbations in
Ribonuclease T1 Substrate Binding. a Study of the Influence of Simulation
Length, Internal Degrees of Freedom and Structure in Free Energy
Perturbations. Mol Simul 10, 255-276.
Elofsson, A., and Nilsson, L. (1993). How Consistent Are Molecular-Dynamics
Simulations - Comparing Structure and Dynamics in Reduced and Oxidized
Escherichia-Coli Thioredoxin. J Mol Biol 233, 766-780.
Eriksson, M. A., Berglund, H., Härd, T., and Nilsson, L. (1993). A
Comparison of Nitrogen-15 NMR Relaxation Measurements With a Molecular
Dynamics Simulation: Backbone Dynamics of the Glucocorticoid Receptor
DNA-Binding Domain. Proteins 17, 375-390.
Whitley, P., Nilsson, L., and von Heijne, G. (1993). Three-Dimensional Model
For the Membrane Domain of Escherichia Coli Leader Peptidase Based On
Disulfide Mapping. Biochemistry 32, 8534-8539.
Vogel, H., Nilsson, L., Rigler, R., Meder, S., Boheim, G., Beck, W., Kurth,
H. H., and Jung, G. (1993). Structural Fluctuations Between 2 Conformational
States of a Transmembrane Helical Peptide Are Related to Its Channel-
Forming Properties in Planar Lipid-Membranes. Eur J Biochem 212, 305-313.
1992
De Loof, H., Nilsson, L., and Rigler, R. (1992). Molecular Dynamics
Simulation of Galanin in Aqueous and Nonaqueous Solution. J Am Chem Soc 114,
4028-4035.
Härd, T., and Nilsson, L. (1992). Free-Energy Calculations Predict Sequence
Specificity in DNA-Drug Complexes. Nucleosides & Nucleotides 11, 167-173.
Nilsson, L., Ahgrenstalhandske, A., Sjogren, A. S., Hahne, S., and Sjoberg,
B. M. (1992). Computer-Graphics Modeling and Molecular-Dynamics Simulation
of the Core of the Self Splicing Intervening Sequence of the T4 Nrdb
Messenger-Rna in the Presence of the Guanosine Cofactor. Nucleosides &
Nucleotides 11, 159-166.
Patel, N., Berglund, H., Nilsson, L., Rigler, R., McLaughlin, L. W., and
Graslund, A. (1992). Thermodynamics of Interaction of a Fluorescent DNA
Oligomer with the Antitumor Drug Netropsin. European Journal of Biochemistry
203, 361-366.
1991
Elofsson, A., Rigler, R., Nilsson, L., Roslund, J., Krause, G., and
Holmgren, A. (1991). Motion of Aromatic Side Chains, Picosecond
Fluorescence, and Internal Energy Transfer in Escherichia Coli Thioredoxin
Studied By Site-Directed Mutagenesis, Time-Resolved Fluorescence
Spectroscopy, and Molecular Dynamics Simulations. Biochemistry 30,
9648-9656.
Patel, N., Graslund, A., Berglund, H., Nilsson, L., Rigler, R., and
McLaughlin, L. W. (1991). Interaction of a Minor Groove Binder With a
Fluorescent Dna Oligomer Containing the Eco Ri Recognition Sequence.
Nucleosides & Nucleotides 10, 547-548.
Rigler, R., Wennerberg, A., Cooke, R. M., Elofsson, A., Nilsson, L., Vogel,
H., Holley, L. H., Carlquist, M., Langel, U., Bartfai, T., and Campbell, I.
D. (1991). On the Solution Structure of Galanin. In Galanin, T. Hökfelt, and
T. Bartfai, eds. (London, MacMillan), pp. 17-25.
1990
Elofsson, A., Nilsson, L., and Rigler, R. (1990). Studies On Somatostatin
With Time-Resolved Spectroscopy and Molecular Dynamics Simulations. Int J
Pept Protein Res 36, 297-301.
Knapp, E.-W., and Nilsson, L. (1990). Can Electron Transfer Be Influenced by
Protein Dynamics: The Transfer from Cytochrome C to the Special Pair in
Photosynthetic Reaction Centers. In Reaction Centers in Photosynthetic
Bacteria, M.-E. Michel-Beyerl, ed. (Heidelberg, Springer Verlag), pp.
437-450.
Knapp, E.-W., and Nilsson, L. (1990). Protein Dynamics in the Photosynthetic
Reaction Center: The Electron Transfer from Cytochrome C to the Special
Pair. In Perspectives in Photosynthesis, J. Jortner, and B. Pullman, eds.
(Dordrecht, Kluwer Academic Publishers), pp. 389-412.
Nilsson, L., Åhgren-Stålhandske, A., Sjögren, A. S., Hahne, S., and Sjöberg,
B.-M. (1990). Three-Dimensional Model and Molecular Dynamics Simulation of
the Active Site of the Self-Splicing Intervening Sequence of the
Bacteriophage T4 nrdb Messenger RNA. Biochemistry 29, 10317-10322.
Nordlund, T. M., Wu, P., Andersson, S., Nilsson, L., Rigler, R., Gräslund,
A., McLaughlin, L. W., and Gildea, B. (1990). Structural Dynamics of DNA
Sensed by Fluorescence from Chemically Modified Bases. SPIE 1204, 344-353. |
The Molecular Modeling
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