Bacia Lab

Research

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                                                          We have positions available in the Bacia lab.
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Membrane remodeling by proteins

Eukaryotic cells have a very complex organization, featuring various, membrane-enclosed internal compartments. As a consequence, ‘cargo’ molecules need to be sorted and transported between these compartments. To facilitate transport, the formation of small vesicles from a donor lipid bilayer is mediated by coat proteins, which interact with the membrane. We are interested in how coat proteins accomplish the process of remodeling a lipid bilayer into a bud and finally into a separate vesicle. Important aspects of budding processes can be artificially reconstituted and studied in vitro using purified proteins and artificial membrane systems.

Schematic view of the formation of a protein-coated vesicle from a lipid bilayer


Advantages of in vitro reconstitution

(Left) Protein purification. (Middle) Confocal microscopy of the COPII coat reconstituted on giant liposomes (from Bacia et al., Sci. Rep. 2013, doi:10.1038/srep00017). Scale bar = 10 µm. (Right) COPII coat structure from cryo electron microscopy (from Zanetti et al., eLife 2013, doi: 10.7554/eLife.00951). Scale bar = 100 nm.
Reconstitution represents a ‘bottom-up’ approach. A complicated biological process is taken apart and the various reactants can subsequently be examined by putting them together in any desired combination. To accomplish this, we express the proteins recombinantly, purify them and add them to artificial lipid bilayers. Among the advantages of using artificial membrane systems compared to biological cells is that we can control the composition of the lipids and choose among different types of spatial configurations. Moreover, artificial systems allow for a more flexible choice of biochemical, biophysical and advanced light and electron microscopy techniques for characterizing the proteins and the lipid environment.


Artificial membrane systems

Liposomes can be prepared in various sizes, ranging from tens of nanometers to tens of micrometers. Reconstitution of integral membrane proteins into liposomes (i.e. the formation of proteoliposomes) as well as the peripheral binding of coat proteins to liposomes is analyzed using both biochemical and biophysical assays.

(A) FCS (fluorescence correlation spectroscopy) analysis of membrane protein reconstitution. The protein carries a fluorescent label. Free protein in solution diffuses fast (red curve), whereas proteoliposomes diffuse much more slowly (purple curve). (B) Biochemical assay for membrane protein reconstitution.


Using dual-color fluorescence cross-correlation spectroscopy (FCCS), the success of membran protein reconstitution can be assessed within minutes. (from Simeonov et al., Biophys. Chem. 2013, doi: 10.1016/j.bpc.2013.08.003)

Dual-color FCCS (see below) allows to obtain quantitative binding curves of protein (or ligand) binding to freely diffusing liposomes (from Kruger et al., BioRxiv 2017, DOI 10.1101/146464 , now published in Biophys. J. 2017, doi: 10.1016/j.bpj.2017.06.023)


Very large liposomes, so-called Giant Unilamellar Vesicles (GUVs), prepared by the electroformation method are on the order of 10 µm in size, making them well-suited for studies by confocal fluorescence microscopy and fluorescence correlation spectroscopy (FCS, see below).

(A) Electroformation setup for producing Giant Unilamellar Vesicle; (B) Dye-labeled Giant Unilamellar Vesicles in a test tube; (C) Confocal slice image of Giant Unilamellar Vesicles

Langmuir monolayers are prepared at the buffer/air interface. The interaction of proteins with the monolayers can be studied using infrared reflection absorption spectroscopy (IRRAS).

Determination of the orientation of the COPII-protein Sar1p at a lipid monolayer by IRRAS (from Schwieger et al., Polymers 2017, doi: 10.3390/polym9110612)


Lipid phase behavior

We are interested in dynamic lateral heterogeneities in membranes from natural components (proteins, lipids) and synthetic components (artificial amphiphiles and polyphiles).
 
Dendritic, star-shaped domains with sixfold symmetry formed in membranes from DPPC and X-shaped bolapolyphiles (from Werner et al., Polymers 2017, doi:10.3390/polym9100476, see also Werner et al., Chem. Eur. J. 2015, doi 10.1002/chem.201405994). The molecular structure of the bolapolyphile influences the domain shape.

Fluorescence correlation spectroscopy (FCS) is a very useful tool for examining mobility and interactions in a variety of systems including membranes. FCS is highly sensitive to small differences in the diffusion rates of proteins and lipids, which allows for instance to characterize differences in phase behavior of lipid bilayers. FCS is used to analyze the binding of diffusible ligands to membrane receptors, such as membrane proteins or glycolipids. Changes in the fluorescence brightness parameter reveal membrane protein oligomerization. Moreover, the use of dual-color fluorescence cross-correlation (dcFCCS) allows to assess protein-protein binding in cases, where binding does not lead to significant changes in diffusion rates. The dual-color cross-correlation technique can also be employed to detect dynamic co-localization of labeled cargo molecules in small, mobile carriers, such as transport vesicles. DcFCCS allows to analyze binding processes with complex stoichiometries, including the binding of proteins to liposomes. Owing to the use of fluorescent labels, FCS is highly specific and can be applied both to artificial, reconstituted systems and directly to living cells.

Parameters accessible by FCS (for details see: Bacia et al., Nat. Methods 2006)

Schematic view of an FCS setup with dual color FCCS capabilityFCS is typically performed on a setup that is similar to a confocal microscope. One or more laser lines are focused in the sample and the fluorescence is collected through the same objective. A pinhole serves to delimit the detection volume. The fluorescence emission(s) from the label(s) are selected by means of emission filter(s) and the fluorescence intensity as a function of time is recorded by avalanche photodiode detectors. Different methods of analysis are available to extract information from the fluorescence fluctuations, which occur as labeled molecule diffuse through the focus. Correlation analysis yields an autocorrelation curve, whose amplitude is inversely related to the concentration of the fluorescent particles. The decay time of the correlation curve reflects the diffusional mobility of the particles. In dual-color FCCS, the relative amplitude of the cross-correlation curve depends on the fraction of double-labeled (i.e., bound) particles.

Principle of FCS and dcFCCS measurements, for details see Bacia et al., Nat. Methods 2006

Equipment

HALOmem is equipped with state-of-the art equipment for protein expression and purification (e.g. Äkta FPLC systems), protein analysis and physico-chemical analysis (FT-IR spectroscopy, dynamic light scattering, Langmuir film balances). Fluorescence correlation spectroscopy (FCS) and related techniques are used for single-molecule-sensitive diffusion and interaction analysis of membrane proteins and lipids in reconstituted membrane systems. Fluorescence auto- and cross-correlation measurements in combination with high sensitivity confocal fluorescence imaging are performed on our Zeiss ConfoCor3/LSM710 setup. TIRF and super-resolution microscopy are carried out on our Zeiss Elyra microscope. Samples for cryo electron microscopy are prepared using our Leica grid plunger and imaged in collaboration with the university imaging facility.

People

See contact page for fax number, mailing address and how to find us on campus.

Telephone numbers: +49-345-55-XXXXX (see below for extensions)

Group leader extension e-mail
Prof. Dr. Kirsten Bacia -24924 .(JavaScript must be enabled to view this email address)
Administrative Assistant
Claudia Hochbach -24830 .(JavaScript must be enabled to view this email address)
Technical Assistant
Claudia Müller -22817 (office) -24813 (lab) .(JavaScript must be enabled to view this email address)
Staff scientists
Dr. Sebastian Daum -22817 (office) -24813 (lab) .(JavaScript must be enabled to view this email address)
PD Dr. Annette Meister -25826 (office) .(JavaScript must be enabled to view this email address)
PhD students
Mona Grimmer -22817 (office) -24816 (lab) .(JavaScript must be enabled to view this email address)
Stefan Werner -24955 (office) .(JavaScript must be enabled to view this email address)
Jan Ebenhan -22817 (office) -24813 (lab) .(JavaScript must be enabled to view this email address)
Students
Paul Czyzykowski -22817 (office) -24813 (lab)

Publications

Poppe S, Poppe M, Ebert H, Prehm M, Chen Ch, Liu F, Werner S, Bacia K, Tschierske C (2017) “Effects of Lateral and Terminal Chains of X-Shaped Bolapolyphiles with Oligo(phenylene ethynylene) Cores on Self-Assembly Behaviour. Part 1: Transition between Amphiphilic and Polyphilic Self-Assembly in the Bulk”. Polymers 9(10), 471, DOI: 10.3390/polym9100471

Werner S, Ebenhan J, Poppe M, Poppe S, Ebert H, Tschierske C, Bacia K (2017) “Effects of Lateral and Terminal Chains of X-Shaped Bolapolyphiles with Oligo(phenylene ethynylene) Cores on Self-Assembly Behavior. Part 2: Domain Formation by Self-Assembly in Lipid Bilayer Membranes”. Polymers 9(10), 476, DOI 10.3390/polym9100476

Schwieger C, Meister A, Daum S, Blume A, Bacia K (2017) “Binding of the GTPase Sar1 to a Lipid Membrane Monolayer: Insertion and Orientation studied by Infrared-Reflection-Absorption Spectroscopy”. Polymers, 9, 612, DOI 10.3390/polym9110612

Krüger D, Ebenhan J, Werner S, Bacia K (2017) “Measuring Protein Binding to Lipid Vesicles by Fluorescence Cross-Correlation Spectroscopy”. Biophys. Journal, Vol. 113, Issue 6, 1311-1320, DOI 10.1016/j.bpj.2017.06.023

Schaller-Laudel S, Latowski D, Jemioła-Rzemińska M, Strzałka K, Daum S, Bacia K, Wilhelm C, Goss R. (2017) “Influence of thylakoid membrane lipids on the structure of aggregated light-harvesting complexes of the diatom Thalassiosira pseudonana and the green alga Mantoniella squamata”. Physiol Plant. 2017 Jul;160(3):339-358, DOI 10.1111/ppl.12565 

Achilles A, Baerenwald R, Lechner BD, Werner S, Ebert H, Tschierske C, Blume A, Bacia K, Saalwaechter K (2016), Self-​Assembly of X-​Shaped Bolapolyphiles in Lipid Membranes: Solid-​State NMR Investigations, Langmuir, 32(3), 673-682,  DOI 10.1021/acs.langmuir.5b03712

Werner S, Ebert H, Lechner BD, Lange F, Achilles A, Bärenwald R, Poppe S, Blume A, Saalwächter K, Tschierske C, Bacia K (2015), “Dendritic Domains with Hexagonal Symmetry Formed by X-Shaped Bolapolyphiles in Lipid Membranes”, Chem. Eur. J., 21: 8840-8850, DOI 10.1002/chem.201405994

Lechner BD, Ebert H, Prehm M, Werner S, Meister A, Hause G, Beerlink A, Saalwächter K, Bacia K, Tschierske C, Blume A (2015), “Temperature-Dependent In-Plane Structure Formation of an X-Shaped Bolapolyphile within Lipid Bilayers”, Langmuir, 31(9):2839-2850, DOI 10.1021/la504903d

Schwieger C, Achilles A, Scholz S, Rüger J, Bacia, K, Saalwächter K, Kressler J, Blume A (2014), ” Binding of amphiphilic and triphilic block copolymers to lipid model membranes: the role of perfluorinated moieties”, Soft Matter, 10(33): 6147-6160, DOI 10.1039/C4SM00830H

Daum S, Krüger D, Meister A, Auerswald J, Prinz S, Briggs JA, Bacia K (2014), “Insights from reconstitution reactions of COPII vesicle formation using pure components and low mechanical perturbation”, Biol Chem, 395(7-8):801-812, DOI 10.1515/hsz-2014-0117

Schulz M, Olubummo A, Bacia K, Binder WH (2014), “Lateral surface engineering of hybrid lipid–BCP vesicles and selective nanoparticle embedding”, Soft Matter, 10(6): 831-839, DOI 10.1039/C3SM52040D

Bacia K (2013) “Intracellular transport mechanisms (Highlight: Nobel Prize for Medicine 2013).”, Angew Chem Int Ed, DOI 10.1002/anie.201308937, Intrazelluläre Transportmechanismen (Highlight: Nobelpreis für Medizin 2013), Angew Chem DOI 10.1002/ange.201308937

Simeonov P, Werner S, Haupt C, Tanabe M, Bacia K (2013), “Membrane Protein Reconstitution into Liposomes Guided by Dual-Color Fluorescence Cross-Correlation Spectroscopy”, Biophys. Chem., DOI 10.1016/j.bpc.2013.08.003, open access

Zanetti G, Prinz S,  Daum S, Meister A, Schekman R, Bacia K, Briggs JAG (2013), “The structure of the COPII transport-vesicle coat assembled on membranes”, eLife, DOI 10.7554/eLife.00951, open access

Schulz M, Werner S, Bacia K, Binder WH (2012), “Controlling Molecular Recognition with Lipid/Polymer Domains in Vesicle Membranes”, Angewandte Chemie Intern. Ed., DOI 10.1002/anie.201204959

Faini M, Prinz S, Beck R, Schorb M, Riches JD, Bacia K, Brügger B, Wieland FT, Briggs JAG (2012), “The Structures of COPI-Coated Vesicles Reveal Alternate Coatomer Conformations and Interactions”, Science, DOI 10.1126/science.1221443

Olubummo A, Schulz M, Lechner BD, Scholtysek P, Bacia K, Blume A, Kressler J, Binder WH (2012), “Controlling the Localization of Polymer-Functionalized Nanoparticles in Mixed Lipid/Polymer Membranes”, ACS Nano, DOI 10.1021/nn3023602

Bacia K, Petrasek Z, Schwille P (2012), “Correcting for Spectral Cross-Talk in Dual-Color Fluorescence Cross-Correlation Spectroscopy”, ChemPhysChem, DOI 10.1002/cphc.201100801, open access

Schulz M, Glatte D, Meister A, Scholtysek P, Kerth A, Blume A, Bacia K, Binder W (2011), “Hybrid lipid/polymer giant unilamellar vesicles: effects of incorporated biocompatible PIB–PEO block copolymers on vesicle properties”, Soft Matter, DOI 10.1039/C1SM05725A

Bacia K, Futai E, Prinz S, Meister A, Daum S, Glatte D, Briggs JAG, Schekman R (2011), “Multibudded tubules formed by COPII on artificial liposomes”, Sci Rep. 1, 17 nature.com/srep open access

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Ewers H, Römer W, Smith AE, Bacia K, Dmitrieff S, Chai W, Mancini R, Kartenbeck J, Chambon V, Berland L, Oppenheim A, Schwarzmann G, Feizi T, Schwille P, Sens P, Helenius A & Johannes L (2010), “GM1 structure determines SV40-induced membrane invagination and infection” Nat Cell Biol. 12(1), 11-18 Pubmed

Bacia K, Haustein E & Schwille P, “Fluorescence Correlation Spectroscopy: Principles and Applications”, Chapter 39 (p. 609) in: Imaging: A Laboratory Manual, Cold Spring Harbor Laboratory Press, 2010, ed. Rafael Yuste, ISBN 978-0879699352

Schön P, García-Sáez AJ, Malovrh P, Bacia K, Anderluh G & Schwille P (2008), “Equinatoxin II permeabilizing activity depends on the presence of sphingomyelin and lipid phase coexistence.” Biophys J. 95(2),691-698 Pubmed

Bacia K & Schwille P (2007), “Fluorescence correlation spectroscopy.” Methods Mol Biol. 398, 73-84 Pubmed

Bacia K & Schwille P (2007), “Practical guidelines for dual-color fluorescence cross-correlation spectroscopy.” Nat Protoc. 2(11), 2842-2856 Pubmed

Becker CF, Seidel R, Jahnz M, Bacia K, Niederhausen T, Alexandrov K, Schwille P, Goody RS& Engelhard M (2006), “C-terminal fluorescence labeling of proteins for interaction studies on the single-molecule level.” Chembiochem. 7(6), 891-895 Pubmed

Bacia K, Kim SA & Schwille P (2006), “Fluorescence cross-correlation spectroscopy in living cells.” Nat Methods. 3(2), 83-89 Pubmed

Kim SA, Heinze KG, Bacia K, Waxham MN & Schwille P (2005), “Two-photon cross-correlation analysis of intracellular reactions with variable stoichiometry.” Biophys J. 88(6), 4319-4336 Pubmed

Bacia K, Schwille P & Kurzchalia T (2005), “Sterol structure determines the separation of phases and the curvature of the liquid-ordered phase in model membranes.” Proc Natl Acad Sci U S A. 102(9), 3272-3277 Pubmed

Schwille P, Kahya N & Bacia K, “Protein and Lipid Partitioning in Locally Heterogeneous Model Membranes”, Chapter 14 (p. 337) in: Protein-Lipid Interactions, Wiley-VCH, 2005, ed. Lukas K. Tamm, ISBN 978-3527311514

Bacia K, Scherfeld D, Kahya N & Schwille P (2004), “Fluorescence correlation spectroscopy relates rafts in model and native membranes.” Biophys J. 87(2), 1034-1043 Pubmed

Bacia K, Schuette CG, Kahya N, Jahn R & Schwille P (2004), “SNAREs prefer liquid-disordered over “raft” (liquid-ordered) domains when reconstituted into giant unilamellar vesicles.” J Biol Chem. 279(36), 37951-37955 Pubmed

Kahya N, Scherfeld D, Bacia K & Schwille P (2004), “Lipid domain formation and dynamics in giant unilamellar vesicles explored by fluorescence correlation spectroscopy.” J Struct Biol. 147(1), 77-89 Pubmed

Kahya N, Scherfeld D, Bacia K, Poolman B & Schwille P (2003), “Probing lipid mobility of raft-exhibiting model membranes by fluorescence correlation spectroscopy.” J Biol Chem. 278(30), 28109-28115 Pubmed

Bacia K & Schwille P (2003), “A dynamic view of cellular processes by in vivo fluorescence auto- and cross-correlation spectroscopy.” Methods. 29(1), 74-85 Pubmed

Bacia K, Majoul IV & Schwille P (2002), “Probing the endocytic pathway in live cells using dual-color fluorescence cross-correlation analysis.” Biophys J. 83(2), 1184-1193 Pubmed

Keyhani NO, Bacia K & Roseman S (2000), “The transport/phosphorylation of N,N’-diacetylchitobiose in Escherichia coli. Characterization of phospho-IIB(Chb) and of a potential transition state analogue in the phosphotransfer reaction between the proteins IIA(Chb) AND IIB(Chb).” J Biol Chem. 275(42), 33102-33109 Pubmed