Title: How Outer Coordination Sphere Modifications Can Impact Metal Structures in Proteins: A Crystallographic Evaluation

Abstract

A challenging objective of de novo metalloprotein design is to control of the outer coordination spheres of an active site to fine tune metal properties. The well-defined three stranded coiled coils, TRI and CoilSer peptides, are used to address this question. Substitution of Cys for Leu yields a thiophilic site within the core. Metals such as Hg^II, Pb^II, and AsIII result in trigonal planar or trigonal pyramidal geometries; however, spectroscopic studies have shown that Cd^II forms three-, four- or five-coordinate Cd^IIS₃(OH₂)_x (in which x=0–2) when the outer coordination spheres are perturbed. Unfortunately, there has been little crystallographic examination of these proteins to explain the observations. Here, the high-resolution X-ray structures of apo- and mercurated proteins are compared to explain the modifications that lead to metal coordination number and geometry variation. It reveals that Ala substitution for Leu opens a cavity above the Cys site allowing for water excess, facilitating Cd^IIS₃(OH₂). Replacement of Cys by Pen restricts thiol rotation, causing a shift in the metal-binding plane, which displaces water, forming CdIIS₃. Residue d-Leu, above the Cys site, reorients the side chain towards the Cys layer, diminishing the space for water accommodation yielding Cd^IIS₃, whereas d-Leu below opens more space, allowing formore » equal Cd^IIS₃(OH₂) and Cd^IIS₃(OH₂)₂. These studies provide insights into how to control desired metal geometries in metalloproteins by using coded and non-coded amino acids.« less

Authors:

Ruckthong, Leela  ^[1];

• Search DOE PAGES for author "Ruckthong, Leela"
• Search DOE PAGES for ORCID "0000-0001-9352-2534"

Stuckey, Jeanne A.  ^[2];

• Search DOE PAGES for author "Stuckey, Jeanne A."
• Search DOE PAGES for ORCID "0000-0002-4192-8900"

Pecoraro, Vincent L.  ^[3]

• Search DOE PAGES for author "Pecoraro, Vincent L."
• Search DOE PAGES for ORCID "0000-0002-1540-5735"

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+ Show Author Affiliations

1. Department of ChemistryUniversity of Michigan Ann Arbor Michigan 48109 USA;Department of ChemistryFaculty of ScienceKing Mongkut's University of Technology, Thonburi (KMUTT), Bang Mod, Thung Khru Bangkok 10140 Thailand
2. Life Sciences InstituteUniversity of Michigan Ann Arbor Michigan 48109 USA;Department of Biological ChemistryUniversity of Michigan Ann Arbor Michigan 48109 USA
3. Department of ChemistryUniversity of Michigan Ann Arbor Michigan 48109 USA

Publication Date:

Thu Apr 25 00:00:00 EDT 2019

Research Org.:

Argonne National Lab. (ANL), Argonne, IL (United States)

Sponsoring Org.:

USDOE Office of Science (SC)

Contributing Org.:

Advanced Photon Source (APS), Argonne National Laboratory (ANL), Argonne, IL (US)

OSTI Identifier:

1542983

Grant/Contract Number:  

AC02–06CH11357

Resource Type:

Accepted Manuscript

Journal Name:

Chemistry - A European Journal

Additional Journal Information:

Journal Volume: 25; Journal Issue: 27; Journal ID: ISSN 0947-6539

Publisher:

ChemPubSoc Europe

Country of Publication:

United States

Language:

ENGLISH

Subject:

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; d-amino acids; de novo protein engineering; metalloprotein engineering; nonnatural amino acids