Opportunities and challenges for assigning cofactors in cryo-EM density maps of chlorophyll-containing proteins

Christopher J. Gisriel; Jimin Wang; Gary W. Brudvig; Donald A. Bryant

doi:10.1038/s42003-020-01139-1

Opportunities and challenges for assigning cofactors in cryo-EM density maps of chlorophyll-containing proteins

Christopher J. Gisriel, Jimin Wang, Gary W. Brudvig, Donald A. Bryant

Biochemistry & Molecular Biology

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

19 Scopus citations

Abstract

The accurate assignment of cofactors in cryo-electron microscopy maps is crucial in determining protein function. This is particularly true for chlorophylls (Chls), for which small structural differences lead to important functional differences. Recent cryo-electron microscopy structures of Chl-containing protein complexes exemplify the difficulties in distinguishing Chl b and Chl f from Chl a. We use these structures as examples to discuss general issues arising from local resolution differences, properties of electrostatic potential maps, and the chemical environment which must be considered to make accurate assignments. We offer suggestions for how to improve the reliability of such assignments.

Original language	English (US)
Article number	408
Journal	Communications Biology
Volume	3
Issue number	1
DOIs	https://doi.org/10.1038/s42003-020-01139-1
State	Published - Dec 1 2020

All Science Journal Classification (ASJC) codes

Medicine (miscellaneous)
Biochemistry, Genetics and Molecular Biology(all)
Agricultural and Biological Sciences(all)

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10.1038/s42003-020-01139-1

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title = "Opportunities and challenges for assigning cofactors in cryo-EM density maps of chlorophyll-containing proteins",

abstract = "The accurate assignment of cofactors in cryo-electron microscopy maps is crucial in determining protein function. This is particularly true for chlorophylls (Chls), for which small structural differences lead to important functional differences. Recent cryo-electron microscopy structures of Chl-containing protein complexes exemplify the difficulties in distinguishing Chl b and Chl f from Chl a. We use these structures as examples to discuss general issues arising from local resolution differences, properties of electrostatic potential maps, and the chemical environment which must be considered to make accurate assignments. We offer suggestions for how to improve the reliability of such assignments.",

author = "Gisriel, {Christopher J.} and Jimin Wang and Brudvig, {Gary W.} and Bryant, {Donald A.}",

note = "Funding Information: This work was supported by National Science Foundation grant MCB-1613022 to D.A.B., Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences grant DE-FG02-05ER15646 to G.W.B., and the Forest B.H. and Elizabeth D.W. Brown Postdoctoral Fellowship for Plant Science to C.J.G. We thank Professors Peter Moore (Yale University) and Juliette Lecomte (Johns Hopkins University) for critical commentaries on our manuscript during its preparation. Publisher Copyright: {\textcopyright} 2020, The Author(s).",

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AU - Bryant, Donald A.

N1 - Funding Information: This work was supported by National Science Foundation grant MCB-1613022 to D.A.B., Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences grant DE-FG02-05ER15646 to G.W.B., and the Forest B.H. and Elizabeth D.W. Brown Postdoctoral Fellowship for Plant Science to C.J.G. We thank Professors Peter Moore (Yale University) and Juliette Lecomte (Johns Hopkins University) for critical commentaries on our manuscript during its preparation. Publisher Copyright: © 2020, The Author(s).

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N2 - The accurate assignment of cofactors in cryo-electron microscopy maps is crucial in determining protein function. This is particularly true for chlorophylls (Chls), for which small structural differences lead to important functional differences. Recent cryo-electron microscopy structures of Chl-containing protein complexes exemplify the difficulties in distinguishing Chl b and Chl f from Chl a. We use these structures as examples to discuss general issues arising from local resolution differences, properties of electrostatic potential maps, and the chemical environment which must be considered to make accurate assignments. We offer suggestions for how to improve the reliability of such assignments.

AB - The accurate assignment of cofactors in cryo-electron microscopy maps is crucial in determining protein function. This is particularly true for chlorophylls (Chls), for which small structural differences lead to important functional differences. Recent cryo-electron microscopy structures of Chl-containing protein complexes exemplify the difficulties in distinguishing Chl b and Chl f from Chl a. We use these structures as examples to discuss general issues arising from local resolution differences, properties of electrostatic potential maps, and the chemical environment which must be considered to make accurate assignments. We offer suggestions for how to improve the reliability of such assignments.

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Opportunities and challenges for assigning cofactors in cryo-EM density maps of chlorophyll-containing proteins

Abstract

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