Microsoft word - serrano1984-2005.doc

Serrano Lab Publications 1984-2005
1984

Serrano L.,Diez J.,Avila J.,Maccioni R.
"Controlled proteolysis of tubulin with subtilisin: Structural and functional consequences"
J.submicrosc.Cytol. 16(1), 55-56 (1984)
Serrano L.,Avila J.,Maccioni R
"Limited proteolysis of tubulin and the binding site for colchicine"
J.Biol.Chem. 259, 6607-6611 (1984)
Serrano L.,Avila J.,Maccioni R.
"Controlled proteolysis of tubulin by subtilisin: Localization of the binding site for MAP2"
Biochemistry 23, 4675-4681 (1984)
Serrano L., De la Torre J., Maccioni R.,Avila J.
"Involvement of the carboxy-terminal domain of tubulin in the regulation of its assembly"
Proc.Nat.Acad.Sci.U.S.A 81, 5989-5993 (1984)
1985

Maccioni R.,Serrano L,Avila J.
"Structural and functional domains of tubulin"
Bioessays 2, 156-159 (1985)
Serrano L.,Avila J
"The interactions of tubulin subunits in the tubulin dimer"
Biochemical J. 230, 551-556 (1985)
Serrano L.,Montejo E.,Hernandez M,A.,Avila J.
"Localization of the binding site for Tau protein"
Eur. J. of Biochem. 135, 595-600 (1985)
Wandosell F., Serrano L.,Avila J.
"Calcium binding protein of D.melanogaster which activates AMPc phosphodiesterase: comparison with
brain porcine calmodulin"
Arch. Biochem.Biophys.Methods. 247, 147-154 (1985)
1986

Serrano L.,Wandosell F.,De la Torre J.,Avila J.
"Proteolytical modifications of tubulin" Methods in Enzimology 134, 179-190 (1986) Serrano L., Wandosell F., Diez J., Avila J. "The combined use of limited proteolysis and differential peptide staining for protein characterization" J.Biochem.Biophys.Methods. 12, 281-283 (1986) Serrano L., De la Torre J., Maccioni R., Avila J. "The role of the carboxy-terminal region of tubulin in the regulation of its self-assembly" Annals of the New York Academy of Sciences. 466, 642-644 (1986) Wandosell F.,Serrano L.,Hernandez M.A.,Avila J. "Phosphorylation of tubulin by a calmodulin dependent kinase" J.Biol.Chem. 261, 10332-10334 (1986) Maccioni R., Serrano L., Avila J.,CannR. "Characterization and structural aspects of the enhanced assembly of tubulin after removal of its C-terminal domain" Eur.J.Biochem. 56, 375-381 (1986) Serrano L.,Valencia A., Caballero R.,Avila J. "Localization of the high affinity calcium binding site on tubulin molecule” J.Biol.Chem. 261, 7076-7081 (1986) Wandosell F., Villanueva N., Serrano L., Avila J. "Analysis of drug-tubulin interaction by trypsin cleavage: Comparison for colchicine, podophyllotoxin,vinblastine, and taxol" Comp.Biochem. and Physiol.B 85,3, 635-638 (1986) Serrano L.,De la Torre J., Luduena R.F Avila J. "The removal of the carboxy-terminal region of tubulin favours its vinblastine induced aggregation" Arch.Biophys.Bioch. 49, 611-615 (1986) Avila J.,Serrano L., Maccioni R. "Regulation of the colchicine binding to tubulin" Mol.Cell. Biochem. 73, 29 -36 (1986) Serrano L.,Wandosell F., Avila J. "Location of the regions recognized by five commercial antibodies on the tubulin molecule" Anal.Biochemistry. 159, 253-259 (1986) Montejo de Garcini E., Serrano L., Avila J. "Self assembly of microtubule associated protein Tau into filaments ressembling these found in alzheimer disease" BIOCHEM BIOPH RES CO 141, 790-796 (1986)
1987

Serrano, L., Diaz-Nido, J., Wandosell, F. & Avila, J.
“Phosphorylation of tubulin by casein-quinase II its similar to that found "in vivo"”
J. Cell Biology 105, 1731-1739 (1987)
1988

Avila J., Serrano L., Diaz-nido J., Wandosell F., Hernandez M.A.
"Regulation of the polymerization of tubulin"
J.Muscle Research 9(1), 95 (1988)
Serrano L., Wandosell F., De la Torre J., Avila J.
“Effect of specific proteolytic cleavages on tubulin polymer formation"
Biochem J. 252, 683-691 (1988)
Serrano L., Dominguez J., Avila J.
"Zinc binding proteins detected on nitrocellulose paper; Zinc binds to the amino-terminal of tubulin"
Anal.Biochemistry 172, 210-218 (1988)
Diaz-Nido, J., Serrano, L., Mendez, E. & Avila, J.
“A casein-kinase II like activity its involved in phosphorylation of microtubule associated protein MAP1,
during neuroblastome cell differentiation”
J. Cell Biol. 106, 2057-2065 (1988)
Diaz-nido J.,Serrano L., Avila J
"Differential phosphorylation of microtubule proteins by ATP and GTP"
Mol.Cell.Biochem. 79, 73-79 (1988)
Valencia A., Serrano L.,Caballero R., Anderson S.P.,Lacal J.C.
"Conformational alterations detected by circular dichroism, induced in the normal ras p21 by activating point
mutations at positions 12,59 or 61”
Eur.J. of Biochem. 174, 621-627 (1988)
1989

Serrano L., Diaz-Nido J., Hernandez M.A., Avila J.
"Association of casein-kinase II to microtubules"
Experimental cell research 181, 263-272 (1989)
Serrano, L. , Diez, J., Wandosell, F. ,Avila, J. & Little, M.
“Calcium binding properties of the beta-tubulin subunit from chicken erythrocites.”
Biochemistry. Int. 19, 235-246 (1989)
Diaz-nido J., Serrano L., Hernandez M.A, Avila J
"Phosphorylation of microtubule protein in rat brain of different development stages. Comparison with that
found in neuronal cultures"
J. Neuroscience 54, 211-222 (1989)
Matouschek A., Kellis J.T., Serrano L., Fersht A.R.
"Mapping the transition state and pathway of protein folding by protein engineering"
Nature 340, 122-126 (1989)
Serrano L., Fersht A.R.
"Capping and alpha-helix stability"
Nature 342, 296-299 (1989)
1990

Diaz-nido J., Serrano L., Lopez-Otin, C., Vandekerckhove J.,Avila J
"Localization of the main phosphorylation site in brain tubulin"
J.Biol.Chem 265, 13949-13954 (1990)
Serrano L., Horovitz A., Avron B., Bycroft M., Fersht A.R.
"Measurement of the effects of surface electrostatic interactions on enzyme stability using protein
engineering and double-mutant cycles"
Biochemistry 29, 9343-9352 (1990)
Matouschek A., Kellis J.T., Serrano L., Bycroft M., Fersht A.R.
"Transient folding intermediates characterised by protein engineering"
Nature 346, 440-445 (1990)
Bycroft M., Matouschek A., Kellis J., Serrano L., Fersht A.R
"Detection and characterization of a folding intermediate in barnase by NMR"
Nature 340, 488-490 (1990)
Horovitz A., Serrano L., Avron B., Bycroft M., Fersht A.R.
"Strengh and Co-operativity of Contributions of Surface Salt Bridges to Protein Stability"
J. Mol. Biol. 216, 1031-1044 (1990)
1991

Serrano L., Bycroft M., Fersht A.R.
"Aromatic-aromatic interactions and protein stability: Investigation by double-mutant cycles"
J. Mol. Biol. 218, 465-475 (1991)
Horovitz A., Serrano L., Fersht A.R.
“COSMIC analysis of the major alpha-helix of barnase during folding"
J. Mol. Biol. 219, 5-9 (1991)
Fersht A.R., Bycroft M., Horovitz A., Kellis J., Matouschek A. & Serrano L.
“Pathway and stability of protein holding”
Phil. Trans. R. Soc. Lond. B. 332, 171-176 (1991)
1992

Sancho J., Serrano L & Fersht A.
"Histidine residues at the N- and C-termini of alpha-helices: perturbed pKas and protein stability"
Biochemistry 31, 2253-2258 (1992)
Fersht A.R. Serrano L. & Matouschek, A.R.
"The Folding of an Enzyme I"
J. Mol. Biol. 224, 771-782 (1992)
Serrano, L., Kellis, J., Cann, P., Matouschek, A. & Fersht, A.R.
"The Folding of an Enzyme II"
J. Mol. Biol. 224, 783-804 (1992)
Serrano, L., Matouschek, A. & Fersht, A.R.
"The Folding of an Enzyme III"
J. Mol. Biol. 224, 805-818 (1992)
Matouschek, A. Serrano, L. & Fersht, A.R.
"The Folding of an Enzyme IV"
J. Mol. Biol. 224, 819-835 (1992)
Matouschek, A.R., Bycroft, M., Meiering, E., Serrano, L. & Fersht, A.R.
"The Folding of an Enzyme V"
J. Mol. Biol. 224, 837-845 (1992)
Serrano, L., Matouschek, A. & Fersht, A.R.
"The Folding of an Enzyme VI"
J. Mol. Biol. 224, 847-859 (1992)
Serrano, L., Neira, J.L., Sancho, J. & Fersht, A.R.
"Effect of alanine versus glycine in alpha-helices on protein stability”
Nature 356, 453-455 (1992)
Meiering, E., Serrano, L. & Fersht, A.R.
"Effect of active site residues in barnase on activity and stability”
J. Mol. Biol. 225, 585-589 (1992)

Serrano, L., Sancho, J., Hirshberg, M. & Fersht, A.R.
"Helix Stability in Proteins. I. Empirical Correlations Concerning Substitutions of Side-Chains at the N- and
C-caps and the Replacement of Alanine by Glicine or Serine at Solvent-exposed Surfaces”
J. Mol. Biol. 227, 544-559 (1992)
1993

Serrano, L. & Fersht, A.R.
"Principles of protein stability from protein engineering experiments”
Current Opinion in Structural Biology 3, 75-83 (1993)
Serrano, L., Day, T. & Fersht, A.R.
"The step-wise mutation of barnase to binase and a procedure for engineering increased stability of proteins:
An experimental analysis of the evolution of protein stability”
J. Mol. Biol. 233, 305-312 (1993)
Bruix, M., Pascual, J., Santoro, J., Prieto, J., Serrano, L. & Rico, M.
"1H and 15N NMR assignement and solution structure of the chemotactic E. coli CHEY protein”
Eur. J. Biochem. 215, 573-585 (1993)
Filimonov, V.V., Prieto, J., Mateo, P.L. & Serrano, L.
"Thermodynamic analysis of the chemotactic protein from E. coli, CheY”
Biochemistry 32, 12906-12921 (1993)
1994

Serrano, L.
"Protein engineering and the dissection of protein folding pathways”
Curr. Opinion in Structural Biology 3, 75-83 (1994)
Viguera, A.R., Martinez, J.C., Filimonov, V., Mateo, P. & Serrano, L.
"Thermodynamic and kinetic analysis of the SH3 domain of spectrin”
Biochemistry 33, 2142-2150 (1994)
Bellsolell, L., Prieto, J., Serrano, L. & Coll, M.
"Magnesium binding to the bacterial chemotaxis protein CheY results in large conformational changes
involving its functional surface”
J. Mol. Biol. 238, 489-495 (1994)
Muñoz, V., Lopez, E. & Serrano, L.
"Kinetic chracterization of the chemotactic protein from E. coli CheY. Kinetic analysis of the inverse
hydrophobic effect”
Biochemistry 33, 5858-5866 (1994)
Muñoz, V. & Serrano, L.
"Elucidating the folding problem of helical peptides using empirical parameters”
Nature Struct. Biol. 1, 399-409 (1994)
Blanco, F., Rivas, G. & Serrano, L.
“A short linear peptide that folds into a native stable beta-hairpin in aqueous solution"
Nature Struct. Biol. 1, 584-590 (1994)
Viguera, A.R., Arrondo, J.L.R. , Musacchio, Andrea., Saraste, M. & Serrano, L.
“Characterization of the interaction of natural proline-rich peptides with five different SH3 domains”
Biochemistry 33, 10925-10933 (1994)
Muñoz, V. & Serrano, L.
“Intrinsic secondary structure propensities of the amino acids, using statistical phi-psi matrices. Comparison
with experimental scales”
Proteins Struct. Funct. and Genetics 20, 301-311 (1994)
Jimenez, M. A., Muñoz, V., Rico, M. & Serrano, L.
“Helix stop and start signals in peptides and proteins: The capping box does not necessarily prevent helix
elongation”
J. Mol. Biol. 242, 487-496 (1994)
Muñoz, V. & Serrano, L.
“Elucidating the folding problem of helical peptides using empirical parameters, II. Helix macrodipole effects
and rational modification of the helical content of natural peptides”
J. Mol. Biol 245, 275-296 (1994)
Muñoz, V. & Serrano, L.
“Elucidating the folding problem of helical peptides using empirical parameters III: Temperature and pH
dependence”
J. Mol. Biol 245, 297-308 (1994)
Pisabarro, M.T., Ortiz, A.R., Viguera, A.R. Gago, F. & Serrano, L.
“Molecular modeling of the interaction of prolyproline-based peptides with the Abl-SH3 domain: rational
modification of the interaction”
Protein Engineering 7, 1455-1462 (1994)
Pisabarro, M.T., Ortiz, A.R., Serrano, L. & Wade, R.
“Homology modeling of the Abl-SH3 domain”
PROTEINS; Struct. and Function. 20, 203-215 (1994)
1995

Santoro, J., Bruix, M., Pascual, J., Lopez, E., Serrano, L & Rico. M.
“Three dimensional structure of chemotactic CheY protein in aqueous solution by nuclear magnetic
resonance methods”
J. Mol. Biol. 247, 717-725 (1995)
Muñoz, V., Jimenez, M.A. Rico, M. & Serrano, L. “Structural analysis of peptides encompassing all the alpha-helices of three alpha/beta parallel proteins: CheY, Flavodoxin and P21-ras: Implications for alpha-helix stability and the folding of alpha/beta parallel proteins” J. Mol. Biol. 247, 648-669 (1995) Cronet, F., Bellsolell, L., Majolero, M., Sander, C., Coll, M. & Serrano, L. “Investigating the structural determinants of the p21-like triphosphate and Mg2+ binding site” J. Mol. Biol. 249, 654-664 (1995) Muñoz, V., Blanco, F. & Serrano, L. "The "Hydrophobic-staple" motif. A role for loop-residues in alpha-helix stability and protein holding” Nature Struct. Biol. 2, 380-385 (1995) Lopez-Hernandez, E. & Serrano, L. “Empirical Correlation for the Replacement of Ala by Gly: Importance of amino acid secondary intrinsic propensities” PROTEINS: Struct. and Function. 22, 340-349 (1995) Blanco, F.J. & Serrano, L. “Folding of protein G B1 domain studied by the conformational characterization of fragments comprising its secondary structure elements” Eur. J. Biochem. 230, 634-649 (1995) Muñoz, V. & Serrano, L. “Helix Design, Prediction and Stability” Current Opinion in Biotechnology 6, 382-386 (1995) Viguera, A.R. & Serrano, L. “Experimental analysis of the Schellman motif” J. Mol. Biol. 251, 150-160 (1995) Muñoz, V. & Serrano, L. “Intrinsic secondary structure propensities of the amino acids, using statistical phi-psi matrices: comparison with the experimental scales” PROTEINS: Struct. Funct. and Genet. 20, 301-311 (1995) Viguera, A.R. & Serrano, L. “Side-chain interactions between sulfur-containing amino acids and Phe in alpha-helices” Biochemistry 34, 8771-8779 (1995) Viguera, A.R., Blanco, F. & Serrano, L. “The order of secondary structure elements does not determine the structure of a protein but does affect its folding kinetics” J. Mol. Biol. 247, 670-681 (1995) Villegas, V., Azuaga, A., Catasus, Ll., Reverter, D., Mateo, P.L., Aviles, F.X. & Serrano, L.
“Evidence for a two-state transition in the folding process of the activation domain of human
procarboxypeptidase A2”
Biochemistry 34, 15105-15110 (1995)
Serrano, L.
“Comparison between the phi distribution of the amino acids in the protein database and NMR data indicates
that amino acids have various phi propensities in the random-coil conformation”
J. Mol. Biol. 254, 322-333 (1995)
Muñoz, V. & Serrano, L.
“Analysis of i,i+5 and i,i+8 hydrophobic interactions in a helical model peptide bearing the hydrophobic
staple motif”
Biochemistry 34, 15301-15306 (1995)
Muñoz, V., Blanco, F. & Serrano, L.
“The distribution of alpha-helix propensity along the polypeptide chain is not conserved in proteins from the
same family”
Prot. Sci. 4, 1577-1586 (1995)
1996

Viguera, A.R., Jimenez, M.A., Rico, M. & Serrano, L.
“Conformational analysis of peptides corresponding to beta-hairpins and a beta-sheet, that represent the
entire sequence of alpha-spectrin SH3-domain”
J. Mol. Biol. 255, 507-521 (1996)
Villegas, V., Viguera, A.R., Aviles, F.X. & Serrano, L.
“Stabilisation of proteins by rational design of alpha-helix stability using helix/coil transition theory”
Folding & Design 1, 29-34 (1996)
Ramirez-Alvarado, M., Blanco, F.J. & Serrano, L.
“De novo design and structural analysis of a model beta-hairpin peptide system”
Nat. Struct. Biol. 3, 604-612 (1996)
Lopez-Hernandez, E. & Serrano, L.
“Structure of the transition state for folding of the 129aa protein, CheY, resembles that of a smaller protein,
CI-2.”
Folding & Design 1, 43-55 (1996)
Bellsolell, L., Cronet, P., Majolero, M., Serrano, L. & Coll, M.
“The Three-dimensional Structure of Two Mutants of the Signal Transduction Protein CheY Suggest its
Molecular Activation Mechanism”
J. Mol. Biol. 257, 116-128 (1996)
Muñoz, V., Cronet, P., López-Hernández, E. & Serrano, L.
“Analysis of the Effect of Local Interactions in Protein Stability”
Folding & Design 1, 167-178 (1996)

Arrondo, J.L., Blanco, F.J., Serrano, L. & Goñi, F.M.
“Infrared evidence of a beta-hairpin peptide structure in solution”
FEBS 384, 35-37 (1996)
Pisabarro, M. T. & Serrano, L.
“Rational design of specific high affinity ligands for the Abl-SH3 domain”
Biochemistry 35, 10634-10640 (1996)
Muñoz, V. & Serrano, L.
“Local vs non-local interactions in protein folding and stability. An experimentalist point of view”
Folding & Design 1, R71-R77 (1996)
Viguera, A.R. Wilmanns, M. & Serrano, L.
“Different folding transition states could result in the some native structure”
Nat. Struct. Biol. 3, 874-880 (1996)
Viguera, A.R., Virtudes, V., Aviles, F.X. & Serrano, L.
“Favourable native-like helical local interactions can accelerate protein folding”
Folding & Design 2, 23-33 (1996)
1997

López-Hernández, E., Cronet, P., Serrano, L. & Muñoz, V.
“Folding kinetics of Che Y mutants with enhanced native alpha-helix propensities”
J. Mol. Biol. 266, 610-620 (1997)
Muñoz, V. & Serrano, L.
“Development of the multiple sequence approximation within the AGADIR model of alpha-helix formation:
comparison with Zimm-Bragg and Lifson-Roig formalisms”
Biopolymers 41, 495-509 (1997)
Bruix, M, Muñoz, V., Campos-Olivas, R, del Bosque, J.R., Serrano, L. and Rico L.
“Characterisation of the isolated Che Y C-terminal fragment (79-129)--Exploring the structure/stability/folding
relationship of the alpha/beta parallel protein Che Y”
Eur. J. of Biochem. 243, 384-392 (1997)
Blanco, F.J., Ortiz, A.R. & Serrano, L.
“1H and 15N-NMR assignment and solution structure of the SH3 domain of spectrin. Comparison with the
crystal structure”
J. of Biomol. NMR. 9, 347-357 (1997)
Blanco, F.J., Ortiz, A.R. & Serrano, L.
“Role of a nonnative interaction in the folding of the protein G B1 domain as inferred from the conformational
analysis of the alpha-helix fragment”
Folding & Design 2, 123-133 (1997)

Ramirez-Alvarado, M., Serrano, L. & Blanco, F.J.
“Conformational analysis of peptides corresponding to all the secondary structure elements of protein L B1
domain: Secondary structure propensities are not conserved in proteins with the same fold”
Protein Sci. 6, 1-13 (1997)
Prieto, J., Wilmanns, M., Jimenez, M.A., Rico, M. & Serrano, L.
“Non-native interactions in protein folding and stability: Introducing a helical tendency in the all beta-sheet
alpha-spectrin SH3 domain”
J. Mol. Biol. 268, 760-778 (1997)
Prieto, J. & Serrano, L.
“C-capping and Helix stability: The Pro C-capping motif”
J. Mol. Biol. 274, 276-288 (1997)
Viguera, A.R. & Serrano, L.
“Loop length, intramolecular diffusion and protein folding”
Nat. Struct. Biol. 4, 939-946 (1997)
Ramírez-Alvarado, M., Blanco, F.J, Niemann, H. & Serrano, L
“Role of beta-turn residues in beta-hairpin formation and stability in designed peptides”
J. Mol. Biol. 273, 898-912 (1997)
Lacroix E, Bruix M, Lopez-Hernandez E, Serrano L, & Rico M
“Amide hydrogen exchange and internal dynamics in the chemotactic protein CheY from Escherichia coli”
J Mol Biol 271, 472-487 (1997)
1998

Blanco F, Ramirez-Alvarado M , Serrano L.
“Formation and stability of beta-hairpin structures in polypeptides”
Curr Opin Struct Biol 8, 107-111 (1998)
Blanco FJ, Serrano L , Forman-Kay JD.
“High Populations of Non-native Structures in the Denatured State are Compatible with the Formation of the
Native Folded State”
J Mol Biol 284, 1153-1164 (1998)
Kortemme T, Ramirez-Alvarado M , Serrano L.
“Design of a 20-amino acid, three-stranded beta-sheet protein”
Science 281, 253-256 (1998)
Lacroix E, Viguera AR , Serrano L.
“Elucidating the Folding Problem of alpha-Helices: Local Motifs, Long- range Electrostatics, Ionic-strength
Dependence and Prediction of NMR Parameters”
J Mol Biol 284, 173-191 (1998)

Lacroix E, Viguera AR , Serrano L
“Reading protein sequences backwards”
Fold Des 3, 79-85 (1998)
Martinez JC, Pisabarro MT , Serrano L.
“Obligatory steps in protein folding and the conformational diversity of the transition state”
Nat Struct Biol 5, 721-729 (1998)
Petukhov M, Munoz V, Yumoto N, Yoshikawa S , Serrano L.
“Position dependence of non-polar amino acid intrinsic helical propensities”
J Mol Biol 278, 279-289 (1998)
Pisabarro MT, Serrano L , Wilmanns M.
“Crystal structure of the abl-SH3 domain complexed with a designed high- affinity peptide ligand:
implications for SH3-ligand interactions”
J Mol Biol 281, 513-521 (1998)
Ramirez-Alvarado M, Daragan VA, Serrano L , Mayo KH.
“Motional dynamics of residues in a beta-hairpin peptide measured by 13C- NMR relaxation”
Protein Sci 7, 720-729 (1998)
Vazquez MI, Rivas G, Cregut D, Serrano L , Esteban M
“The vaccinia virus 14-kilodalton (A27L) fusion protein forms a triple coiled-coil structure and interacts with
the 21-kilodalton (A17L) virus membrane protein through a C-terminal alpha-helix [In Process Citation]”
J Virol 72, 10126-10137 (1998)
Villegas V, Martinez JC, Aviles FX , Serrano L.
“Structure of the transition state in the folding process of human procarboxypeptidase A2 activation domain
[In Process Citation]”
J Mol Biol 283, 1027-1036 (1998)
Wilcock D, Pisabarro MT, Lopez-Hernandez E, Serrano L , Coll M.
“Structure analysis of two CheY mutants: importance of the hydrogen-bond contribution to protein stability
[In Process Citation]”
Acta Crystallogr D Biol Crystallogr 54, 378-385 (1998)
1999

Blanco, F. J., Angrand, I. & Serrano, L.
“Exploring the conformational properties of the sequence space between two proteins with different folds: an
experimental study”
J Mol Biol 285(2), 741-753 (1999)
Cregut, D., Civera, C., Macias, M. J., Wallon, G. & Serrano, L.
“A tale of two secondary structure elements: when a beta-hairpin becomes an alpha-helix” J Mol Biol 292(2), 389-401 (1999) Cregut, D. & Serrano, L. “Molecular dynamics as a tool to detect protein foldability. A mutant of domain B1 of protein G with non-native secondary structure propensities” Protein Sci 8(2), 271-282 (1999) Domingues, H., Cregut, D., Sebald, W., Oschkinat, H. & Serrano, L. “Rational design of a GCN4-derived mimetic of interleukin-4” Nat Struct Biol 6(7), 652-656 (1999) Filimonov, V. V., Azuaga, A. I., Viguera, A. R., Serrano, L. & Mateo, P. L. “A thermodynamic analysis of a family of small globular proteins: SH3 domains” Biophys Chem 77(2-3), 195-208 (1999) Lacroix, E., Kortemme, T., Lopez de la Paz, M. & Serrano, L “The design of linear peptides that fold as monomeric beta-sheet structures” Curr Opin Struct Biol 9(4), 487-493 (1999) Martinez, J. C. & Serrano, L. “The folding transition state between SH3 domains is conformationally restricted and evolutionarily conserved” Nat Struct Biol 6(11), 1010-1016 (1999) Martinez, J. C., Viguera, A. R., Berisio, R., Wilmanns, M., Mateo, P. L., Filimonov, V. V. & Serrano, L. “Thermodynamic analysis of alpha-spectrin SH3 and two of its circular permutants with different loop lengths: discerning the reasons for rapid folding in proteins” Biochemistry 38(2), 549-559 (1999) Petukhov, M., Cregut, D., Soares, C. M. & Serrano, L. “Local water bridges and protein conformational stability [In Process Citation]” Protein Sci 8(10), 1982-1989 (1999) Petukhov, M., Uegaki, K., Yumoto, N., Yoshikawa, S. & Serrano, L. “Position dependence of amino acid intrinsic helical propensities II: non-charged polar residues: Ser, Thr, Asn, and Gln [In Process Citation]” Protein Sci 8(10), 2144-2150 (1999) Ramirez-Alvarado, M., Kortemme, T., Blanco, F. J. & Serrano, L. “Beta-hairpin and beta-sheet formation in designed linear peptides” Bioorg Med Chem 7(1), 93-103 (1999) Sola, M., Gomis-Ruth, F. X., Serrano, L., Gonzalez, A. & Coll, M “Three-dimensional crystal structure of the transcription factor PhoB receiver domain” J Mol Biol 285(2), 675-687 (1999)
Viguera, A. R. & Serrano, L.
“Stable proline box motif at the N-terminal end of alpha-helices [In Process Citation]”
Protein Sci 8(9), 1733-1742 (1999)
2000

Wallon, G., Rappsilber, J., Mann, M. & Serrano, L.
“Model for stathmin/OP18 binding to tubulin”
Embo J 19(2), 213-222 (2000)
Becskei, A. & Serrano, L.
“Nature. Engineering stability in gene networks by autoregulation.”
Nature 405, 590-593 (2000)
Kortemme, T., Kelly, M. J., Kay, L. E., Forman-Kay, J. & Serrano, L.
“Similarities between the spectrin SH3 domain denatured state and its folding transition state”
J Mol Biol 297(5), 1217-1229 (2000)
Serrano, L.
“The relationship between sequence and structure in elementary folding units”
Adv Protein Chem 53, 49-85 (2000)
Taddei, N., Chiti, F., Fiaschi, T., Bucciantini, M., Capanni, C., Stefani, M., Serrano, L., Dobson, C. M. &
Ramponi, G.
“Stabilisation of alpha-helices by site-directed mutagenesis reveals the importance of secondary structure in
the transition state for acylphosphatase folding [In Process Citation]”
J Mol Biol 300(3), 633-647 (2000)
Fernandez, A. M., Villegas, V., Martinez, J. C., Van Nuland, N. A., Conejero-Lara, F., Aviles, F. X., Serrano,
L., Filimonov, V. V. & Mateo, P. L.
"Thermodynamic analysis of helix-engineered forms of the activation domain of human procarboxypeptidase
A2 [In Process Citation]”
Eur J Biochem 267(19), 5891-5899 (2000)
Villegas, V., Zurdo, J., Filimonov, V. V., Aviles, F. X., Dobson, C. M. & Serrano, L.
“Protein engineering as a strategy to avoid formation of amyloid fibrils”
Protein Sci 9(9), 1700-1708 (2000)
Guerois, R. & Serrano, L.
“The SH3-fold family: experimental evidence and prediction of variations in the folding pathways [In Process
Citation]”
J Mol Biol 304(5), 967-982 (2000)
Idiyatullin, D., Krushelnitsky, A., Nesmelova, I., Blanco, F., Daragan, V. A., Serrano, L. & Mayo, K. H.
“Internal motional amplitudes and correlated bond rotations in an alpha- helical peptide derived from 13C
and 15N NMR relaxation.[In Process Citation]”
Protein Sci 9(11), 2118-2127 (2000)
Sola, M., Lopez-Hernandez, E., Cronet, P., Lacroix, E., Serrano, L., Coll, M. & Parraga, A.
“Towards understanding a molecular switch mechanism: thermodynamic and crystallographic studies of the
signal transduction protein cheY [In Process Citation]”
J Mol Biol 303(2), 213-225 (2000)
Westerholm-Parvinen, A., Vernos, I. & Serrano, L.
“Kinesin subfamily UNC104 contains a FHA domain: boundaries and physicochemical characterization”
FEBS Lett 486(3), 285-290 (2000)
Domingues, H., J. Peters, et al.
"Improving the refolding yield of interleukin-4 through the optimization of local interactions."
J Biotechnol 84(3), 217-230 (2000)
Guerois, R. and L. Serrano
"The SH3-fold family: experimental evidence and prediction of variations in the folding pathways."
J Mol Biol 304(5), 967-982 (2000)
Vega, M. C., J. C. Martinez, et al.
"Thermodynamic and structural characterization of Asn and Ala residues in the disallowed II' region of the
Ramachandran plot."
Protein Sci 9(12), 2322-2328 (2000)
Westerholm-Parvinen, A., I. Vernos, et al.
"Kinesin subfamily UNC104 contains a FHA domain: boundaries and physicochemical characterization."
FEBS Lett 486(3), 285-290 (2000)
2001

Berisio, R. R., Viguera, A. A., Serrano, L. L. & Wilmanns, M. M.
“Atomic resolution structure of a mutant of the spectrin SH3 domain. Acta Crystallogr D”
Biol Crystallogr 57 (Pt2), 337-340 (2001)
Guerois, R. & Serrano, L.
“Protein design based on folding models”
Curr Opin Struct Biol 11(1), 101-106 (2001)
Fisinger, S., L. Serrano, et al.
"Computational estimation of specific side chain interaction energies in alpha helices."
Protein Sci 10(4), 809-818 (2001)
Garcia, P., L. Serrano, et al.
"NMR and SAXS characterization of the denatured state of the chemotactic protein CheY: implications for
protein folding initiation."
Protein Sci 10(6), 1100-1112 (2001)
Viguera, A. R. and L. Serrano
"Bergerac-SH3: "frustation" induced by stabilizing the folding nucleus."
J Mol Biol 311(2), 357-371 (2001)
Becskei, A., B. Seraphin, et al.
"Positive feedback in eukaryotic gene networks: cell differentiation by graded to binary response
conversion."
Embo J 20(10), 2528-2535 (2001)
Guerois, R. and L. Serrano
"Protein design based on folding models."
Curr Opin Struct Biol 11(1), 101-106 (2001)
Lopez de la Paz, M., E. Lacroix, et al.
"Computer-aided design of beta-sheet peptides."
J Mol Biol 312(1), 229-246 (2001)
Ramirez-Alvarado, M., F. J. Blanco, et al.
"Elongation of the BH8 beta-hairpin peptide: Electrostatic interactions in beta-hairpin formation and stability."
Protein Sci 10(7), 1381-1392 (2001)
Choma CT, Tieleman DP, Cregut D, Serrano L, Berendsen HJ.
“Towards the design and computational characterization of a membrane protein.”
J Mol Graph Model. 20(3), 219-234 (2001)
2002

Garcia, P., L. Serrano, et al.
"An NMR view of the folding process of a CheY mutant at the residue level."
Structure (Camb) 10(9), 1173-1185 (2002)
2003

Viguera, A. R. and L. Serrano
"Hydrogen-exchange stability analysis of Bergerac-Src homology 3 variants allows the characterization of a
folding intermediate in equilibrium."
Proc Natl Acad Sci U S A 100(10), 5730-5735 (2003)
2004

de la Paz, M. L. and L. Serrano
"Sequence determinants of amyloid fibril formation."
Proc Natl Acad Sci U S A 101(1), 87-92 (2004)
Kiel, C., L. Serrano, et al.
"A detailed thermodynamic analysis of ras/effector complex interfaces."
J Mol Biol 340(5), 1039-1058 (2004)
Ventura, S. and L. Serrano
"Designing proteins from the inside out."
Proteins 56(1), 1-10 (2004)
Ander, M., Beltrao, P., Di Ventura, B., Ferkinghoff-Borg, J., Foglierini, M., Kaplan, A., Lemerle, C., Tomás-
Oliveira, I. & Serrano, L.
“SmartCell, a framework to simulate cellular processes that combines stochastic approximation with
diffusion and localisation: analysis of simple gene networks”
Systems Biology 1, 129-139 (2004)
2005

Beltrao, P. and L. Serrano
"Comparative Genomics and Disorder Prediction Identify Biologically Relevant SH3 Protein Interactions."
PLoS Comput Biol 1(3), e26 (2005)
Bork, P. and L. Serrano
"Towards cellular systems in 4D."
Cell 121(4), 507-509 (2005)
Esteras-Chopo, A., Serrano, L. & Lopez de la Paz, M.
"The amyloid stretch hypothesis: recruiting proteins toward the dark side".
Proc Natl Acad Sci USA 102, 16672-16677 (2005)
Isalan, M., Lemerle, C. & Serrano, L.
"Engineering gene networks to emulate Drosophila embryonic pattern formation".
PLoS Biol 3, e64 (2005)
Isalan, M., Santori, M. I., Gonzalez, C. & Serrano, L.
"Localized transfection on arrays of magnetic beads coated with PCR products".
Nat Methods 2, 113-118 (2005)
Kiel, C. et al.
"Recognizing and defining true Ras binding domains II: in silico prediction based on homology modelling and
energy calculations".
J Mol Biol 348, 759-775 (2005)
Lemerle, C., Di Ventura, B. & Serrano, L.
"Space as the final frontier in stochastic simulations of biological systems"
FEBS Lett 579, 1789-1794 (2005)
Lopez de la Paz, M., de Mori, G. M., Serrano, L. & Colombo, G. "Sequence dependence of amyloid fibril formation: insights from molecular dynamics simulations". J Mol Biol 349, 583-596 (2005) Maxwell, K. L. et al. "Protein folding: defining a "standard" set of experimental conditions and a preliminary kinetic data set of two-state proteins". Protein Sci 14, 602-616 (2005) Michalodimitrakis, K. M., Sourjik, V. & Serrano, L. "Plasticity in amino acid sensing of the chimeric receptor Taz" Mol Microbiol 58, 257-266 (2005) Neduva, V. et al. "Systematic discovery of new recognition peptides mediating protein interaction networks". PLoS Biol 3, e405 (2005) Reumers, J. et al. "SNPeffect: a database mapping molecular phenotypic effects of human non-synonymous coding SNPs" Nucleic Acids Res 33, D527-D532 (2005) Schymkowitz, J. et al. "The FoldX web server: an online force field". Nucleic Acids Res 33, W382-W388 (2005) Schymkowitz, J. W. et al. "Prediction of water and metal binding sites and their affinities by using the Fold-X force field" Proc Natl Acad Sci U S A 102, 10147-10152 (2005) Wohlgemuth, S. et al. "Recognizing and defining true Ras binding domains I: biochemical analysis" J Mol Biol 348, 741-758 (2005)

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