title: The energy landscape of a selective tumor-homing pentapeptide.
abstract: Recently, a potentially powerful strategy based on phage-display libraries has been presented to target tumors via homing peptides attached to nanoparticles. The Cys-Arg-Glu-Lys-Ala (CREKA) peptide sequence has been identified as a tumor-homing peptide that binds to clotted plasmas proteins present in tumor vessels and interstitium. The aim of this work consists of mapping the conformational profile of CREKA to identify the bioactive conformation. For this purpose, a conformational search procedure based on modified simulated annealing combined with molecular dynamics was applied to three systems that mimic the experimentally used conditions: (i) the free peptide; (ii) the peptide attached to a nanoparticle; and (iii) the peptide inserted in a phage display protein. In addition, the free peptide was simulated in an ionized aqueous solution environment, which mimics the ionic strength of the physiological medium. Accessible minima of all simulated systems reveal a multiple interaction pattern involving the ionized side chains of Arg, Glu, and Lys, which induces a beta-turn motif in the backbone observed in all simulated CREKA systems.
authors.affiliation: Departament d'Enginyeria Química, E. T. S. d'Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, Barcelona E-08028, Spain. david.zanuy@upc.edu
authors.forename: David
authors.initials: D
authors.lastname: Zanuy
authors.forename: Alejandra
authors.initials: A
authors.lastname: Flores-Ortega
authors.forename: Jordi
authors.initials: J
authors.lastname: Casanovas
authors.forename: David
authors.initials: D
authors.lastname: Curcó
authors.forename: Ruth
authors.initials: R
authors.lastname: Nussinov
authors.forename: Carlos
authors.initials: C
authors.lastname: Alemán
mesh_terms: D000595:Amino Acid Sequence; D001120:Arginine / Q000737:chemistry / Q000378:metabolism; D001665:Binding Sites; D003198:Computer Simulation; D018698:Glutamic Acid / Q000737:chemistry / Q000378:metabolism; D008239:Lysine / Q000737:chemistry / Q000378:metabolism; D008969:Molecular Sequence Data; D053758:Nanoparticles / Q000737:chemistry; D009363:Neoplasm Proteins / Q000737:chemistry* / Q000378:metabolism; D009842:Oligopeptides / Q000737:chemistry* / Q000378:metabolism; D010446:Peptide Fragments / Q000737:chemistry* / Q000378:metabolism; D017433:Protein Structure, Secondary; D012996:Solutions / Q000737:chemistry; D013816:Thermodynamics; D013997:Time Factors; D014867:Water / Q000737:chemistry
chemical_list: D009363:Neoplasm Proteins; D009842:Oligopeptides; D010446:Peptide Fragments; D012996:Solutions; D014867:Water; D018698:Glutamic Acid; D001120:Arginine; D008239:Lysine