Self-Reporting Biological Nanosystems to Study and Control Bio-Molecular
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BIOSCOPE Final Publishable Report BIOs cope Project no. NMP4-CT-2003-505211 Project acronym BIOSCOPE Project full name Self-reporting biological nanosystems to study and control bio- molecular mechanisms on the single molecule level Instrument type SPECIFIC TARGETED RESEARCH OR INNOVATION PROJECT Priority name Priority 3: Nanotechnology and nanoscience, knowledge-based multifunctional materials, new production processes and devices (NMP) Final Publishable Report Period covered: from February 1, 2006 to January 31, 2007 Date of preparation: April 19, 2007 Start date of project: Duration: February 1, 2004 36 month Project coordinator name Dr. Tommy Nylander Project coordinator organisation name Revision 2.0 Lund University (Div. Physical Chemistry 1) Page 1 of (26) BIOSCOPE Final Publishable Report BIOs cope www.BIOSCOPE.FKEM1.LU.SE Project execution The aim with BIOSCOPE was to pioneer the development of new leading edge nanoscale research tools and methodologies that will allow unprecedented insight into bio-molecular mechanisms at biological interfaces on the molecular scale. BIOSCOPE consider the biomolecular system itself as a part of the nanoscopic instrument, which in various ways reports to the out-side world about its current local state. Thereby it will be possible to study the local effects on the molecular level when e.g. a protein interacts with a biomembrane surface or when a lipase interacts with a lipid surface. The objectives of BIOSCOPE were: • To develop instrumentation and methods for manipulation of enzymes and enzyme activity at the nanoscale providing insight into the biomolecular mechanisms on a single molecule level. • To develop novel forms of integration, at the nanoscale level, of enzymes and non-biological systems such as nanoparticles, artificial membranes, electrical field or force field traps. • To confine several enzymes to surfaces of nanoparticles or membranes on a less than 10 nm scale in order to achieve a self-organized assembly with a concerted bioaction superior to the simple sum of the same individual enzymes. The function of the nanosystems will be optimized for enzymatic action on biosubstrates. Contractors involved BIOSCOPE is a pan-European consortium where the collective resources both in terms of knowledge in physics, biology, surface and colloid chemistry, synthesis and biochemistry, as well as a combination of a range of experimental techniques reporting on nanoscale organization, theory and modelling will provide the necessary knowledge-base for the new nanoscopic research tools to study bio-molecular mechanisms at interfaces on the single molecular level. Acronym Partner Responsible Main role scientist P1 Physical Chemistry 1, Lund Dr. Tommy How to build structures from ULUND University, Lund, SWEDEN Nylander lipids and showing the structure of nanoscopic objects P2 Nano-Science Center (NSC), Prof. Thomas Showing the effect of UCPH University of Copenhagen, Björnholm enzymes on the substrate on Copenhagen, DENMARK the nanoscopic scale P3 Protein Design, Novozymes A/S, Dr. Allan Building new enzyme Novozymes Bagsvaerd, Denmark Svendsen P4 Laboratory for Photochemistry Prof. Johan Watching very fast changes KUL and Spectroscopy, Katholieke Hofkens in enzymes and changes in University of Leuven, Leuven, the enzymes environment. BELGIUM Measuring the light signal from single enzyme molecule. Page 2 of (26) BIOSCOPE Final Publishable Report Acronym Partner Responsible Main role scientist P5. Centre for Nanoscale Science, Dr. Mathias Making nanosized particles UNILIV Department of Chemistry, The Brust that control enzymes on the University of Liverpool, nanoscopic scale Liverpool, UK P6 Biophysics & Molecular Prof. Hermann Direct measurements of the PHYSLMU Materials, Ludwig-Maximilians- Gaub force a single enzyme Universität, München,Germany molecule feels P7 Institute of Biochemistry, Vilnius, Prof. Making molecules for IBLT LITHUANIA Valdemaras connecting enzymes, enzyme Razumas modification and measuring the electrical signal from enzymes P8 MEMPHYS - Center for Prof. Ole. G. Telling how the properties of SDU Biomembrane Physics, University Mouritsen the soft interface close to the of Southern Denmark Odense, enzyme affect the function of DENMARK the enzyme. Predicting and calculating enzyme and substrate interactions P9 Dep. of Organic Chemistry, Prof. Roeland J. Providing self-assembled KUN Radboud University of Nijmegen, M. Nolte supra-molecular structures THE NETHERLANDS for determining single enzyme molecule action mechanisms Co-ordinator contact details Dr. Tommy Nylander Physical Chemistry 1, Lund University, Center for Chemistry and Chemical Engineering, P.O.Box 124, S-221 00 Lund, SWEDEN Email: [email protected] Phone: +46 46 2228158; Fax: +46 46 2224413 Summary of results BIOSCOPE has provided insight of the biomolecular mechanisms on a single molecule level. This has been made using two approaches: Confocal Microscopy: This is powerful tool to study the activity of single, but it requires that the ezyme is immobilized and does not work for natural substrates. The single enzyme experiment of CalB adsorbed to a hydrophobic surface (Velonia, 2005; Flomenbom, 2005) and TLL linked to the BSA foot labelled with fluorescent probe was studied (Hazitakis, 2006). The waiting times Dt between peaks (bursts of activity) contains the kinetic information. In fact the distribution of waiting times shows non- exponential behavior (Flamenbom, 2006). The appearance of a stretched exponential function implies that the number of conformations is large. This shows that the reaction rate constant, k, is not constant with time, that is TLL shows an oscillating behavior adopting a variety of interconnecting conformations (Figure 1). In fact one might talk of an enzyme molecule that sleeps and works (Engelkamp, 2006). Wide field microscopy: This technique can be used on natural substrates and accounts for the fact that the activity of the enzyme can be affected by its diffusion and vice versa. This method requires imaging of a large area, which means loss of Page 3 of (26) BIOSCOPE Final Publishable Report resolution. The used approach in BIOSCOPE involves two lasers, one for the labelled enzyme and the labelled substrate layer, with minimal overlap in wavelength of laser wavelength and that of the emitted light (Verheijen, 2006; Hofkens, unpublished data, 2007). The movement of the single enzyme molecule could be followed by analysing the mean square displacement versus time. It was possible to follow the hydrolysis of phospholipid layer by means of fluorescence microscopy and simultaneously track single molecules of enzyme (single molecule resolution) acting on phospholipid layers and to monitor the changes in the phospholipids layers (not single molecule resolution). The results indicate that the enzyme docks on the layer for just short periods of time. Figure 1. Schematic figure of the different interconnecting conformations of TLL, which in turn have different rate constant for the hydrolysis of the substrate. BIOSCOPE has developed new concepts for integration (linkers) and reporting at the nanoscale-level of enzymes and non-biological systems. A range of variants of Thermomyces lanuginosus lipase (TLL), but also of Candida antarctica lipase B (CalB), mostly for binding signalling, either binding or action, or attachment to surfaces has been prepared. This has been essential for all the bioconjugated system produced within BIOSCOPE. These two lipases has also been the main enzymes used in the work, but some work also includes Phospholipase A2 (PLA or PLA2) In the past there has been a lack of reporter molecules that report on the activity of lipase and at the same time are amphiphilic and self-assembling as the natural substrate for lipases. This challenge has been met by BIOSCOPE by producing lipid like probes (Valincius, 2005; Ignatjev, 2005; Bulovas, 2006), supported bilayers (Simonsen, 2004) as well as well defined lipid based liquid crystalline nanoparticles (Barauskas, 2006; Popescu 2007). In many cases the synthesised substrates can be detected by electrochemical methods (redox activity) as well as optical methods such Page 4 of (26) BIOSCOPE Final Publishable Report as UV/VIS and fluorescence spectroscopy. Some of the key components of these amphiphilic and self-assembling substrates are presented in Figure 2a. Figure 2a. Examples of reporter molecules, e.g. substrates for lipase, which can report on the enzymatic activity at different type of interfaces. Apart from profluorescent substrate study of single molecule enzyme activity requires some sort of immobilization of the enzyme. Several approaches have been developed for this purpose involving Direct covalent immobilization as well as Non-specific deposition. Some of the approaches used in BIOSCOPE are summarized in Figure 2b (Dirks, 2005; Hazitakis, 2006; Engelkamp, 2006). Clickable Maleimides Clickable Enzymes-Proteins O O O O BSA S O N3 O BSA S O N3 O Clickable dyes O O CALB S CALB S N O N3 O O O O N3 O S O H H NH TLL N SH TLL N O OH Clickable Surface Clickable Surface Clickable polymers and N3 N3 block-copolymers O O O O OH OH OH OH OH N N N N HO 3 N O 3 3 O 3 75 75 75 O HSi HSi HSi HSi HSi HSi HSi O O O O N3 N3 O O O O O O O O O O O O O O O 40 40 Figure 2b. Different linker approaches that have been developed during BIOSCOPE, by KUN. They can be used both to couple to surfaces as well as to form Enzyme dimers. The two new electrochemical (amperometric) techniques to determine the lipase activity have been