Publications
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., in press.
Hart K
& Nilsson L (2008) Investigation of transcription factor Ndt80 affinity
differences for wild type and mutant DNA: a molecular dynamics study.
Proteins, in press.
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., submitted.
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, in press.
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
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.
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.
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
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., and Nilsson, L. (2005). Urea Parametrization for Molecular Dynamics
Simulations. J Mol Struct THEOCHEM 758, 137-146.
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.
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.
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