DNA-Directed Protein Packing within Single Crystals

Peter H. Winegar; Oliver G. Hayes; Janet R. McMillan; C. Adrian Figg; Pamela J. Focia; Chad A. Mirkin

doi:10.1016/j.chempr.2020.03.002

DNA-Directed Protein Packing within Single Crystals

Peter H. Winegar, Oliver G. Hayes, Janet R. McMillan, C. Adrian Figg, Pamela J. Focia, Chad A. Mirkin^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

21 Scopus citations

Abstract

Designed DNA-DNA interactions are investigated for their ability to modulate protein packing within single crystals of mutant green fluorescent proteins (mGFPs) functionalized with a single DNA strand (mGFP-DNA). We probe the effects of DNA sequence, length, and protein-attachment position on the formation and protein packing of mGFP-DNA crystals. Notably, when complementary mGFP-DNA conjugates are introduced to one another, crystals form with nearly identical packing parameters, regardless of sequence if the number of bases is equivalent. DNA complementarity is essential, because experiments with non-complementary sequences produce crystals with different protein arrangements. Importantly, the DNA length and its position of attachment on the protein markedly influence the formation of and protein packing within single crystals. This work shows how designed DNA interactions can be used to influence the growth and packing in X-ray diffraction quality protein single crystals and is thus an important step forward in protein crystal engineering.

Original language	English (US)
Pages (from-to)	1007-1017
Number of pages	11
Journal	Chem
Volume	6
Issue number	4
DOIs	https://doi.org/10.1016/j.chempr.2020.03.002
State	Published - Apr 9 2020

Funding

The authors would like to acknowledge support from the Vannevar Bush Faculty Fellowship program sponsored by the Basic Research Office of the Assistant Secretary of Defense for Research and Engineering and funded by the Office of Naval Research through grant N00014-15-1-0043, as well as support from the Air Force Office of Scientific Research under award FA9550-17-1-0348. We acknowledge staff and instrumentation support from the Structural Biology Facility at Northwestern University, the Robert H Lurie Comprehensive Cancer Center of Northwestern University, and NCI CCSG P30 CA060553. This research used resources of the Advanced Photon Source, a U.S. Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under contract no. DE-AC02-06CH11357. Use of the LS-CAT Sector 21 was supported by the Michigan Economic Development Corporation and the Michigan Technology Tri-Corridor (grant 085P1000817). This study utilized the Recombinant Protein Production Core at Northwestern University. A part of this work was performed in the Northwestern University High-Throughput Analysis Laboratory. This work made use of the IMSERC at Northwestern University, which has received support from the Soft and Hybrid Nanotechnology Experimental (SHyNE) Resource (NSF ECCS-1542205), the State of Illinois, and the International Institute for Nanotechnology (IIN). Molecular graphics created with UCSF Chimera, were developed by the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco, with support from NIH P41-GM103311. J.R.M. gratefully acknowledges the National Science and Engineering Research Council of Canada for a Postgraduate Fellowship. Conceptualization, P.H.W. O.G.H. J.R.M. C.A.F. and C.A.M.; Investigation, P.H.W. O.G.H. J.R.M. C.A.F. and P.J.F.; Writing ? Original Draft, P.H.W. O.G.H. J.R.M. C.A.F. and C.A.M.; Writing ? Review and Editing, P.H.W. O.G.H. J.R.M. C.A.F. P.J.F. and C.A.M.; Funding Acquisition, C.A.M. The following patent is related to this work: PCT/US19/65078 Protein Crystal Engineering through DNA Hybridization Interactions. The authors would like to acknowledge support from the Vannevar Bush Faculty Fellowship program sponsored by the Basic Research Office of the Assistant Secretary of Defense for Research and Engineering and funded by the Office of Naval Research through grant N00014-15-1-0043 , as well as support from the Air Force Office of Scientific Research under award FA9550-17-1-0348 . We acknowledge staff and instrumentation support from the Structural Biology Facility at Northwestern University , the Robert H Lurie Comprehensive Cancer Center of Northwestern University , and NCI CCSG P30 CA060553 . This research used resources of the Advanced Photon Source, a U.S. Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under contract no. DE-AC02-06CH11357. Use of the LS-CAT Sector 21 was supported by the Michigan Economic Development Corporation and the Michigan Technology Tri-Corridor (grant 085P1000817 ). This study utilized the Recombinant Protein Production Core at Northwestern University. A part of this work was performed in the Northwestern University High-Throughput Analysis Laboratory. This work made use of the IMSERC at Northwestern University, which has received support from the Soft and Hybrid Nanotechnology Experimental (SHyNE) Resource (NSF ECCS-1542205 ), the State of Illinois, and the International Institute for Nanotechnology (IIN). Molecular graphics created with UCSF Chimera, were developed by the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco, with support from NIH P41-GM103311 . J.R.M. gratefully acknowledges the National Science and Engineering Research Council of Canada for a Postgraduate Fellowship.

Keywords

DNA
SDG9: Industry, innovation, and infrastructure
crystal engineering
programmable interactions
protein
protein crystallography
protein packing
protein-DNA

ASJC Scopus subject areas

General Chemistry
Biochemistry
Environmental Chemistry
General Chemical Engineering
Biochemistry, medical
Materials Chemistry

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10.1016/j.chempr.2020.03.002

Cite this

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title = "DNA-Directed Protein Packing within Single Crystals",

abstract = "Designed DNA-DNA interactions are investigated for their ability to modulate protein packing within single crystals of mutant green fluorescent proteins (mGFPs) functionalized with a single DNA strand (mGFP-DNA). We probe the effects of DNA sequence, length, and protein-attachment position on the formation and protein packing of mGFP-DNA crystals. Notably, when complementary mGFP-DNA conjugates are introduced to one another, crystals form with nearly identical packing parameters, regardless of sequence if the number of bases is equivalent. DNA complementarity is essential, because experiments with non-complementary sequences produce crystals with different protein arrangements. Importantly, the DNA length and its position of attachment on the protein markedly influence the formation of and protein packing within single crystals. This work shows how designed DNA interactions can be used to influence the growth and packing in X-ray diffraction quality protein single crystals and is thus an important step forward in protein crystal engineering.",

keywords = "DNA, SDG9: Industry, innovation, and infrastructure, crystal engineering, programmable interactions, protein, protein crystallography, protein packing, protein-DNA",

author = "Winegar, {Peter H.} and Hayes, {Oliver G.} and McMillan, {Janet R.} and Figg, {C. Adrian} and Focia, {Pamela J.} and Mirkin, {Chad A.}",

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doi = "10.1016/j.chempr.2020.03.002",

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AU - Winegar, Peter H.

AU - Hayes, Oliver G.

AU - McMillan, Janet R.

AU - Figg, C. Adrian

AU - Focia, Pamela J.

AU - Mirkin, Chad A.

PY - 2020/4/9

Y1 - 2020/4/9

N2 - Designed DNA-DNA interactions are investigated for their ability to modulate protein packing within single crystals of mutant green fluorescent proteins (mGFPs) functionalized with a single DNA strand (mGFP-DNA). We probe the effects of DNA sequence, length, and protein-attachment position on the formation and protein packing of mGFP-DNA crystals. Notably, when complementary mGFP-DNA conjugates are introduced to one another, crystals form with nearly identical packing parameters, regardless of sequence if the number of bases is equivalent. DNA complementarity is essential, because experiments with non-complementary sequences produce crystals with different protein arrangements. Importantly, the DNA length and its position of attachment on the protein markedly influence the formation of and protein packing within single crystals. This work shows how designed DNA interactions can be used to influence the growth and packing in X-ray diffraction quality protein single crystals and is thus an important step forward in protein crystal engineering.

AB - Designed DNA-DNA interactions are investigated for their ability to modulate protein packing within single crystals of mutant green fluorescent proteins (mGFPs) functionalized with a single DNA strand (mGFP-DNA). We probe the effects of DNA sequence, length, and protein-attachment position on the formation and protein packing of mGFP-DNA crystals. Notably, when complementary mGFP-DNA conjugates are introduced to one another, crystals form with nearly identical packing parameters, regardless of sequence if the number of bases is equivalent. DNA complementarity is essential, because experiments with non-complementary sequences produce crystals with different protein arrangements. Importantly, the DNA length and its position of attachment on the protein markedly influence the formation of and protein packing within single crystals. This work shows how designed DNA interactions can be used to influence the growth and packing in X-ray diffraction quality protein single crystals and is thus an important step forward in protein crystal engineering.

KW - DNA

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KW - protein packing

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DNA-Directed Protein Packing within Single Crystals

Abstract

Funding

Keywords

ASJC Scopus subject areas

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Crystal Structure of C148 mGFP-cDNA-1

Crystal Structure of C148 mGFP-cDNA-3

Crystal Structure of C176 mGFP

Cite this

DNA-Directed Protein Packing within Single Crystals

Abstract

Funding

Keywords

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Datasets

Crystal Structure of C148 mGFP-cDNA-1

Crystal Structure of C148 mGFP-cDNA-3

Crystal Structure of C176 mGFP

Cite this