Kvanteprotein center

Publiceret Januar 2012

Kvanteprotein centeret startede som et Dansk Grundforkningscenter i 2001 med en bevilling på ca 35 millioner, der blev givet for forskning i beregning og experimenter i protein processer, der omhandlede electron strukturer og dynamik både med hensyn til kvantemekaniske og klassiske molekylær dynamiske beregninger sammenholdt med eksperimenter i spektroskopi og mikroskopi.

I disse processer er der udført beregninger over electron strukturer for proteiner, der indgår i gen-reperation og photosynthese processerne ved hjælp af tætheds-functional teori (DFT) metoder og desuden ved hjælp af molekylær mekanik, når solvent molekyler skal indrages i analysen. For at kunne sammenligne teori med experimenter er der udregnet vibrations spektre for mindre peptid molekyler og nukleotider, hvor sidstnævnte direkte indgår i processerne og som til en vis grad kan generatiseres til større proteiner.

Nye teoretiske og eksperimentelle metoder er konstrueret og brugt i analysen af protein processer. Af særlig betydning har været eksperimenter i akustiske tryk forsøg med en resonerende akustisk celle og med enkeltmolekyle spektroskopi ved brug af nanopartiler i Raman spredning og tidsopløst fluorescens spektroskopi.

Desuden er der foretaget kemiske undersøgelser udført parallelt til og sammenholdt med kvantemekaniske beregninger af spektre.

Et stort antal artikler er blevet publiceret over beregninger af vibrationelle spektre af peptider og dele af større proteiner i vandig opløsning. Af de vigtigste resultater kan nævnes:

  1. Konstruktur af en ny teori for fler-elektron processer i fotosyntesen.
  2. Beregninger og spectral analyse af membran proteiner.
  3. Elektroniske processer i metalloproteiner.
  4. SERS (Surface enhanced Raman Scattering) analyse af enkelt molekyler.
  5. Konstruktion af en ny DFT (Tæthedsfunktional teori) baseret på strømme og med magnetfelter, CFT.
  6. Simulering med molekylær dynamik af vandkanal proteinet, Aquaporin

I det følgende gives en mere udførlig gennemgang på engelsk af nogle projekter i vores center.

Research at Quantum Protein Centre

QuP is a research centre at Physics whose primary mission is to calculate electronic structures of proteins and other bio-molecules and then analyze their biological function and carry out relevant experiments in spectroscopy. At QuP we also design new detectors, for e.g. spectroscopy, and have succeeded in designing new vibronic laser instruments for chiral and time-resolved measurements, thus gaining important new knowledge of the structure, dynamics and function of bio molecules. An important aspect of the center is to perform theoretical studies, such as QMMM calculations, on the bio-molecules we study experimentally.

Of research highlights can be mentioned the following:

1. Computational physics and chemistry project: The electronic structure of small peptide molecules in solvent are being calculated by the use of Density Functional Theory. Firstly, classical Molecular Dynamics programs are being used to positioning the solvent molecules and then the electronic orbital states of the various conformational states are being calculated. Finally the Raman scattering and VA/VCD vibrational spectra are being calculated and compared to experimental spectroscopy data [1,2].

2. Project on membrane protein: Using Raman spectroscopy we have been able to study a large complex protein (the Na+K+ ATPase) in its lipid environment and obtained in situ information about conformational changes underlying its catalytic function. Specifically we have shown the structural importance of the 30 amino acid N-terminal part of the sequence in stabilizing the protein [3].

3. Project on protein stability and folding: We have been able to construct a pressure cell for studying protein folding in situ simultaneously at very large pressures. When tested in Raman scattering we observed surprising changes in the internal protein structure [14]. Furthermore we have identified long time modes on H-bonds in proteins using both model calculation and X-ray data [4] and we have seen cation-p effects in integral membrane proteins [3].

4. Project on single-molecule detection: We report on utilizing Surface Enhanced Raman Scattering on small molecules (pentapeptides) as well as on a large protein (Myoglobin) for finding specific vibrational modes that can be used for identifying unique dynamic features shown in the review of [8].

5. Project on transport through channel proteins:A novel technique has been developed to stabilize multiple biometrical membranes for the study of transport properties in membrane channel proteins using fluorescence microscopy integrated into Raman experiments. It is and essential, basic element in the EU-project “Industrial biomimetic water membranes” that received funding and gave rise to the company “Aquaporin” for water rinsing [6,7,8].

6. Project on electronic structures of gene-repair proteins: Quantum mechanical studies of gene repair proteins, e.g. photolyase, where new insight is obtained in the elctronic replenishing process. We developed a theory for radiation-less process, the bio-Auger process. Also a DFT/MD study on Lactam hydrolysis catalyzed by metallo-beta-lactamases gave important results about antibiotics [9].

7. Project on diffusion limited ion-protein interaction dynamics: At the subcellular level functional ion-protein interactions occur due to random encounters between these. We have developed a theoretical modelling framework to describe such interactions between diffusing Ca2+ ions and buffers in connection with synaptic transmission, and will expand the investigation to encompass other ion-protein interactions (for example Zn2+ and metallothionein)[10].

8. Project on electronic structure and processes of photosynthetic complex: A study is about the energy balance in the photosynthetic process and the replenishing of the electrons after being excited by photons. A special process, which we call a Bio-Auger mechanism, similar to the usually known Auger mechanism but at much lower energy, will be able to transfer an electron from an excited state to an even higher level while an outside electron fills the hole arising from the photo-excitation in ground state [11,12].

9. Project on acoustic pressure denaturation and refolding of proteins: A sample cell is designed and constructed to reveal protein dynamics on the nano- to micro-second scale. This is done by sending an acoustic wave through a resonating sample cell of protein in an aqueous solution while monitoring the sample by Raman scattering. The cell is designed so as to be in resonance with a wave of around 1 MHz and above. Such an acoustic wave can generate an oscillating pressure of roughly 25 Bar which has been demonstrated to be enough for partial denaturation [13]. We also made high pressure-jump experiments with fluorescence using a similar cell designed in our lab and where almost full denaturation of proteins at around 1000 bar with time-resolved fluorescence spectre were obtained at faster than µ-sec scales [14].

10. Project on the chiral and topological structure of peptides and proteins: Opiate peptides with different D and L amino-acids are being studied using Molecular Dynamics methods in order to understand their binding to a drug receptor molecule and their functional properties [15]. Also chiral spectroscopy experiments on enantiomer molecules, being e.g. inhibitors to transporter proteins, are studied. Furthermore topological properties of proteins are studied by differential line-geometry providing a topological classification of protein folds based on knot-invariant Gauss integrals [16] and which are used for fold prediction from sequence [17].

Related references:

Jalkanen, K.J., Bohr, H. G. and Suhai, S. in Theoretical and Computational Genome Research, Plenum Press, New York (1997), pp 255-277.

Jalkanen, K., Nieminen, R. M., Frimand, K., Bohr, J., Bohr, H., Wade, R.C. Tajkhorshid, E. and Suhai, S., “A comparison of aqueous solvent models used in the calculation of the Raman and ROA spectra of L-alanine, Chemical Physics 265, 125-151 (2001).

Nielsen, C.H. Abdali, S., Lundbæk, J.A. and Cornelius, F. Raman spectral studies of conformational changes in the sodium potassium ATPase. Spectroscopy (2006).

Austin, RH; Xie, AH; van der Meer, L; Redlich, B; Lindgård, PA; Frauenfelder, H; Fu, D. 2005. Picosecond thermometer in the amide I band of myoglobin. PHYSICAL REVIEW LETTERS 94 (12): art. no.-128101.

Bohr, H.G. and F.B. Malik: ‘Evidence of Auger-like transitions in the repair stage of ultra-violet mutated DNA’, Physics Letters A, 10049 (2006).

Jensen, MØ; Tajkhorshid, E; Schulten, K. (2003). Electrostatic tuning of permeation and selectivity in aquaporin water channels. BIOPHYSICAL JOURNAL 85 (5): 2884-2899.

Tajkhorshid, K.E., Nollert, P., Jensen M.Ø., Miercke, L.J.W., O’Connell, J., RM Stroud, R.M., Schulten, K., Science, 296 (5567), 525 (2002).

Kneipp Katrin; Kneipp Harald; Bohr Henrik G. (2006) Surface-Enhanced Raman Scattering: Physics and applications. Book Series: TOPICS IN APPLIED PHYSICS Volume: 103 Pages: 261-277.

Olsen, L, Antony, J., Ryde, U., Adolph, H.W.; Hemmingsen, L. 2003. “Lactam hydrolysis catalyzed by mononuclear metallo-beta-lactamases”: A density functional study. JOURNAL OF PHYSICAL CHEMISTRY B 107 (10): 2366-2375.

Petersen, FNR; Jensen, MØ; Nielsen CH, “Interfacial Tryptophan Residues: A role for the cation-pi effect?”, Biophysical Journal, 89, 3985-3996.

Bohr, H. Greisen, P. and Malik, F.B. “Excited state processes in Photosynthetic molecules”, Condensed Matter Theories, 23, 329-338 (2009).

Bohr, H. and Malik, F.B., “A schematic model for energy and charge transfer in the chlorophyll complex”, Theoretical Chemistry account, TCA, (2011) 130, 1203-1200.

Abitan, H.A., Lindgaard, P.A., Nielsen, B.G., M.S. Larsen and Bohr, H.G., “Hydration shells exchange charge with their protein”, Journal of Physics, Condensed Matter 22, 365102 (2010).

Dumont, C., Emilsson, T. and Gruebele, M., “Reaching the protein folding speed limit with large, sub-microsecond pressure jumps”, (Use of high-pressure cell from QuP), Nature Methods, 6, 515 (2009).

Nielsen B.G., Jensen, M.Ø., and Bohr, H.G., “The Probability Distribution of Side-chain Conformations in [Leu] and [Met]enkephalin Determines the Potency and Selectivity to µ and ? Opiate Receptors.” Biopolymers 71, 577-92 (2003).

Røgen, P. and Bohr, H.,”A new family of global protein shape descriptors.” Mathematical Biosciences 182, 167-181 (2003).

Nielsen, B.G., Røgen, P. and Bohr, H.G., “Gauss-integral based representation of protein structure for predicting the fold class from sequence”, Mathematical and computer modelling, 43, 401-412 (2006).