151
|
Gógl G, Biri-Kovács B, Póti ÁL, Vadászi H, Szeder B, Bodor A, Schlosser G, Ács A, Turiák L, Buday L, Alexa A, Nyitray L, Reményi A. Dynamic control of RSK complexes by phosphoswitch-based regulation. FEBS J 2017; 285:46-71. [PMID: 29083550 DOI: 10.1111/febs.14311] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 10/18/2017] [Accepted: 10/25/2017] [Indexed: 12/19/2022]
Abstract
Assembly and disassembly of protein-protein complexes needs to be dynamically controlled and phosphoswitches based on linear motifs are crucial in this process. Extracellular signal-regulated kinase 2 (ERK2) recognizes a linear-binding motif at the C-terminal tail (CTT) of ribosomal S6 kinase 1 (RSK1), leading to phosphorylation and subsequent activation of RSK1. The CTT also contains a classical PDZ domain-binding motif which binds RSK substrates (e.g. MAGI-1). We show that autophosphorylation of the disordered CTT promotes the formation of an intramolecular charge clamp, which efficiently masks critical residues and indirectly hinders ERK binding. Thus, RSK1 CTT operates as an autoregulated phosphoswitch: its phosphorylation at specific sites affects its protein-binding capacity and its conformational dynamics. These biochemical feedbacks, which form the structural basis for the rapid dissociation of ERK2-RSK1 and RSK1-PDZ substrate complexes under sustained epidermal growth factor (EGF) stimulation, were structurally characterized and validated in living cells. Overall, conformational changes induced by phosphorylation in disordered regions of protein kinases, coupled to allosteric events occurring in the kinase domain cores, may provide mechanisms that contribute to the emergence of complex signaling activities. In addition, we show that phosphoswitches based on linear motifs can be functionally classified as ON and OFF protein-protein interaction switches or dimmers, depending on the specific positioning of phosphorylation target sites in relation to functional linear-binding motifs. Moreover, interaction of phosphorylated residues with positively charged residues in disordered regions is likely to be a common mechanism of phosphoregulation. DATABASE Structural data are available in the PDB database under the accession numbers 5N7D, 5N7F and 5N7G. NMR spectral assignation data are available in the BMRB database under the accession numbers 27213 and 27214.
Collapse
Affiliation(s)
- Gergő Gógl
- Department of Biochemistry, ELTE Eötvös Loránd University, Budapest, Hungary.,Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Beáta Biri-Kovács
- Department of Biochemistry, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Ádám L Póti
- Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Henrietta Vadászi
- Department of Biochemistry, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Bálint Szeder
- Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Andrea Bodor
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Gitta Schlosser
- MTA-ELTE Research Group of Peptide Chemistry, Hungarian Academy of Sciences, ELTE Eötvös Loránd University, Budapest, Hungary
| | - András Ács
- MS Proteomics Research Group, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Lilla Turiák
- MS Proteomics Research Group, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - László Buday
- Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Anita Alexa
- Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - László Nyitray
- Department of Biochemistry, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Attila Reményi
- Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| |
Collapse
|
152
|
Yuan H, Zhang J, Cai Y, Wu S, Yang K, Chan HCS, Huang W, Jin WB, Li Y, Yin Y, Igarashi Y, Yuan S, Zhou J, Tang GL. GyrI-like proteins catalyze cyclopropanoid hydrolysis to confer cellular protection. Nat Commun 2017; 8:1485. [PMID: 29133784 PMCID: PMC5684135 DOI: 10.1038/s41467-017-01508-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 09/12/2017] [Indexed: 02/01/2023] Open
Abstract
GyrI-like proteins are widely distributed in prokaryotes and eukaryotes, and recognized as small-molecule binding proteins. Here, we identify a subfamily of these proteins as cyclopropanoid cyclopropyl hydrolases (CCHs) that can catalyze the hydrolysis of the potent DNA-alkylating agents yatakemycin (YTM) and CC-1065. Co-crystallography and molecular dynamics simulation analyses reveal that these CCHs share a conserved aromatic cage for the hydrolytic activity. Subsequent cytotoxic assays confirm that CCHs are able to protect cells against YTM. Therefore, our findings suggest that the evolutionarily conserved GyrI-like proteins confer cellular protection against diverse xenobiotics via not only binding, but also catalysis.
Collapse
Affiliation(s)
- Hua Yuan
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Jinru Zhang
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Yujuan Cai
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Sheng Wu
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Kui Yang
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - H C Stephen Chan
- Faculty of Life Sciences, University of Bradford, Bradford, West Yorkshire, BD7 1DP, UK
| | - Wei Huang
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Wen-Bing Jin
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Yan Li
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Yue Yin
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Yasuhiro Igarashi
- Biotechnology Research Center, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Shuguang Yuan
- Laboratory of Physical Chemistry of Polymers and Membranes, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH B3 495 (Bâtiment CH) Station 6, CH-1015, Lausanne, Switzerland.
| | - Jiahai Zhou
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China.
| | - Gong-Li Tang
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China.
| |
Collapse
|
153
|
Horváth G, Biczók L, Majer Z, Kovács M, Micsonai A, Kardos J, Toke O. Structural insight into a partially unfolded state preceding aggregation in an intracellular lipid-binding protein. FEBS J 2017; 284:3637-3661. [DOI: 10.1111/febs.14264] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 08/15/2017] [Accepted: 09/05/2017] [Indexed: 12/15/2022]
Affiliation(s)
- Gergő Horváth
- Laboratory for NMR Spectroscopy; Research Centre for Natural Sciences; Hungarian Academy of Sciences; Budapest Hungary
| | - László Biczók
- Institute of Materials and Environmental Chemistry; Research Centre for Natural Sciences; Hungarian Academy of Sciences; Budapest Hungary
| | - Zsuzsa Majer
- Institute of Chemistry; Eötvös Loránd University; Budapest Hungary
| | - Mihály Kovács
- Department of Biochemistry; ELTE-MTA ‘Momentum’ Motor Enzymology Research Group; Eötvös Loránd University; Budapest Hungary
| | - András Micsonai
- Department of Biochemistry; MTA-ELTE NAP B Neuroimmunology Research Group; Institute of Biology; Eötvös Loránd University; Budapest Hungary
| | - József Kardos
- Department of Biochemistry; MTA-ELTE NAP B Neuroimmunology Research Group; Institute of Biology; Eötvös Loránd University; Budapest Hungary
| | - Orsolya Toke
- Laboratory for NMR Spectroscopy; Research Centre for Natural Sciences; Hungarian Academy of Sciences; Budapest Hungary
| |
Collapse
|
154
|
Evaluation of the absolute affinity of neuraminidase inhibitor using steered molecular dynamics simulations. J Mol Graph Model 2017; 77:137-142. [PMID: 28854402 DOI: 10.1016/j.jmgm.2017.08.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 08/18/2017] [Accepted: 08/21/2017] [Indexed: 11/20/2022]
Abstract
The absolute free energy difference of binding (ΔG) between neuraminidase and its inhibitor was evaluated using fast pulling of ligand (FPL) method over steered molecular dynamics (SMD) simulations. The metric was computed through linear interaction approximation. Binding nature was described by free energy differences of electrostatic and van der Waals (vdW) interactions. The finding indicates that vdW metric is dominant over electrostatics in binding process. The computed values are in good agreement with experimental data with a correlation coefficient of R=0.82 and error of σΔGexp=2.2kcal/mol. The results were observed using Amber99SB-ILDN force field in comparison with CHARMM27 and GROMOS96 43a1 force fields. Obtained results may stimulate the search for an Influenza therapy.
Collapse
|
155
|
Wang JB, Ilie A, Yuan S, Reetz MT. Investigating Substrate Scope and Enantioselectivity of a Defluorinase by a Stereochemical Probe. J Am Chem Soc 2017; 139:11241-11247. [DOI: 10.1021/jacs.7b06019] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Jian-bo Wang
- Department
of Chemistry, Philipps-University, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany
| | - Adriana Ilie
- Department
of Chemistry, Philipps-University, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany
| | - Shuguang Yuan
- Laboratory
of Physical Chemistry of Polymers and Membranes, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH B3 495 (Bâtiment CH) Station
6, CH-1015 Lausanne, Switzerland
| | - Manfred T. Reetz
- Department
of Chemistry, Philipps-University, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany
| |
Collapse
|
156
|
EGCG inhibits the oligomerization of amyloid beta (16-22) hexamer: Theoretical studies. J Mol Graph Model 2017; 76:1-10. [PMID: 28658644 DOI: 10.1016/j.jmgm.2017.06.018] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Revised: 06/16/2017] [Accepted: 06/19/2017] [Indexed: 11/21/2022]
Abstract
An extensive replica exchange molecular dynamics (REMD) simulation was performed to investigate the progress patterns of the inhibition of (-)-epigallocatechin-3-gallate (EGCG) on the Aβ16-22 hexamer. Structural variations of the oligomers without and with EGCG were monitored and analyzed in detail. It has been found that EGCG prevents the formation of Aβ oligomer through two different ways by either accelerating the Aβ oligomerization or reducing the β-content of the hexamer. It also decreases the potential "highly toxic" conformations of Aβ oligomer, which is related to the conformations having high order β-sheet sizes. Both electrostatic and van der Waals interaction energies are found to be involved to the binding process. Computed results using quantum chemical methods show that the π-π stacking is a critical factor of the interaction between EGCG and the peptides. As a result, the binding free energy of the EGCG to the Aβ peptides is slightly larger than that of the curcumin.
Collapse
|
157
|
Non-linearity of the collagen triple helix in solution and implications for collagen function. Biochem J 2017; 474:2203-2217. [PMID: 28533266 PMCID: PMC5632799 DOI: 10.1042/bcj20170217] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 05/18/2017] [Accepted: 05/22/2017] [Indexed: 12/29/2022]
Abstract
Collagen adopts a characteristic supercoiled triple helical conformation which requires a repeating (Xaa-Yaa-Gly)n sequence. Despite the abundance of collagen, a combined experimental and atomistic modelling approach has not so far quantitated the degree of flexibility seen experimentally in the solution structures of collagen triple helices. To address this question, we report an experimental study on the flexibility of varying lengths of collagen triple helical peptides, composed of six, eight, ten and twelve repeats of the most stable Pro-Hyp-Gly (POG) units. In addition, one unblocked peptide, (POG)10unblocked, was compared with the blocked (POG)10 as a control for the significance of end effects. Complementary analytical ultracentrifugation and synchrotron small angle X-ray scattering data showed that the conformations of the longer triple helical peptides were not well explained by a linear structure derived from crystallography. To interpret these data, molecular dynamics simulations were used to generate 50 000 physically realistic collagen structures for each of the helices. These structures were fitted against their respective scattering data to reveal the best fitting structures from this large ensemble of possible helix structures. This curve fitting confirmed a small degree of non-linearity to exist in these best fit triple helices, with the degree of bending approximated as 4–17° from linearity. Our results open the way for further studies of other collagen triple helices with different sequences and stabilities in order to clarify the role of molecular rigidity and flexibility in collagen extracellular and immune function and disease.
Collapse
|
158
|
Zhang L, Kang H, Vázquez FX, Toledo-Sherman L, Luan B, Zhou R. Molecular Mechanism of Stabilizing the Helical Structure of Huntingtin N17 in a Micellar Environment. J Phys Chem B 2017; 121:4713-4721. [DOI: 10.1021/acs.jpcb.7b01476] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Leili Zhang
- Computational
Biology Center, IBM Thomas J. Watson Research Center, Yorktown
Heights, New York 10598, United States
| | - Hongsuk Kang
- Computational
Biology Center, IBM Thomas J. Watson Research Center, Yorktown
Heights, New York 10598, United States
| | - Francisco X. Vázquez
- Computational
Biology Center, IBM Thomas J. Watson Research Center, Yorktown
Heights, New York 10598, United States
| | | | - Binquan Luan
- Computational
Biology Center, IBM Thomas J. Watson Research Center, Yorktown
Heights, New York 10598, United States
| | - Ruhong Zhou
- Computational
Biology Center, IBM Thomas J. Watson Research Center, Yorktown
Heights, New York 10598, United States
| |
Collapse
|
159
|
Fisette O, Wingbermühle S, Schäfer LV. Partial Dissociation of Truncated Peptides Influences the Structural Dynamics of the MHCI Binding Groove. Front Immunol 2017; 8:408. [PMID: 28458665 PMCID: PMC5394104 DOI: 10.3389/fimmu.2017.00408] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 03/22/2017] [Indexed: 12/29/2022] Open
Abstract
Antigen processing on MHCI involves the exchange of low-affinity peptides by high-affinity, immunodominant ones. This peptide editing process is mediated by tapasin and ERAAP at the peptide C- and N-terminus, respectively. Since tapasin does not contact the peptide directly, a sensing mechanism involving conformational changes likely allows tapasin to distinguish antigen-loaded MHCI molecules from those occupied by weakly bound, non-specific peptides. To understand this mechanism at the atomic level, we performed molecular dynamics simulations of MHCI allele B*44:02 loaded with peptides truncated or modified at the C- or N-terminus. We show that the deletion of peptide anchor residues leads to reversible, partial dissociation of the peptide from MHCI on the microsecond timescale. Fluctuations in the MHCI α2-1 helix segment, bordering the binding groove and cradled by tapasin in the PLC, are influenced by the peptide C-terminus occupying the nearby F-pocket. Simulations of tapasin complexed with MHCI bound to a low-affinity peptide show that tapasin widens the MHCI binding groove near the peptide C-terminus and weakens the attractive forces between MHCI and the peptide. Our simulations thus provide a detailed, spatially resolved picture of MHCI plasticity, revealing how peptide loading status can affect key structural regions contacting tapasin.
Collapse
Affiliation(s)
- Olivier Fisette
- Center for Theoretical Chemistry, Faculty of Chemistry and Biochemistry, Ruhr-University, Bochum, Germany
| | - Sebastian Wingbermühle
- Center for Theoretical Chemistry, Faculty of Chemistry and Biochemistry, Ruhr-University, Bochum, Germany
| | - Lars V. Schäfer
- Center for Theoretical Chemistry, Faculty of Chemistry and Biochemistry, Ruhr-University, Bochum, Germany
| |
Collapse
|
160
|
Bagherzadeh K, Maleki M, Golestani A, Khajeh K, Amanlou M. Chondrotinase ABC I thermal stability is enhanced by site-directed mutagenesis: a molecular dynamic simulations approach. J Biomol Struct Dyn 2017; 36:679-688. [DOI: 10.1080/07391102.2017.1294110] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Kowsar Bagherzadeh
- Razi Drug Research Center, Iran University of Medical Sciences, Tehran, Iran
- Faculty of Pharmacy and Pharmaceutical Sciences Research Center, Department of Medicinal Chemistry, Tehran University of Medical Sciences, Tehran, Iran
| | - Monireh Maleki
- Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Abolfazl Golestani
- Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Khosro Khajeh
- Faculty of Biological Sciences, Department of Biochemistry, Tarbiat Modares University, Tehran, Iran
| | - Massoud Amanlou
- Faculty of Pharmacy and Pharmaceutical Sciences Research Center, Department of Medicinal Chemistry, Tehran University of Medical Sciences, Tehran, Iran
| |
Collapse
|
161
|
Truong DT, Nguyen MT, Vu VV, Ngo ST. Fast pulling of ligand approach for the design of β-secretase 1 inhibitors. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.01.032] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|
162
|
Fedeli D, Montani M, Bordoni L, Galeazzi R, Nasuti C, Correia-Sá L, Domingues VF, Jayant M, Brahmachari V, Massaccesi L, Laudadio E, Gabbianelli R. In vivo and in silico studies to identify mechanisms associated with Nurr1 modulation following early life exposure to permethrin in rats. Neuroscience 2017; 340:411-423. [DOI: 10.1016/j.neuroscience.2016.10.071] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Revised: 10/24/2016] [Accepted: 10/29/2016] [Indexed: 01/16/2023]
|
163
|
Ngo ST, Luu XC, Nguyen MT, Le CN, Vu VV. In silico studies of solvated F19W amyloid β (11–40) trimer. RSC Adv 2017. [DOI: 10.1039/c7ra07187f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
REMD studies shows that F19W mutation does not change in the overall structure of Aβ11–40 trimer significantly but increases it flexibility, consistent with the observed formation of the same fibril structures at slower rates.
Collapse
Affiliation(s)
- Son Tung Ngo
- Computational Chemistry Research Group
- Ton Duc Thang University
- Ho Chi Minh City
- Vietnam
- Faculty of Applied Sciences
| | - Xuan-Cuong Luu
- NTT Hi-Tech Institute
- Nguyen Tat Thanh University
- Ho Chi Minh City
- Vietnam
| | | | - Chinh N. Le
- NTT Hi-Tech Institute
- Nguyen Tat Thanh University
- Ho Chi Minh City
- Vietnam
| | - Van V. Vu
- NTT Hi-Tech Institute
- Nguyen Tat Thanh University
- Ho Chi Minh City
- Vietnam
| |
Collapse
|
164
|
Ngo ST, Hung HM, Truong DT, Nguyen MT. Replica exchange molecular dynamics study of the truncated amyloid beta (11–40) trimer in solution. Phys Chem Chem Phys 2017; 19:1909-1919. [DOI: 10.1039/c6cp05511g] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The structure of the 3Aβ11–40 oligomer is determined for the first time using T-REMD simulations.
Collapse
Affiliation(s)
- Son Tung Ngo
- Computational Chemistry Research Group
- Ton Duc Thang University
- Ho Chi Minh City
- Vietnam
- Faculty of Applied Sciences
| | | | - Duc Toan Truong
- Department of Theoretical Physics
- Ho Chi Minh City University of Science
- Ho Chi Minh City
- Vietnam
| | - Minh Tho Nguyen
- Computational Chemistry Research Group
- Ton Duc Thang University
- Ho Chi Minh City
- Vietnam
- Faculty of Applied Sciences
| |
Collapse
|
165
|
Fisette O, Päslack C, Barnes R, Isas JM, Langen R, Heyden M, Han S, Schäfer LV. Hydration Dynamics of a Peripheral Membrane Protein. J Am Chem Soc 2016; 138:11526-35. [PMID: 27548572 DOI: 10.1021/jacs.6b07005] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Water dynamics in the hydration shell of the peripheral membrane protein annexin B12 were studied using MD simulations and Overhauser DNP-enhanced NMR. We show that retardation of water motions near phospholipid bilayers is extended by the presence of a membrane-bound protein, up to around 10 Å above that protein. Near the membrane surface, electrostatic interactions with the lipid head groups strongly slow down water dynamics, whereas protein-induced water retardation is weaker and dominates only at distances beyond 10 Å from the membrane surface. The results can be understood from a simple model based on additive contributions from the membrane and the protein to the activation free energy barriers of water diffusion next to the biomolecular surfaces. Furthermore, analysis of the intermolecular vibrations of the water network reveals that retarded water motions near the membrane shift the vibrational modes to higher frequencies, which we used to identify an entropy gradient from the membrane surface toward the bulk water. Our results have implications for processes that take place at lipid membrane surfaces, including molecular recognition, binding, and protein-protein interactions.
Collapse
Affiliation(s)
- Olivier Fisette
- Center for Theoretical Chemistry, Faculty of Chemistry and Biochemistry, Ruhr-University , 44780 Bochum, Germany
| | - Christopher Päslack
- Center for Theoretical Chemistry, Faculty of Chemistry and Biochemistry, Ruhr-University , 44780 Bochum, Germany.,Max-Planck Institut für Kohlenforschung , 45470 Mülheim an der Ruhr, Germany
| | - Ryan Barnes
- Department of Chemistry and Biochemistry and Department of Chemical Engineering, University of California, Santa Barbara , Santa Barbara, California 93106, United States
| | - J Mario Isas
- Department of Biochemistry and Molecular Biology, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California , Los Angeles, California 90089, United States
| | - Ralf Langen
- Department of Biochemistry and Molecular Biology, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California , Los Angeles, California 90089, United States
| | - Matthias Heyden
- Max-Planck Institut für Kohlenforschung , 45470 Mülheim an der Ruhr, Germany
| | - Songi Han
- Department of Chemistry and Biochemistry and Department of Chemical Engineering, University of California, Santa Barbara , Santa Barbara, California 93106, United States
| | - Lars V Schäfer
- Center for Theoretical Chemistry, Faculty of Chemistry and Biochemistry, Ruhr-University , 44780 Bochum, Germany
| |
Collapse
|
166
|
Awoonor-Williams E, Rowley CN. Evaluation of Methods for the Calculation of the pKa of Cysteine Residues in Proteins. J Chem Theory Comput 2016; 12:4662-73. [DOI: 10.1021/acs.jctc.6b00631] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ernest Awoonor-Williams
- Department of Chemistry, Memorial University of Newfoundland, St.
John’s, Newfoundland and Labrador A1B 3X9, Canada
| | - Christopher N. Rowley
- Department of Chemistry, Memorial University of Newfoundland, St.
John’s, Newfoundland and Labrador A1B 3X9, Canada
| |
Collapse
|
167
|
Antalek M, Pace E, Hedman B, Hodgson KO, Chillemi G, Benfatto M, Sarangi R, Frank P. Solvation structure of the halides from x-ray absorption spectroscopy. J Chem Phys 2016; 145:044318. [PMID: 27475372 PMCID: PMC4967075 DOI: 10.1063/1.4959589] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 07/11/2016] [Indexed: 11/14/2022] Open
Abstract
Three-dimensional models for the aqueous solvation structures of chloride, bromide, and iodide are reported. K-edge extended X-ray absorption fine structure (EXAFS) and Minuit X-ray absorption near edge (MXAN) analyses found well-defined single shell solvation spheres for bromide and iodide. However, dissolved chloride proved structurally distinct, with two solvation shells needed to explain its strikingly different X-ray absorption near edge structure (XANES) spectrum. Final solvation models were as follows: iodide, 8 water molecules at 3.60 ± 0.13 Å and bromide, 8 water molecules at 3.40 ± 0.14 Å, while chloride solvation included 7 water molecules at 3.15 ± 0.10 Å, and a second shell of 7 water molecules at 4.14 ± 0.30 Å. Each of the three derived solvation shells is approximately uniformly disposed about the halides, with no global asymmetry. Time-dependent density functional theory calculations simulating the chloride XANES spectra following from alternative solvation spheres revealed surprising sensitivity of the electronic state to 6-, 7-, or 8-coordination, implying a strongly bounded phase space for the correct structure during an MXAN fit. MXAN analysis further showed that the asymmetric solvation predicted from molecular dynamics simulations using halide polarization can play no significant part in bulk solvation. Classical molecular dynamics used to explore chloride solvation found a 7-water solvation shell at 3.12 (-0.04/+0.3) Å, supporting the experimental result. These experiments provide the first fully three-dimensional structures presenting to atomic resolution the aqueous solvation spheres of the larger halide ions.
Collapse
Affiliation(s)
- Matthew Antalek
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, USA
| | - Elisabetta Pace
- Laboratori Nazionali di Frascati-INFN, P.O. Box 13, 00044 Frascati, Italy
| | - Britt Hedman
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, USA
| | - Keith O Hodgson
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Giovanni Chillemi
- CINECA, SCAI-SuperComputing Applications and Innovation Department, Via dei Tizii 6, 00185 Roma, Italy
| | - Maurizio Benfatto
- Laboratori Nazionali di Frascati-INFN, P.O. Box 13, 00044 Frascati, Italy
| | - Ritimukta Sarangi
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, USA
| | - Patrick Frank
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, USA
| |
Collapse
|
168
|
Vermaas JV, Trebesch N, Mayne CG, Thangapandian S, Shekhar M, Mahinthichaichan P, Baylon JL, Jiang T, Wang Y, Muller MP, Shinn E, Zhao Z, Wen PC, Tajkhorshid E. Microscopic Characterization of Membrane Transporter Function by In Silico Modeling and Simulation. Methods Enzymol 2016; 578:373-428. [PMID: 27497175 PMCID: PMC6404235 DOI: 10.1016/bs.mie.2016.05.042] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Membrane transporters mediate one of the most fundamental processes in biology. They are the main gatekeepers controlling active traffic of materials in a highly selective and regulated manner between different cellular compartments demarcated by biological membranes. At the heart of the mechanism of membrane transporters lie protein conformational changes of diverse forms and magnitudes, which closely mediate critical aspects of the transport process, most importantly the coordinated motions of remotely located gating elements and their tight coupling to chemical processes such as binding, unbinding and translocation of transported substrate and cotransported ions, ATP binding and hydrolysis, and other molecular events fueling uphill transport of the cargo. An increasing number of functional studies have established the active participation of lipids and other components of biological membranes in the function of transporters and other membrane proteins, often acting as major signaling and regulating elements. Understanding the mechanistic details of these molecular processes require methods that offer high spatial and temporal resolutions. Computational modeling and simulations technologies empowered by advanced sampling and free energy calculations have reached a sufficiently mature state to become an indispensable component of mechanistic studies of membrane transporters in their natural environment of the membrane. In this article, we provide an overview of a number of major computational protocols and techniques commonly used in membrane transporter modeling and simulation studies. The article also includes practical hints on effective use of these methods, critical perspectives on their strengths and weak points, and examples of their successful applications to membrane transporters, selected from the research performed in our own laboratory.
Collapse
Affiliation(s)
- J V Vermaas
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States; University of Illinois at Urbana-Champaign, Urbana, IL, United States; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - N Trebesch
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States; University of Illinois at Urbana-Champaign, Urbana, IL, United States; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - C G Mayne
- University of Illinois at Urbana-Champaign, Urbana, IL, United States; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - S Thangapandian
- University of Illinois at Urbana-Champaign, Urbana, IL, United States; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - M Shekhar
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States; University of Illinois at Urbana-Champaign, Urbana, IL, United States; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - P Mahinthichaichan
- University of Illinois at Urbana-Champaign, Urbana, IL, United States; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - J L Baylon
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States; University of Illinois at Urbana-Champaign, Urbana, IL, United States; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - T Jiang
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States; University of Illinois at Urbana-Champaign, Urbana, IL, United States; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Y Wang
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States; University of Illinois at Urbana-Champaign, Urbana, IL, United States; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - M P Muller
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States; University of Illinois at Urbana-Champaign, Urbana, IL, United States; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, United States; College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - E Shinn
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States; University of Illinois at Urbana-Champaign, Urbana, IL, United States; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Z Zhao
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States; University of Illinois at Urbana-Champaign, Urbana, IL, United States; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - P-C Wen
- University of Illinois at Urbana-Champaign, Urbana, IL, United States; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - E Tajkhorshid
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States; University of Illinois at Urbana-Champaign, Urbana, IL, United States; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, United States; College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, United States.
| |
Collapse
|
169
|
Sajó R, Tőke O, Hajdú I, Jankovics H, Micsonai A, Dobó J, Kardos J, Vonderviszt F. Structural plasticity of the Salmonella FliS flagellar export chaperone. FEBS Lett 2016; 590:1103-13. [PMID: 27003324 DOI: 10.1002/1873-3468.12149] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 03/15/2016] [Accepted: 03/17/2016] [Indexed: 11/11/2022]
Abstract
The Salmonella FliS flagellar export chaperone is a highly α-helical protein. Proteolytic experiments suggest that FliS has a compact core. However, the calorimetric melting profile of FliS does not show any melting transition in the 25-110 °C temperature range. Circular dichroism measurements reveal that FliS is losing its helical structure over a broad temperature range upon heating. These observations indicate that FliS unfolds in a noncooperative way and its native state shows features reminiscent of the molten globule state of proteins possessing substantial structural plasticity. As FliS has several binding partners within the cell, conformational adaptability seems to be an essential requirement to fulfill its multiple roles.
Collapse
Affiliation(s)
- Ráchel Sajó
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Orsolya Tőke
- Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - István Hajdú
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Hajnalka Jankovics
- Bio-Nanosystems Laboratory, Research Institute for Chemical and Process Engineering, University of Pannonia, Veszprém, Hungary
| | - András Micsonai
- MTA-ELTE NAP B Neuroimmunology Research Group, Department of Biochemistry, Institute of Biology, Eötvös Loránd University, Budapest, Hungary
| | - József Dobó
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - József Kardos
- MTA-ELTE NAP B Neuroimmunology Research Group, Department of Biochemistry, Institute of Biology, Eötvös Loránd University, Budapest, Hungary
| | - Ferenc Vonderviszt
- Bio-Nanosystems Laboratory, Research Institute for Chemical and Process Engineering, University of Pannonia, Veszprém, Hungary.,Institute of Technical Physics and Materials Science, Centre for Energy Research, Hungarian Academy of Sciences, Budapest, Hungary
| |
Collapse
|
170
|
Collagen interactions: Drug design and delivery. Adv Drug Deliv Rev 2016; 97:69-84. [PMID: 26631222 DOI: 10.1016/j.addr.2015.11.013] [Citation(s) in RCA: 163] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 11/19/2015] [Accepted: 11/20/2015] [Indexed: 12/25/2022]
Abstract
Collagen is a major component in a wide range of drug delivery systems and biomaterial applications. Its basic physical and structural properties, together with its low immunogenicity and natural turnover, are keys to its biocompatibility and effectiveness. In addition to its material properties, the collagen triple-helix interacts with a large number of molecules that trigger biological events. Collagen interactions with cell surface receptors regulate many cellular processes, while interactions with other ECM components are critical for matrix structure and remodeling. Collagen also interacts with enzymes involved in its biosynthesis and degradation, including matrix metalloproteinases. Over the past decade, much information has been gained about the nature and specificity of collagen interactions with its partners. These studies have defined collagen sequences responsible for binding and the high-resolution structures of triple-helical peptides bound to its natural binding partners. Strategies to target collagen interactions are already being developed, including the use of monoclonal antibodies to interfere with collagen fibril formation and the use of triple-helical peptides to direct liposomes to melanoma cells. The molecular information about collagen interactions will further serve as a foundation for computational studies to design small molecules that can interfere with specific interactions or target tumor cells. Intelligent control of collagen biological interactions within a material context will expand the effectiveness of collagen-based drug delivery.
Collapse
|
171
|
Fu I, Case DA, Baum J. Dynamic Water-Mediated Hydrogen Bonding in a Collagen Model Peptide. Biochemistry 2016; 54:6029-37. [PMID: 26339765 DOI: 10.1021/acs.biochem.5b00622] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In the canonical (G-X-Y)(n) sequence of the fibrillar collagen triple helix, stabilizing direct interchain hydrogen bonding connects neighboring chains. Mutations of G can disrupt these interactions and are linked to connective tissue diseases. Here we integrate computational approaches with nuclear magnetic resonance (NMR) to obtain a dynamic view of hydrogen bonding distributions in the (POG)(4)(-)(POA)-(POG)(5) peptide, showing that the solution conformation, dynamics, and hydrogen bonding deviate from the reported X-ray crystal structure in many aspects. The simulations and NMR data provide clear evidence of inequivalent environments in the three chains. Molecular dynamics (MD) simulations indicate direct interchain hydrogen bonds in the leading chain, water bridges in the middle chain, and nonbridging waters in the trailing chain at the G → A substitution site. Theoretical calculations of NMR chemical shifts using a quantum fragmentation procedure can account for the unusual downfield NMR chemical shifts at the substitution sites and are used to assign the resonances to the individual chains. The NMR and MD data highlight the sensitivity of amide shifts to changes in the acceptor group from peptide carbonyls to water. The results are used to interpret solution NMR data for a variety of glycine substitutions and other sequence triplet interruptions to provide new connections between collagen sequences, their associated structures, dynamical behavior, and their ability to recognize collagen receptors.
Collapse
Affiliation(s)
- Iwen Fu
- Department of Chemistry and Chemical Biology and BioMaPS Institute, Rutgers University , Piscataway, New Jersey 08854, United States
| | - David A Case
- Department of Chemistry and Chemical Biology and BioMaPS Institute, Rutgers University , Piscataway, New Jersey 08854, United States
| | - Jean Baum
- Department of Chemistry and Chemical Biology and BioMaPS Institute, Rutgers University , Piscataway, New Jersey 08854, United States
| |
Collapse
|
172
|
Torabi R, Bagherzadeh K, Ghourchian H, Amanlou M. An investigation on the interaction modes of a single-strand DNA aptamer and RBP4 protein: a molecular dynamic simulations approach. Org Biomol Chem 2016; 14:8141-53. [DOI: 10.1039/c6ob01094f] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Monitoring and evaluating structural and functional alternations in RBP4 induced by its specific aptamer binding to design new aptamers for diagnostic and therapeutic purposes with reduced insulin resistance.
Collapse
Affiliation(s)
- Raheleh Torabi
- Laboratory of Microanalysis
- Institute of Biochemistry & Biophysics
- University of Tehran
- Tehran
- Iran
| | - Kowsar Bagherzadeh
- Razi Drug Research Center
- Iran University of Medical Sciences
- Tehran
- Iran
- Department of Medicinal Chemistry
| | - Hedayatollah Ghourchian
- Laboratory of Microanalysis
- Institute of Biochemistry & Biophysics
- University of Tehran
- Tehran
- Iran
| | - Massoud Amanlou
- Department of Medicinal Chemistry
- Faculty of Pharmacy and Drug Design and Development Research Center
- Tehran University of Medical Sciences
- Tehran
- Iran
| |
Collapse
|
173
|
The non-octarepeat copper binding site of the prion protein is a key regulator of prion conversion. Sci Rep 2015; 5:15253. [PMID: 26482532 PMCID: PMC4651146 DOI: 10.1038/srep15253] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 09/14/2015] [Indexed: 01/01/2023] Open
Abstract
The conversion of the prion protein (PrPC) into prions plays a key
role in transmissible spongiform encephalopathies. Despite the importance for
pathogenesis, the mechanism of prion formation has escaped detailed characterization
due to the insoluble nature of prions. PrPC interacts with copper
through octarepeat and non-octarepeat binding sites. Copper coordination to the
non-octarepeat region has garnered interest due to the possibility that this
interaction may impact prion conversion. We used X-ray absorption spectroscopy to
study copper coordination at pH 5.5 and 7.0 in human PrPC constructs,
either wild-type (WT) or carrying pathological mutations. We show that mutations and
pH cause modifications of copper coordination in the non-octarepeat region. In the
WT at pH 5.5, copper is anchored to His96 and His111, while at pH 7 it is
coordinated by His111. Pathological point mutations alter the copper coordination at
acidic conditions where the metal is anchored to His111. By using in vitro
approaches, cell-based and computational techniques, we propose a model whereby
PrPC coordinating copper with one His in the non-octarepeat
region converts to prions at acidic condition. Thus, the non-octarepeat region may
act as the long-sought-after prion switch, critical for disease onset and
propagation.
Collapse
|
174
|
Fuchs JE, Waldner BJ, Huber RG, von Grafenstein S, Kramer C, Liedl KR. Independent Metrics for Protein Backbone and Side-Chain Flexibility: Time Scales and Effects of Ligand Binding. J Chem Theory Comput 2015; 11:851-60. [DOI: 10.1021/ct500633u] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Julian E. Fuchs
- Institute
of General, Inorganic and Theoretical Chemistry, and Center for Molecular
Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain
80-82, A-6020 Innsbruck, Tyrol, Austria
- Centre
for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Birgit J. Waldner
- Institute
of General, Inorganic and Theoretical Chemistry, and Center for Molecular
Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain
80-82, A-6020 Innsbruck, Tyrol, Austria
| | - Roland G. Huber
- Institute
of General, Inorganic and Theoretical Chemistry, and Center for Molecular
Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain
80-82, A-6020 Innsbruck, Tyrol, Austria
- Bioinformatics
Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, Matrix #07-01, 138671 Singapore
| | - Susanne von Grafenstein
- Institute
of General, Inorganic and Theoretical Chemistry, and Center for Molecular
Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain
80-82, A-6020 Innsbruck, Tyrol, Austria
| | - Christian Kramer
- Institute
of General, Inorganic and Theoretical Chemistry, and Center for Molecular
Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain
80-82, A-6020 Innsbruck, Tyrol, Austria
| | - Klaus R. Liedl
- Institute
of General, Inorganic and Theoretical Chemistry, and Center for Molecular
Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain
80-82, A-6020 Innsbruck, Tyrol, Austria
| |
Collapse
|