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  • High-Resolution NMR Reveals Secondary Structure and Folding of Amino Acid Transporter from Outer Chloroplast Membrane James D. Zook1, Trivikram R. Molugu2, Neil E. Jacobsen2, Guangxin Lin2,3, Jürgen Soll4, Brian R. Cherry1,

    Michael F. Brown2,5, Petra Fromme1*

    1 Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona, United States of America, 2 Department of Chemistry and Biochemistry, University

    of Arizona, Tucson, Arizona, United States of America, 3 Saudi Basic Industries Corporation, Mount Vernon, Indiana, United States of America, 4 Department of Biology,

    Ludwig-Maximilians-University, München, Germany, 5 Department of Physics, University of Arizona, Tucson, Arizona, United States of America

    Abstract

    Solving high-resolution structures for membrane proteins continues to be a daunting challenge in the structural biology community. In this study we report our high-resolution NMR results for a transmembrane protein, outer envelope protein of molar mass 16 kDa (OEP16), an amino acid transporter from the outer membrane of chloroplasts. Three-dimensional, high- resolution NMR experiments on the 13C, 15N, 2H-triply-labeled protein were used to assign protein backbone resonances and to obtain secondary structure information. The results yield over 95% assignment of N, HN, CO, Ca, and Cb chemical shifts, which is essential for obtaining a high resolution structure from NMR data. Chemical shift analysis from the assignment data reveals experimental evidence for the first time on the location of the secondary structure elements on a per residue basis. In addition T1Z and T2 relaxation experiments were performed in order to better understand the protein dynamics. Arginine titration experiments yield an insight into the amino acid residues responsible for protein transporter function. The results provide the necessary basis for high-resolution structural determination of this important plant membrane protein.

    Citation: Zook JD, Molugu TR, Jacobsen NE, Lin G, Soll J, et al. (2013) High-Resolution NMR Reveals Secondary Structure and Folding of Amino Acid Transporter from Outer Chloroplast Membrane. PLoS ONE 8(10): e78116. doi:10.1371/journal.pone.0078116

    Editor: Oleg Y. Dmitriev, University of Saskatchewan, Canada

    Received October 26, 2012; Accepted September 16, 2013; Published October 29, 2013

    This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.

    Funding: This work was supported by the U.S. National Institutes of Health (GM095583 to P.F. and EY012049 and EY018891 to M.F.B). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

    Competing Interests: Although one of the authors is currently employed by the commercial company ‘‘SABIC,’’ all contributions to this work including data collection and evaluation was performed while under the employment of the University of Arizona, Tucson. The authors include this information for purposes of transparency. This does not alter the authors’ adherence to all the PLOS ONE policies on sharing data and materials.

    * E-mail: pfromme@asu.edu

    Introduction

    Integral membrane proteins are a rapidly growing field of

    interest in structural biology and biochemistry. They are

    responsible for a plethora of cell functions, ranging from energy

    generation by enzymes involved in respiration and photosynthesis

    such as ATP synthase [1], to cell signaling as shown by the large

    number of integral membrane receptors [2]. However, structure

    determination of these proteins remains a formidable challenge.

    While most of the 300 structures of membrane proteins solved so

    far are determined by X-ray diffraction, crystallization is difficult

    and is a major bottleneck for solving membrane structures [3,4].

    Improvements in magnetic resonance technology provide new

    methods as a powerful tool for in-depth analysis of the structure

    and function of membrane proteins. Although nuclear magnetic

    resonance (NMR) spectroscopy shows great promise in the field of

    structure determination, it remains a challenge for membrane

    proteins for several reasons. One such hurdle involves obtaining

    high yields of isotope-enriched proteins that are structurally stable

    in detergent micelles at concentrations high enough to produce

    adequate signal to noise. A further challenge is specific to proteins

    that are largely a-helical (as seen by many transmembrane proteins), which display spectra that have a narrow chemical shift

    dispersion in the 1H dimension. This narrow 1H dispersion,

    combined with the increased number of residues present in larger

    membrane proteins, yields a problem with regard to peak overlap

    in high-resolution NMR spectra. Yet another obstacle to consider

    is the necessity of solubilizing the protein in detergent micelles,

    which are used to maintain protein structural integrity. This

    increase in size of the complex results in slower rotational

    averaging, and therefore decreased transverse relaxation times [5].

    One integral membrane protein that has shown promise as a

    target for NMR study is the outer envelope protein with a

    molecular mass of 16 kDa (OEP16) from the chloroplast

    membrane [6]. OEP16 is a transmembrane (TM) protein that

    shares some sequence homologies (52%) to a putative protein from

    the mitochondrial membrane translocase of the inner membrane

    (TIM) that may be part of the protein translocase complex

    (UniProtKB Accession number: ABF95523.1). Notably, OEP16 is

    located within the outer membrane of chloroplasts, and forms a

    channel for selective diffusion of amino acids into the intermem-

    brane space. This pore-forming protein is remarkably selective,

    and may supply the chloroplast organelle with the amino acids for

    use in protein expression [7]. The first structural information for

    OEP16 was based on hydropathy plots from the amino acid

    PLOS ONE | www.plosone.org 1 October 2013 | Volume 8 | Issue 10 | e78116

  • sequence and circular dichroism (CD) experiments in phosphati-

    dylcholine liposomes [7]. These studies hypothesized that OEP16

    may consist of three TM helices with the N-terminus of the protein

    forming a b-sheet [7,8]. A later model suggested a four TM-helix bundle [9], which contrasts with the textbook view that nearly all

    outer membrane channels form b-barrels. Yet improved CD spectral data support the four-helix bundle hypothesis [6]. Dimers

    have been considered from cross-linking studies [7]; electron

    micrographs have led to the suggestion of trimer formation [10];

    and moreover hexameric and higher oligomeric forms have been

    hypothesized from gel filtration data [6].

    This paper reports the results of NMR experiments for OEP16

    in sodium dodecyl sulfate (SDS) detergent micelles. High yields of

    recombinantly expressed 15N-enriched OEP16 in minimal media

    have been previously reported [6]. These results give a starting

    point for expression and purification of the uniformly 15N, 13C, 2H-labeled protein needed for 3D NMR experiments. We show

    the first experimental evidence for how the protein traverses the

    membrane, and how the individual amino acid residues contribute

    to the secondary structure of the protein. We establish that OEP16

    consists of four TM helices and identify the residues for helix

    formation. Relaxation measurements report on intramolecular

    dynamics [11,12], and help to estimate the isotropic global

    correlation time that provides insight into the multimeric state of

    the protein, which is under debate in the literature. Chemical shift

    perturbation is used to elucidate the residues that are responsible

    for the selectivity and diffusion of amino acid molecules through

    OEP16. Results of this study reveal nearly complete assignment of

    the N, H, CO, Ca, and Cb chemical shifts, which is essential for a

    NMR high-resolution structure. In addition, a functional study

    performed via arginine titration provides data that reveals specific

    ligand binding to OEP16.

    Materials and Methods

    Protein Expression and Purification For the NMR experiments, U-13C,15N-labeled and 80%

    perdeuterated recombinant OEP16 was expressed by using a

    slightly modified procedure compared to Ni et al. [6]. A 5-mL

    preculture was prepared in Lysogeny Broth (LB) media that was

    allowed to incubate at 310 K overnight, shaking at 200 rpm. The

    preculture was added directly to a 1-L culture of M9 media, with 15N-ammonium chloride as the sole 15N-nitrogen source and 13C-

    glucose as the sole 13C-carbon source. Perdeuteration was

    achieved by growing the cells in 80% 2H2O solution. For

    experiments only requiring 15N-labeled protein, cell growth was

    performed in a similar manner without perdeuteration, employing 15N-ammonium chloride as the sole nitrogen source, and non-

    enriched D-glucose as the carbon source.

    Protein expression was induced at OD600 = 0.8 using 1 mM

    isopropyl-b-D-1-thiogalactopyranoside (IPTG) [6], and allowing it to incubate for an additional 5 h. Purification and reconstitution of

    OEP16