title: A Protocol for the Design of Protein and Peptide Nanostructure Self-Assemblies Exploiting Synthetic Amino Acids.
abstract: In recent years there has been increasing interest in nanostructure design based on the self-assembly properties of proteins and polymers. Nanodesign requires the ability to predictably manipulate the properties of the self-assembly of autonomous building blocks, which can fold or aggregate into preferred conformational states. The design includes functional synthetic materials and biological macromolecules. Autonomous biological building blocks with available 3D structures provide an extremely rich and useful resource. Structural databases contain large libraries of protein molecules and their building blocks with a range of sizes, shapes, surfaces, and chemical properties. The introduction of engineered synthetic residues or short peptides into these building blocks can greatly expand the available chemical space and enhance the desired properties. Herein, we summarize a protocol for designing nanostructures consisting of self-assembling building blocks, based on our recent works. We focus on the principles of nanostructure design with naturally occurring proteins and synthetic amino acids, as well as hybrid materials made of amyloids and synthetic polymers.
authors.affiliation: Department of Computer Science, The University of Massachusetts Boston, 100 Morrissey Blvd., Boston, MA, 02125, USA. nurit.haspel@umb.edu.
authors.forename: Nurit
authors.initials: N
authors.lastname: Haspel
authors.affiliation: Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, OH, 44325, USA.
authors.forename: Jie
authors.initials: J
authors.lastname: Zheng
authors.affiliation: Departament d'Enginyeria Química, E. T. S. d'Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, 08028, Barcelona, Spain.|Center for Research in Nano-Engineering, Universitat Politècnica de Catalunya, Campus Sud, Edifici C', C/Pasqual i Vila s/n, E-08028, Barcelona, Spain.
authors.forename: Carlos
authors.initials: C
authors.lastname: Aleman
authors.affiliation: Departament d'Enginyeria Química, E. T. S. d'Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, 08028, Barcelona, Spain.
authors.forename: David
authors.initials: D
authors.lastname: Zanuy
authors.affiliation: Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Sackler Inst. of Molecular Medicine, Tel Aviv University, Tel Aviv, 69978, Israel.|Basic Science Program, Leidos Biomedical Research, Inc., Frederick, MD, 21702, USA.|Cancer and Inflammation Program, National Cancer Institute, Frederick, MD, 21702, USA.
authors.forename: Ruth
authors.initials: R
authors.lastname: Nussinov
mesh_terms: D000596:Amino Acids / Q000737:chemistry; D000682:Amyloid / Q000737:chemistry / Q000235:genetics; D003198:Computer Simulation; D030562:Databases, Protein; D008958:Models, Molecular; D009154:Mutation; D049329:Nanostructures; D010455:Peptides / Q000737:chemistry / Q000235:genetics; D011487:Protein Conformation; D015202:Protein Engineering / Q000379:methods*; D011506:Proteins / Q000737:chemistry / Q000235:genetics
chemical_list: D000596:Amino Acids; D000682:Amyloid; D010455:Peptides; D011506:Proteins
keywords: Amyloid peptides; Beta-helical proteins; Computational nanodesign; Hybrid materials; Nanostructures; Peptide-based nanodesign; Self-assembly; Synthetic amino acids