1
|
Sahtoe DD, Coscia A, Mustafaoglu N, Miller LM, Olal D, Vulovic I, Yu TY, Goreshnik I, Lin YR, Clark L, Busch F, Stewart L, Wysocki VH, Ingber DE, Abraham J, Baker D. Transferrin receptor targeting by de novo sheet extension. Proc Natl Acad Sci U S A 2021; 118:e2021569118. [PMID: 33879614 PMCID: PMC8092486 DOI: 10.1073/pnas.2021569118] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The de novo design of polar protein-protein interactions is challenging because of the thermodynamic cost of stripping water away from the polar groups. Here, we describe a general approach for designing proteins which complement exposed polar backbone groups at the edge of beta sheets with geometrically matched beta strands. We used this approach to computationally design small proteins that bind to an exposed beta sheet on the human transferrin receptor (hTfR), which shuttles interacting proteins across the blood-brain barrier (BBB), opening up avenues for drug delivery into the brain. We describe a design which binds hTfR with a 20 nM Kd, is hyperstable, and crosses an in vitro microfluidic organ-on-a-chip model of the human BBB. Our design approach provides a general strategy for creating binders to protein targets with exposed surface beta edge strands.
Collapse
Affiliation(s)
- Danny D Sahtoe
- Department of Biochemistry, University of Washington, Seattle, WA 98195
- Institute for Protein Design, University of Washington, Seattle, WA 98195
- HHMI, University of Washington, Seattle, WA 98195
| | - Adrian Coscia
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115
| | - Nur Mustafaoglu
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA 02115
| | - Lauren M Miller
- Department of Biochemistry, University of Washington, Seattle, WA 98195
- Institute for Protein Design, University of Washington, Seattle, WA 98195
| | - Daniel Olal
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115
| | - Ivan Vulovic
- Department of Biochemistry, University of Washington, Seattle, WA 98195
- Institute for Protein Design, University of Washington, Seattle, WA 98195
| | - Ta-Yi Yu
- Institute for Protein Design, University of Washington, Seattle, WA 98195
- Department of Bioengineering, University of Washington, Seattle, WA 98195
| | - Inna Goreshnik
- Department of Biochemistry, University of Washington, Seattle, WA 98195
- Institute for Protein Design, University of Washington, Seattle, WA 98195
| | - Yu-Ru Lin
- Department of Biochemistry, University of Washington, Seattle, WA 98195
- Institute for Protein Design, University of Washington, Seattle, WA 98195
| | - Lars Clark
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115
| | - Florian Busch
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
| | - Lance Stewart
- Department of Biochemistry, University of Washington, Seattle, WA 98195
- Institute for Protein Design, University of Washington, Seattle, WA 98195
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
| | - Donald E Ingber
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA 02115
- Department of Surgery and Vascular Biology Program, Harvard Medical School and Boston Children's Hospital, Boston, MA 02115
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02539
| | - Jonathan Abraham
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115;
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195;
- Institute for Protein Design, University of Washington, Seattle, WA 98195
- HHMI, University of Washington, Seattle, WA 98195
| |
Collapse
|
2
|
Hsia Y, Mout R, Sheffler W, Edman NI, Vulovic I, Park YJ, Redler RL, Bick MJ, Bera AK, Courbet A, Kang A, Brunette TJ, Nattermann U, Tsai E, Saleem A, Chow CM, Ekiert D, Bhabha G, Veesler D, Baker D. Design of multi-scale protein complexes by hierarchical building block fusion. Nat Commun 2021; 12:2294. [PMID: 33863889 PMCID: PMC8052403 DOI: 10.1038/s41467-021-22276-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 02/08/2021] [Indexed: 12/13/2022] Open
Abstract
A systematic and robust approach to generating complex protein nanomaterials would have broad utility. We develop a hierarchical approach to designing multi-component protein assemblies from two classes of modular building blocks: designed helical repeat proteins (DHRs) and helical bundle oligomers (HBs). We first rigidly fuse DHRs to HBs to generate a large library of oligomeric building blocks. We then generate assemblies with cyclic, dihedral, and point group symmetries from these building blocks using architecture guided rigid helical fusion with new software named WORMS. X-ray crystallography and cryo-electron microscopy characterization show that the hierarchical design approach can accurately generate a wide range of assemblies, including a 43 nm diameter icosahedral nanocage. The computational methods and building block sets described here provide a very general route to de novo designed protein nanomaterials.
Collapse
Affiliation(s)
- Yang Hsia
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Biological Physics, Structure and Design Graduate Program, University of Washington, Seattle, WA, USA
| | - Rubul Mout
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - William Sheffler
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Natasha I Edman
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Ivan Vulovic
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Molecular Engineering Graduate Program, University of Washington, Seattle, WA, USA
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Rachel L Redler
- Department of Cell Biology and Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA
| | - Matthew J Bick
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Asim K Bera
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Alexis Courbet
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Alex Kang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - T J Brunette
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Una Nattermann
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Biological Physics, Structure and Design Graduate Program, University of Washington, Seattle, WA, USA
| | - Evelyn Tsai
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Ayesha Saleem
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Cameron M Chow
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Damian Ekiert
- Department of Cell Biology and Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA
- Department of Microbiology, New York University School of Medicine, New York, NY, USA
| | - Gira Bhabha
- Department of Cell Biology and Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
| |
Collapse
|
3
|
Divine R, Dang HV, Ueda G, Fallas JA, Vulovic I, Sheffler W, Saini S, Zhao YT, Raj IX, Morawski PA, Jennewein MF, Homad LJ, Wan YH, Tooley MR, Seeger F, Etemadi A, Fahning ML, Lazarovits J, Roederer A, Walls AC, Stewart L, Mazloomi M, King NP, Campbell DJ, McGuire AT, Stamatatos L, Ruohola-Baker H, Mathieu J, Veesler D, Baker D. Designed proteins assemble antibodies into modular nanocages. Science 2021; 372:eabd9994. [PMID: 33795432 PMCID: PMC8592034 DOI: 10.1126/science.abd9994] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 11/23/2020] [Accepted: 02/10/2021] [Indexed: 12/11/2022]
Abstract
Multivalent display of receptor-engaging antibodies or ligands can enhance their activity. Instead of achieving multivalency by attachment to preexisting scaffolds, here we unite form and function by the computational design of nanocages in which one structural component is an antibody or Fc-ligand fusion and the second is a designed antibody-binding homo-oligomer that drives nanocage assembly. Structures of eight nanocages determined by electron microscopy spanning dihedral, tetrahedral, octahedral, and icosahedral architectures with 2, 6, 12, and 30 antibodies per nanocage, respectively, closely match the corresponding computational models. Antibody nanocages targeting cell surface receptors enhance signaling compared with free antibodies or Fc-fusions in death receptor 5 (DR5)-mediated apoptosis, angiopoietin-1 receptor (Tie2)-mediated angiogenesis, CD40 activation, and T cell proliferation. Nanocage assembly also increases severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pseudovirus neutralization by α-SARS-CoV-2 monoclonal antibodies and Fc-angiotensin-converting enzyme 2 (ACE2) fusion proteins.
Collapse
MESH Headings
- Angiopoietins/chemistry
- Angiopoietins/immunology
- Angiopoietins/metabolism
- Antibodies/chemistry
- Antibodies/immunology
- Antibodies, Monoclonal/chemistry
- Antibodies, Monoclonal/immunology
- Antibodies, Neutralizing/chemistry
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/chemistry
- Antibodies, Viral/immunology
- B-Lymphocytes/immunology
- CD40 Antigens/chemistry
- CD40 Antigens/immunology
- CD40 Antigens/metabolism
- Cell Line, Tumor
- Cell Proliferation
- Computer Simulation
- Genes, Synthetic
- Humans
- Immunoglobulin Fc Fragments/chemistry
- Lymphocyte Activation
- Models, Molecular
- Nanostructures
- Protein Binding
- Protein Engineering
- Receptor, TIE-2/metabolism
- Receptors, TNF-Related Apoptosis-Inducing Ligand/immunology
- Receptors, TNF-Related Apoptosis-Inducing Ligand/metabolism
- SARS-CoV-2/immunology
- Signal Transduction
- T-Lymphocytes/immunology
- T-Lymphocytes/physiology
Collapse
Affiliation(s)
- Robby Divine
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Ha V Dang
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - George Ueda
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Jorge A Fallas
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Ivan Vulovic
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - William Sheffler
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Shally Saini
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
| | - Yan Ting Zhao
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
- Oral Health Sciences, School of Dentistry, University of Washington, Seattle, WA 98195, USA
| | - Infencia Xavier Raj
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
| | | | - Madeleine F Jennewein
- Vaccines and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98019, USA
| | - Leah J Homad
- Vaccines and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98019, USA
| | - Yu-Hsin Wan
- Vaccines and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98019, USA
| | - Marti R Tooley
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Franziska Seeger
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Ali Etemadi
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Medical Biotechnology Department, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences (TUMS), Tehran, Iran
| | | | - James Lazarovits
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Alex Roederer
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Lance Stewart
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Mohammadali Mazloomi
- Medical Biotechnology Department, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences (TUMS), Tehran, Iran
| | - Neil P King
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | | | - Andrew T McGuire
- Vaccines and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98019, USA
- Department of Global Health, University of Washington, Seattle, WA 98195, USA
| | - Leonidas Stamatatos
- Vaccines and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98019, USA
- Department of Global Health, University of Washington, Seattle, WA 98195, USA
| | - Hannele Ruohola-Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
| | - Julie Mathieu
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
- Department of Comparative Medicine, University of Washington, Seattle, WA 98195, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| |
Collapse
|
4
|
Divine R, Dang HV, Ueda G, Fallas JA, Vulovic I, Sheffler W, Saini S, Zhao YT, Raj IX, Morawski PA, Jennewein MF, Homad LJ, Wan YH, Tooley MR, Seeger F, Etemadi A, Fahning ML, Lazarovits J, Roederer A, Walls AC, Stewart L, Mazloomi M, King NP, Campbell DJ, McGuire AT, Stamatatos L, Ruohola-Baker H, Mathieu J, Veesler D, Baker D. Designed proteins assemble antibodies into modular nanocages. bioRxiv 2020:2020.12.01.406611. [PMID: 33299994 PMCID: PMC7724662 DOI: 10.1101/2020.12.01.406611] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Antibodies are widely used in biology and medicine, and there has been considerable interest in multivalent antibody formats to increase binding avidity and enhance signaling pathway agonism. However, there are currently no general approaches for forming precisely oriented antibody assemblies with controlled valency. We describe the computational design of two-component nanocages that overcome this limitation by uniting form and function. One structural component is any antibody or Fc fusion and the second is a designed Fc-binding homo-oligomer that drives nanocage assembly. Structures of 8 antibody nanocages determined by electron microscopy spanning dihedral, tetrahedral, octahedral, and icosahedral architectures with 2, 6, 12, and 30 antibodies per nanocage match the corresponding computational models. Antibody nanocages targeting cell-surface receptors enhance signaling compared to free antibodies or Fc-fusions in DR5-mediated apoptosis, Tie2-mediated angiogenesis, CD40 activation, and T cell proliferation; nanocage assembly also increases SARS-CoV-2 pseudovirus neutralization by α-SARS-CoV-2 monoclonal antibodies and Fc-ACE2 fusion proteins. We anticipate that the ability to assemble arbitrary antibodies without need for covalent modification into highly ordered assemblies with different geometries and valencies will have broad impact in biology and medicine.
Collapse
Affiliation(s)
- Robby Divine
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Ha V. Dang
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - George Ueda
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Jorge A. Fallas
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Ivan Vulovic
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - William Sheffler
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Shally Saini
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
| | - Yan Ting Zhao
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
- Oral Health Sciences, School of Dentistry, University of Washington, Seattle, WA 98195, USA
| | - Infencia Xavier Raj
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
| | | | - Madeleine F. Jennewein
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA, USA
| | - Leah J. Homad
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA, USA
| | - Yu-Hsin Wan
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA, USA
| | - Marti R. Tooley
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Franzika Seeger
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Ali Etemadi
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Medical Biotechnology Department, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences (TUMS), Tehran, Iran
| | | | - James Lazarovits
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Alex Roederer
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Alexandra C. Walls
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Lance Stewart
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Mohammadali Mazloomi
- Medical Biotechnology Department, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences (TUMS), Tehran, Iran
| | - Neil P. King
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | | | - Andrew T. McGuire
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA, USA
- University of Washington, Department of Global Health, Seattle, WA, USA
| | - Leonidas Stamatatos
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA, USA
- University of Washington, Department of Global Health, Seattle, WA, USA
| | - Hannele Ruohola-Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
| | - Julie Mathieu
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
- Department of Comparative Medicine, University of Washington, Seattle, WA 98195, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| |
Collapse
|
5
|
Towse CL, Hopping G, Vulovic I, Daggett V. Nature versus design: the conformational propensities of D-amino acids and the importance of side chain chirality. Protein Eng Des Sel 2014; 27:447-55. [PMID: 25233851 PMCID: PMC4204638 DOI: 10.1093/protein/gzu037] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 08/04/2014] [Accepted: 08/11/2014] [Indexed: 11/12/2022] Open
Abstract
D-amino acids are useful building blocks for de novo peptide design and they play a role in aging-related diseases associated with gradual protein racemization. For amino acids with achiral side chains, one should be able to presume that the conformational propensities of L- and D-amino acids are a reflection of one another due to the straightforward geometric inversion at the Cα atom. However, this presumption does not account for the directionality of the backbone dipole and the inverted propensities have never been definitively confirmed in this context. Furthermore, there is little known of how alternative side chain chirality affects the backbone conformations of isoleucine and threonine. Using a GGXGG host-guest pentapeptide system, we have completed exhaustive sampling of the conformational propensities of the D-amino acids, including D-allo-isoleucine and D-allo-threonine, using atomistic molecular dynamics simulations. Comparison of these simulations with the same systems hosting the cognate L-amino acids verifies that the intrinsic backbone conformational propensities of the D-amino acids are the inverse of their cognate L-enantiomers. Where amino acids have a chiral center in their side chain (Thr, Ile) the β-configuration affects the backbone sampling, which in turn can confer different biological properties.
Collapse
Affiliation(s)
- Clare-Louise Towse
- Department of Bioengineering, University of Washington, Seattle, WA 98195-5013, USA
| | - Gene Hopping
- Department of Bioengineering, University of Washington, Seattle, WA 98195-5013, USA
| | - Ivan Vulovic
- Department of Bioengineering, University of Washington, Seattle, WA 98195-5013, USA
| | - Valerie Daggett
- Department of Bioengineering, University of Washington, Seattle, WA 98195-5013, USA
| |
Collapse
|