National Doctoral Programme in
Informational and Structural Biology

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Publications 1999

• Aitio H, Annila A, Heikkinen S, Thulin E, Drakenberg T & Kilpeläinen I. (1999) NMR assignments, secondary structure, and global fold of calerythrin, an EF-hand calcium-binding protein from Saccharopolyspora erythraea. Protein Sci. 8(12):2580-8.
• Annila A, Aitio H, Thulin E &. Drakenberg T. (1999) Recognition of protein folds via dipolar couplings J. Biol. NMR 14:223-230.
• Baykov AA, Cooperman BS, Goldman A & Lahti R. (1999) Cytoplasmic inorganic pyrophosphatases. Progr. Mol. Subcell. Biol. 23:127-150.
• Baykov AA, Hyytiä T, Turkina M, Efimova I, Kasho V, Goldman A, Cooperman B & Lahti R. (1999) Functional characterization of Escherichia coli inorganic pyrophosphatase in zwitterionic buffers. Eur. J. Biochem. 260:308-317.
• Denessiouk KA, Denesyuk, AI, Lehtonen, JV, Korpela T & Johnson MS. (1999) Common structural elements in the architecture of the cofactor-binding domains in unrelated families of pyridoxal phosphate-dependent enzymes. Proteins: Struct. Funct. Genet. 35(2):250-261.
• Efimova IS, Salminen A, Pohjanjoki P, Lapinniemi J, Magretova N, Cooperman BS, Goldman A, Lahti R & Baykov AA. (1999) Directed mutagenesis studies of the metal binding site at the subunit interface of Escherichia coli inorganic pyrophosphatase. J. Biol. Chem. 274:3294-3299.
• Heikinheimo P, Goldman A, Jeffries C & Ollis DL. (1999) Of barn owls and bankers: a lush variety of alpha/beta hydrolases. Structure Fold. Des. 7:141-146.
• Heikkinen S. (1999) Some applications of RF-gradients and excitation sculpting in NMR spectroscopy. Acta Universitatis Ouluensis A326. (Dissertation).
• Heikkinen S & Kilpeläinen I. (1999) Gradient BIRDR: A method to select uncoupled magnetization. J. Magn. Reson. 137:93-99.
• Heikkinen S, Aitio H, Permi P, Folmer R, Lappalainen K & Kilpeläinen I. (1999) J-multiplied HSQC (MJ-HSQC): a new method for measuring 3J(HNHalpha) couplings in 15N-labeled proteins. J. Magn. Reson. 137(1):243-6.
• Huhtala MT, Pentikäinen O & Johnson MS. (1999) A dimeric ternary complex of FGFR, heparin and FGF-1 leads to an 'electrostatic sandwich' model for heparin binding. Structure 7:699-709.
• Ivaska J, Käpylä J, Pentikäinen O, Hoffren A-M, Hermonen J, Huttunen P, Johnson MS & Heino J. (1999) A peptide inhibiting the collagen binding function of integrin alpha2I domain. J. Biol. Chem. 274:3513-3521.
• Kuusinen A, Abele R, Madden DR & Keinänen K. (1999) Oligomerization and ligand-binding properties of the ectodomain of the AMPA receptor subunit GluRD. J. Biol. Chem. 274:28937-28943.
• Lehtonen JV, Denessiouk KA, & Johnson MS. (1999) Speeding up comparison of three-dimensional protein structures. CSC News 11 (4):16-18.
• Lehtonen JV, Denessiouk KA, May ACW & Johnson MS. (1999) Finding local structural similarities among families of unrelated protein structures: A generic non-linear algorithm. Proteins: Struct. Funct. Genet. 34 (3):341-355.
• Leppänen V-M, Nummelin H, Hansen T, Lahti R, Schäfer G & Goldman A. (1999) The structure and structural basis of thermostability in Sulfolobus acidocaldarius inorganic pyro-phosphatase. Protein Sci. 8:1218-1231.
• Nyrönen TH, Suontamo R & Pikänen I (1999) Why betaine crystallizes in high local C8 symmetry. Ab initio MO and DFT study of anhydrous betaine and betaine monohydrate. Theor. Chem. Acc. 191:209-214.
• Nyrönen TH & Suontamo R. (1999) Fundamental study of high symmetry C8 clusters. CSC Report on Scientific Computing 1997-1998, ed. J Haataja, CSC, Espoo, pp. 100-102.
• Nyrönen TH & Johnson MS. (1999) Huipputeknologia: Tietokoneavusteinen lääkkeensuunnitelu. Prisma TV program, ed. Tomi Salminen, Finland TV1.
• Nyrönen T & Johnson MS. (1999) Customized molecules - engineering new drugs with biocomputing. In: High Technology Today. The Finish Academies of Technology, Finland. pp. 78-79.
• Okoh MP & Vihinen M. (1999) Pleckstrin homology domains of Tec family protein kinases. Biochem. Biophys. Res. Comm. 265:151-157.
• Pentikäinen O, Hoffren A-M, Ivaska J, Käpylä J, Nyrönen T, Heino J & Johnson MS. (1999) RKKH peptides from the snake venom metalloproteinase of Bothrops jararaca bind near the metal ion-dependent adhesion site of the human integrin alpha2 I-domain. J. Biol. Chem. 274(44):31493-31505.
• Permi P, Sorsa T, Kilpelainen I & Annila A. (1999) HN(alpha/beta-COCA-J) experiment for measurement of (1)J(C'C(alpha)) couplings from two-dimensional [(15)N, (1)H] correlation spectrum. J. Magn. Reson. 141(1):44-51.
• Permi P, Kilpeläinen I & Heikkinen S. (1999) An improved J-multiplied method for the measurement of 3JHNHa from two-dimensional 15N, 1H correlation spectrum. Magn. Res. Chem. 37:821-826.
• Permi P, Heikkinen S, Kilpeläinen I & Annila A. (1999) Measurement of (1)J(NC') and (2)J(H(N))(C') couplings from spin-state-selective two-dimensional correlation spectrum. J. Magn. Reson. 140(1):32-40.
• Permi P, Heikkinen S, Kilpeläinen I & Annila A. (1999) Measurement of homonuclear (2)J-couplings from spin-state selective double-/zero-quantum two-dimensional NMR spectra. J. Magn. Reson. 139(2):273-80.
• Ramstedt B & Slotte JP. (1999) Interaction of cholesterol with sphingomyelins and acyl-chain matched phosphatidylcholines - a comparative study of the effects of the chain length. Biophys. J. 76:908-915.
• Ramstedt B & Slotte JP. (1999) Comparison of the biophysical properties of racemic and D-erythro-N-acyl-sphingomyelins. Biophys. J. 77:1498-1506.
• Ramstedt B, Leppimäki P, Axberg M & Slotte JP. (1999) Analysis of natural and synthetic sphingomyelins using high-performance thin-layer chromatography. Eur. J. Biochem. 266:997-1002.
• Salminen A, Efimova IS, Parfenyev AN, Magretova NN, Mikalahti K, Goldman A, Baykov AA & Lahti R. (1999) Reciprocal effects of substitutions at the subunit interfaces in hexameric pyrophosphatase of Escherichia coli. J. Biol. Chem. 274:33989-33904.
• Salminen T, Varis M, Nyrönen T, Pihlavisto M, Hoffren A-M, Lönnberg T, Marjamäki A, Frang H, Savola J-M, Scheinin M & Johnson MS. (1999) Three-dimensional models of alpha-2A-adrenergic receptor complexes provide a structural explanation for ligand binding. J. Biol. Chem. 274(33):23405-23413.
• Salminen TA, Nymalm Y, Kankare J, Käpylä J, Heino J & Johnson MS. (1999) Production, crystallization and preliminary X-ray analysis of the human integrin alpha1 I domain. Acta Cryst. D 55:1365-1367.
• Schell U, Helin S, Kajander T, Schlömann M & Goldman A. (1999) Structural basis for the activity of two muconate cycloisomerase variants towards substituted muconates. Proteins: Struct. Funct. Genet. 34:125-136.
• Sivula T, Salminen A, Parfenyev AN, Pohjanjoki P, Goldman A, Cooperman BS, Baykov AA & Lahti R. (1999) Evolutionary aspects of inorganic pyrophosphatase. FEBS Lett 454:75-80.