Selected Peer-reviewed Publications

Click here to see a current listing of Dr. Ramírez-Alvarado's publications.

• Ramírez-Alvarado, M., Blanco, F. J., and Serrano, L. (1996) De novo design and structural analysis of a model b-hairpin peptide system. Nat. Struct. Biol., 3, 604-612.
• Ramírez-Alvarado, M., Serrano, L., and Blanco, F. J. (1997) 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 Science, 6, 162-174.
• Ramírez-Alvarado, M., Blanco, F. J., Niemann, H., and Serrano, L. (1997) Role of b-turn residues in b-hairpin formation and stability in designed peptides. J. Mol., Biol., 273, 898-912.
• Blanco, F.J., Ramírez-Alvarado, M., and Serrano, L. (1998) Formation and stability of b-hairpin structures in polypeptides. Curr. Opinion Struct. Biol., 8, 107-111.
• Ramírez-Alvarado, M., Daragan, V. A., Serrano, L., and Mayo, K. H. (1998) Motional dynamics of residues in a b-hairpin peptide measured by 13C-NMR relaxation. Protein Science 7, 720-729.
• Ramírez-Alvarado, M.*, Kortemme, T.*, and Serrrano, L. (1998) Design of a 20-amino acid, three-stranded b-sheet protein. Science, 281, 253-256. *Two first authors
• Ramírez-Alvarado, M., Kortemme, T., Blanco, F. J., and Serrano, L. (1999) b-hairpin and b-sheet formation in designed linear peptides. Bioorganic and Medicinal Chemistry, 7, 93-103.
• Ramírez-Alvarado, M., Merkel, J. S., and Regan, L. (2000) A systematic exploration of the influence of the protein stability on amyloid fibril formation in vitro. Proc. Natl. Acad. Sci. USA, 97, 8979-8984.
• Nesmelova, I., Krushelnitsky, A., Idiyatullin, D., Blanco, F., Ramírez-Alvarado, M., Daragan, V.A., Serrano, L., and Mayo, K.H. (2001) Conformational exchange on the microseocond time scale in alpha helix and beta-hairpin peptides measured by (13)C NMR transverse relaxation. Biochemistry 40, 2844-53
• Ramírez-Alvarado, M., Blanco, F. J., and Serrano, L. (2001) Elongation of the BH8 b-hairpin peptide: Electrostatic interactions in b-hairpin formation and stability. Protein Science, 7, 1381-1392.
• López de la Paz, M., Lacroix, E., Ramírez-Alvarado, M., and Serrano, L. (2001) Computer aided design of b-sheets. J. Mol. Biol. 312, 229-246.
• Ramírez-Alvarado, M., and Regan, L. (2002) Does the location of a mutation determine the ability to form amyloid fibrils? J. Mol. Biol. 323, 17-22.
• Ramírez-Alvarado, M., Cocco, M. J., and Regan, L. (2003) Mutations in the B1 domain of protein G that delay the onset of amyloid fibril formation in vitro. Protein Science, 12, 567-76.
• Khurana, R., Ionescu-Zanetti, C., Pope, M., Li, J., Nielson, L., Ramírez-Alvarado, M., Regan, L., Fink, A. L., and Carter, S. A. (2003) A general model for amyloid fibril assembly based on morphological studies using atomic force microscopy. Biophys. J. 85, 1135-1144.
• Abraham RS, Geyer SM, Ramirez Alvarado M., Price-Troska TL, Gertz MA, Fonseca R. (2004) Analysis of somatic hypermutation and antigenic selection in the clonal B cell in immunoglobulin light chain amyloidosis (AL). J Clin Immunol. 2004 Jul;24(4):340-53
• Wang, L., Nguyen, T. V., McLaughlin, R. W., Sikkink, L. A., Ramírez-Alvarado, M., and Weinshilboum, R. (2005) Human thiopurine S-methyltransferase pharmacogenetics: variant allozyme misfolding and aggresome formation. Proc. Natl. Acad. Sci. U.S.A., 102:9394-9399.
• Wang, J., Gulich, S., Bradford, C., Ramírez-Alvarado, M., and Regan, L. (2005) A twisted four-sheeted model for an amyloid fibril. Structure,. 13, 1279-1288.
• Carrigan, P. E., Sikkink, L.A., Smith, D.F., Ramírez-Alvarado, M. (2006) Domain:Domain interactions within Hop, the Hsp70/Hsp90 Organizing Protein, Are Required for Protein Stability and Structure. Protein Sci, 15(3):522-32.
• Kandimalla KK, Curran GL, Holasek SS, Gilles EJ, Wengenack TM, Ramirez-Alvarado, M., Poduslo JF. Physiological and biophysical factors that influence Alzheimer's disease amyloid plaque targeting of native and putrescine modified human amyloid beta 40. J Pharmacol Exp Ther 2006 Jul; 318(1):17-25.
• McLaughlin RW, De Stigter JK, Sikkink LA, Baden EM, Ramirez-Alvarado, M.. The effects of sodium sulfate, glycosaminoglycans, and Congo red on the structure, stability, and amyloid formation of an immunoglobulin light-chain protein. Protein Sci 2006 Jul; 15(7):1710-22.
• Ramirez-Alvarado, M., De Stigter, J. K., Baden, E. M., Sikkink, L. A., and McLaughlin, R. W. Immunoglobulin light chain and systemic AL amyloidosis, 2007,in press. (Chapter submitted by invitation to the book “Protein Misfolding, Aggregation and Conformational Diseases” Edited by Uversky and Fink by Springer Publishers).
• Riley, K. Ramirez-Alvarado, M. Maher, L.J. (2007) RNA-p53 interactions in vitro. Biochemistry, 46(9):2480-7. PMID: 17288451
• Poduslo, J. F., Ramakrishnan, M., Holasek, S. S., Ramirez-Alvarado, M., Kandimalla, K., Gilles, E. J., Curran, G. L., Wengenack, T. M. (2007) In vivo Targeting of Antibody Fragments to the Nervous System for Alzheimer’s Disease Immunotherapy and Molecular Imaging of Amyloid Plaques. J. Neurochem 102(2):420-33. PMID: 17596213.
• Sikkink, L.A., Ramirez-Alvarado, M. (2007). Biochemical and Aggregation Analysis of Bence Jones Proteins from Different Light Chain Diseases. Amyloid, in press.
• Sikkink LA, Ramirez-Alvarado, M. Biochemical and aggregation analysis of Bence Jones proteins from different light chain diseases. Amyloid 2008 Mar; 15(1):29-39.
• Sikkink, L.A. and Ramirez-Alvarado, M. (2008) Salts Enhance Both Protein Stability and Amyloid Formation of an Immunoglobulin Light Chain. Biophysical Chemistry, Jun;135(1-3):25-31.
• Baden EM, Owen BA, Peterson FC, Volkman BF, Ramirez-Alvarado, M., Thompson JR. Altered dimer interface decreases stability in an amyloidogenic protein. J Biol Chem 2008 Jun 6; 283(23):15853-60.
• Kaplan B, Ramirez-Alvarado, M., Dispenzieri A, Zeldenrust SR, Leung N, Livneh A, Gallo G. (2008) Isolation and biochemical characterization of plasma monoclonal free light chains in amyloidosis and multiple myeloma: a pilot study of intact and truncated forms of light chains and their charge properties. Clin Chem Lab Med. 46(3):335-41.
• Ramakrishnan, M., Wengenack, T.M., Kandimalla, K.K., Curran, G.L., Gilles, E.J., Ramirez-Alvarado, M., Lin, J., Garwood, Jack, C.R., Poduslo, J.F. (2008) Selective Contrast Enhancement of Individual Alzheimer's Disease Amyloid Plaques Using a Polyamine and Gd-DOTA Conjugated Antibody Fragment Against Fibrillar Abeta42 for Magnetic Resonance Molecular Imaging. Pharm. Res., Apr 29. [Epub ahead of print].
• Arendt, BK, Ramirez-Alvarado, M., Sikkink, LA, Keats, J, Ahmann, GJ, Dispenzieri, A, Fonseca, R, Ketterling, RP, Knudson, RA, Mulvihill, EM, Tschumper, RC, Wu, X, Zeldenrust, SR, and Jelinek, DF. (2008) Biologic and Genetic Characterization of the Novel Amyloidogenic Lambda Light Chain-Secreting Human Cell Lines, ALMC-1 and ALMC-2. Blood, Sep 1;112(5):1931-41.
• Baden, EM, Randles EG, Aboagye, AK, Thompson, JR, Ramirez-Alvarado, M. Structural insights into the role of mutations in amyloidogenesis. (2008) J. Biol. Chem., Sept 2, in press.