51
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Bach S, Visnow E, Panthöfer M, Gorelik T, Buzanich AG, Gurlo A, Kolb U, Emmerling F, Lind C, Tremel W. Hydrate Networks under Mechanical Stress – A Case Study for Co
3
(PO
4
)
2
·8H
2
O. Eur J Inorg Chem 2016. [DOI: 10.1002/ejic.201501481] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Sven Bach
- Institute of Inorganic Chemistry and Analytical Chemistry, Johannes Gutenberg University, Duesbergweg 10–14, 55128 Mainz, Germany, http://www.ak‐tremel.chemie.uni‐mainz.de/
- Graduate School Materials Science in Mainz, Staudinger Weg 9, 55128 Mainz, Germany
| | - Eduard Visnow
- Institute of Inorganic Chemistry and Analytical Chemistry, Johannes Gutenberg University, Duesbergweg 10–14, 55128 Mainz, Germany, http://www.ak‐tremel.chemie.uni‐mainz.de/
| | - Martin Panthöfer
- Institute of Inorganic Chemistry and Analytical Chemistry, Johannes Gutenberg University, Duesbergweg 10–14, 55128 Mainz, Germany, http://www.ak‐tremel.chemie.uni‐mainz.de/
| | - Tatiana Gorelik
- Institute of Physical Chemistry, Johannes Gutenberg University, Jakob‐Welderweg 11, 55099 Mainz, Germany
| | - Ana Guilherme Buzanich
- Federal Institute for Materials Research and Testing, Richard‐Willstätter‐Straße 11, 12489 Berlin, Germany
| | - Aleksander Gurlo
- Fachgebiet Keramische Werkstoffe, Institut für Werkstoffwissenschaften und ‐technologie, Technische Universität Berlin, Hardenbergerstrasse 40, 10623 Berlin, Germany
| | - Ute Kolb
- Institute of Physical Chemistry, Johannes Gutenberg University, Jakob‐Welderweg 11, 55099 Mainz, Germany
| | - Franziska Emmerling
- Federal Institute for Materials Research and Testing, Richard‐Willstätter‐Straße 11, 12489 Berlin, Germany
| | - Cora Lind
- Department of Chemistry and Biochemistry, The University of Toledo, Toledo, Ohio 43606‐3390, USA
| | - Wolfgang Tremel
- Institute of Inorganic Chemistry and Analytical Chemistry, Johannes Gutenberg University, Duesbergweg 10–14, 55128 Mainz, Germany, http://www.ak‐tremel.chemie.uni‐mainz.de/
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52
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Clifton LA, Ciesielski F, Skoda MWA, Paracini N, Holt SA, Lakey JH. The Effect of Lipopolysaccharide Core Oligosaccharide Size on the Electrostatic Binding of Antimicrobial Proteins to Models of the Gram Negative Bacterial Outer Membrane. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:3485-94. [PMID: 27003358 PMCID: PMC4854487 DOI: 10.1021/acs.langmuir.6b00240] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 02/28/2016] [Indexed: 05/23/2023]
Abstract
Understanding the electrostatic interactions between bacterial membranes and exogenous proteins is crucial to designing effective antimicrobial agents against Gram-negative bacteria. Here we study, using neutron reflecometry under multiple isotopic contrast conditions, the role of the uncharged sugar groups in the outer core region of lipopolysaccharide (LPS) in protecting the phosphate-rich inner core region from electrostatic interactions with antimicrobial proteins. Models of the asymmetric Gram negative outer membrane on silicon were prepared with phopshatidylcholine (PC) in the inner leaflet (closest to the silicon), whereas rough LPS was used to form the outer leaflet (facing the bulk solution). We show how salt concentration can be used to reversibly alter the binding affinity of a protein antibiotic colicin N (ColN) to the anionic LPS confirming that the interaction is electrostatic in nature. By examining the interaction of ColN with two rough LPS types with different-sized core oligosaccharide regions we demonstrate the role of uncharged sugars in blocking short-range electrostatic interactions between the cationic antibiotics and the vulnerable anionic phosphate groups.
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Affiliation(s)
- Luke A Clifton
- ISIS Pulsed Neutron and Muon Source, Science and Technology Facilities Council, Rutherford Appleton Laboratory , Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 OQX, United Kingdom
| | - Filip Ciesielski
- Department of Plant Sciences, University of Oxford , Oxford, OX1 3RB, United Kingdom
| | - Maximilian W A Skoda
- ISIS Pulsed Neutron and Muon Source, Science and Technology Facilities Council, Rutherford Appleton Laboratory , Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 OQX, United Kingdom
| | - Nicolò Paracini
- Institute for Cell and Molecular Biosciences, Newcastle University , Framlington Place, Newcastle upon Tyne, NE2 4HH, United Kingdom
| | - Stephen A Holt
- Bragg Institute, Australian Nuclear Science and Technology Organisation , Locked Bag 2001, Kirrawee DC, New South Wales 2232, Australia
| | - Jeremy H Lakey
- Institute for Cell and Molecular Biosciences, Newcastle University , Framlington Place, Newcastle upon Tyne, NE2 4HH, United Kingdom
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53
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Garcia-Fandiño R, Piñeiro Á, Trick JL, Sansom MSP. Lipid Bilayer Membrane Perturbation by Embedded Nanopores: A Simulation Study. ACS NANO 2016; 10:3693-3701. [PMID: 26943498 DOI: 10.1021/acsnano.6b00202] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
A macromolecular nanopore inserted into a membrane may perturb the dynamic organization of the surrounding lipid bilayer. To better understand the nature of such perturbations, we have undertaken a systematic molecular dynamics simulation study of lipid bilayer structure and dynamics around three different classes of nanopore: a carbon nanotube, three related cyclic peptide nanotubes differing in the nature of their external surfaces, and a model of a β-barrel nanopore protein. Periodic spatial distributions of several lipid properties as a function of distance from the nanopore were observed. This was especially clear for the carbon nanotube system, for which the density of lipids, the bilayer thickness, the projection of lipid head-to-tail vectors onto the membrane plane, and lipid lateral diffusion coefficients exhibited undulatory behavior as a function of the distance from the surface of the channel. Overall, the differences in lipid behavior as a function of the nanopore structure reveal local adaptation of the bilayer structure and dynamics to different embedded nanopore structures. Both the local structure and dynamic behavior of lipids around membrane-embedded nanopores are sensitive to the geometry and nature of the outer surface of the macromolecule/molecular assembly forming the pore.
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Affiliation(s)
- Rebeca Garcia-Fandiño
- Center for Research in Biological Chemistry and Molecular Materials (CIQUS), University of Santiago de Compostela , 15782 Santiago de Compostela, Spain
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Ángel Piñeiro
- Soft Matter & Molecular Biophysics Group, Department of Applied Physics, Faculty of Physics, University of Santiago de Compostela , 15782 Santiago de Compostela, Spain
| | - Jemma L Trick
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, United Kingdom
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54
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Hong S, Kim D. Interaction between bound water molecules and local protein structures: A statistical analysis of the hydrogen bond structures around bound water molecules. Proteins 2015; 84:43-51. [PMID: 26518137 DOI: 10.1002/prot.24953] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 09/21/2015] [Accepted: 10/15/2015] [Indexed: 11/10/2022]
Abstract
Water molecules play an important role in protein folding and protein interactions through their structural association with proteins. Examples of such structural association can be found in protein crystal structures, and can often explain protein functionality in the context of structure. We herein report the systematic analysis of the local structures of proteins interacting with water molecules, and the characterization of their geometric features. We first examined the interaction of water molecules with a large local interaction environment by comparing the preference of water molecules in three regions, namely, the protein-protein interaction (PPI) interfaces, the crystal contact (CC) interfaces, and the non-interfacial regions. High preference of water molecules to the PPI and CC interfaces was found. In addition, the bound water on the PPI interface was more favorably associated with the complex interaction structure, implying that such water-mediated structures may participate in the shaping of the PPI interface. The pairwise water-mediated interaction was then investigated, and the water-mediated residue-residue interaction potential was derived. Subsequently, the types of polar atoms surrounding the water molecules were analyzed, and the preference of the hydrogen bond acceptor was observed. Furthermore, the geometries of the structures interacting with water were analyzed, and it was found that the major structure on the protein surface exhibited planar geometry rather than tetrahedral geometry. Several previously undiscovered characteristics of water-protein interactions were unfolded in this study, and are expected to lead to a better understanding of protein structure and function.
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Affiliation(s)
| | - Dongsup Kim
- Department of Bio and Brain Engineering, KAIST, Daejeon, South Korea
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55
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Persch E, Dumele O, Diederich F. Molekulare Erkennung in chemischen und biologischen Systemen. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201408487] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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56
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Persch E, Dumele O, Diederich F. Molecular recognition in chemical and biological systems. Angew Chem Int Ed Engl 2015; 54:3290-327. [PMID: 25630692 DOI: 10.1002/anie.201408487] [Citation(s) in RCA: 419] [Impact Index Per Article: 46.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Indexed: 12/13/2022]
Abstract
Structure-based ligand design in medicinal chemistry and crop protection relies on the identification and quantification of weak noncovalent interactions and understanding the role of water. Small-molecule and protein structural database searches are important tools to retrieve existing knowledge. Thermodynamic profiling, combined with X-ray structural and computational studies, is the key to elucidate the energetics of the replacement of water by ligands. Biological receptor sites vary greatly in shape, conformational dynamics, and polarity, and require different ligand-design strategies, as shown for various case studies. Interactions between dipoles have become a central theme of molecular recognition. Orthogonal interactions, halogen bonding, and amide⋅⋅⋅π stacking provide new tools for innovative lead optimization. The combination of synthetic models and biological complexation studies is required to gather reliable information on weak noncovalent interactions and the role of water.
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Affiliation(s)
- Elke Persch
- Laboratorium für Organische Chemie, Departement Chemie und Angewandte Biowissenschaften, ETH Zürich, Vladimir-Prelog-Weg 3, 8093 Zürich (Switzerland)
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57
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Visscher KM, Kastritis PL, Bonvin AMJJ. Non-interacting surface solvation and dynamics in protein-protein interactions. Proteins 2015; 83:445-58. [DOI: 10.1002/prot.24741] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Revised: 11/10/2014] [Accepted: 11/26/2014] [Indexed: 12/14/2022]
Affiliation(s)
- Koen M. Visscher
- Bijvoet Center for Biomolecular Research; Faculty of Science-Chemistry, Utrecht University; 3584CH Utrecht The Netherlands
| | - Panagiotis L. Kastritis
- Bijvoet Center for Biomolecular Research; Faculty of Science-Chemistry, Utrecht University; 3584CH Utrecht The Netherlands
| | - Alexandre M. J. J. Bonvin
- Bijvoet Center for Biomolecular Research; Faculty of Science-Chemistry, Utrecht University; 3584CH Utrecht The Netherlands
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58
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Structure of the extracellular domain of matrix protein 2 of influenza A virus in complex with a protective monoclonal antibody. J Virol 2015; 89:3700-11. [PMID: 25609808 DOI: 10.1128/jvi.02576-14] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The extracellular domain of influenza A virus matrix protein 2 (M2e) is conserved and is being evaluated as a quasiuniversal influenza A vaccine candidate. We describe the crystal structure at 1.6 Å resolution of M2e in complex with the Fab fragment of an M2e-specific monoclonal antibody that protects against influenza A virus challenge. This antibody binds M2 expressed on the surfaces of cells infected with influenza A virus. Five out of six complementary determining regions interact with M2e, and three highly conserved M2e residues are critical for this interaction. In this complex, M2e adopts a compact U-shaped conformation stabilized in the center by the highly conserved tryptophan residue in M2e. This is the first description of the three-dimensional structure of M2e. IMPORTANCE M2e of influenza A is under investigation as a universal influenza A vaccine, but its three-dimensional structure is unknown. We describe the structure of M2e stabilized with an M2e-specific monoclonal antibody that recognizes natural M2. We found that the conserved tryptophan is positioned in the center of the U-shaped structure of M2e and stabilizes its conformation. The structure also explains why previously reported in vivo escape viruses, selected with a similar monoclonal antibody, carried proline residue substitutions at position 10 in M2.
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59
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Abstract
We investigate the role of water molecules in 89 protein–RNA complexes taken from the Protein Data Bank. Those with tRNA and single-stranded RNA are less hydrated than with duplex or ribosomal proteins. Protein–RNA interfaces are hydrated less than protein–DNA interfaces, but more than protein–protein interfaces. Majority of the waters at protein–RNA interfaces makes multiple H-bonds; however, a fraction do not make any. Those making H-bonds have preferences for the polar groups of RNA than its partner protein. The spatial distribution of waters makes interfaces with ribosomal proteins and single-stranded RNA relatively ‘dry’ than interfaces with tRNA and duplex RNA. In contrast to protein–DNA interfaces, mainly due to the presence of the 2′OH, the ribose in protein–RNA interfaces is hydrated more than the phosphate or the bases. The minor groove in protein–RNA interfaces is hydrated more than the major groove, while in protein–DNA interfaces it is reverse. The strands make the highest number of water-mediated H-bonds per unit interface area followed by the helices and the non-regular structures. The preserved waters at protein–RNA interfaces make higher number of H-bonds than the other waters. Preserved waters contribute toward the affinity in protein–RNA recognition and should be carefully treated while engineering protein–RNA interfaces.
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Affiliation(s)
- Amita Barik
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur-721302, India
| | - Ranjit Prasad Bahadur
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur-721302, India
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60
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Vajda T, Perczel A. Role of water in protein folding, oligomerization, amyloidosis and miniprotein. J Pept Sci 2014; 20:747-59. [PMID: 25098401 DOI: 10.1002/psc.2671] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 06/03/2014] [Accepted: 06/06/2014] [Indexed: 01/02/2023]
Abstract
The essential involvement of water in most fundamental extra-cellular and intracellular processes of proteins is critically reviewed and evaluated in this article. The role of water in protein behavior displays structural ambivalence; it can protect the disordered peptide-chain by hydration or helps the globular chain-folding, but promotes also the protein aggregation, as well (see: diseases). A variety of amyloid diseases begins as benign protein monomers but develops then into toxic amyloid aggregates of fibrils. Our incomplete knowledge of this process emphasizes the essential need to reveal the principles of governing this oligomerization. To understand the biophysical basis of the simpler in vitro amyloid formation may help to decipher also the in vivo way. Nevertheless, to ignore the central role of the water's effect among these events means to receive an uncompleted picture of the true phenomenon. Therefore this review represents a stopgap role, because the most published studies--with a few exceptions--have been neglected the crucial importance of water in the protein research. The following questions are discussed from the water's viewpoint: (i) interactions between water and proteins, (ii) protein hydration/dehydration, (iii) folding of proteins and miniproteins, (iv) peptide/protein oligomerization, and (v) amyloidosis.
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Affiliation(s)
- Tamás Vajda
- MTA-ELTE Protein Modelling Research Group, Eötvös Loránd University and Laboratory of Structural Chemistry & Biology, Institute of Chemistry, Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest, 1117, Hungary
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61
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Lensink MF, Moal IH, Bates PA, Kastritis PL, Melquiond ASJ, Karaca E, Schmitz C, van Dijk M, Bonvin AMJJ, Eisenstein M, Jiménez-García B, Grosdidier S, Solernou A, Pérez-Cano L, Pallara C, Fernández-Recio J, Xu J, Muthu P, Praneeth Kilambi K, Gray JJ, Grudinin S, Derevyanko G, Mitchell JC, Wieting J, Kanamori E, Tsuchiya Y, Murakami Y, Sarmiento J, Standley DM, Shirota M, Kinoshita K, Nakamura H, Chavent M, Ritchie DW, Park H, Ko J, Lee H, Seok C, Shen Y, Kozakov D, Vajda S, Kundrotas PJ, Vakser IA, Pierce BG, Hwang H, Vreven T, Weng Z, Buch I, Farkash E, Wolfson HJ, Zacharias M, Qin S, Zhou HX, Huang SY, Zou X, Wojdyla JA, Kleanthous C, Wodak SJ. Blind prediction of interfacial water positions in CAPRI. Proteins 2014; 82:620-32. [PMID: 24155158 PMCID: PMC4582081 DOI: 10.1002/prot.24439] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 09/16/2013] [Accepted: 09/26/2013] [Indexed: 12/30/2022]
Abstract
We report the first assessment of blind predictions of water positions at protein-protein interfaces, performed as part of the critical assessment of predicted interactions (CAPRI) community-wide experiment. Groups submitting docking predictions for the complex of the DNase domain of colicin E2 and Im2 immunity protein (CAPRI Target 47), were invited to predict the positions of interfacial water molecules using the method of their choice. The predictions-20 groups submitted a total of 195 models-were assessed by measuring the recall fraction of water-mediated protein contacts. Of the 176 high- or medium-quality docking models-a very good docking performance per se-only 44% had a recall fraction above 0.3, and a mere 6% above 0.5. The actual water positions were in general predicted to an accuracy level no better than 1.5 Å, and even in good models about half of the contacts represented false positives. This notwithstanding, three hotspot interface water positions were quite well predicted, and so was one of the water positions that is believed to stabilize the loop that confers specificity in these complexes. Overall the best interface water predictions was achieved by groups that also produced high-quality docking models, indicating that accurate modelling of the protein portion is a determinant factor. The use of established molecular mechanics force fields, coupled to sampling and optimization procedures also seemed to confer an advantage. Insights gained from this analysis should help improve the prediction of protein-water interactions and their role in stabilizing protein complexes.
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Affiliation(s)
- Marc F Lensink
- Interdisciplinary Research Institute USR3078 CNRS, University Lille North of France, Villeneuve d'Ascq, France
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62
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Talon R, Coquelle N, Madern D, Girard E. An experimental point of view on hydration/solvation in halophilic proteins. Front Microbiol 2014; 5:66. [PMID: 24600446 PMCID: PMC3930881 DOI: 10.3389/fmicb.2014.00066] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Accepted: 02/04/2014] [Indexed: 11/23/2022] Open
Abstract
Protein-solvent interactions govern the behaviors of proteins isolated from extreme halophiles. In this work, we compared the solvent envelopes of two orthologous tetrameric malate dehydrogenases (MalDHs) from halophilic and non-halophilic bacteria. The crystal structure of the MalDH from the non-halophilic bacterium Chloroflexus aurantiacus (Ca MalDH) solved, de novo, at 1.7 Å resolution exhibits numerous water molecules in its solvation shell. We observed that a large number of these water molecules are arranged in pentagonal polygons in the first hydration shell of Ca MalDH. Some of them are clustered in large networks, which cover non-polar amino acid surface. The crystal structure of MalDH from the extreme halophilic bacterium Salinibacter ruber (Sr) solved at 1.55 Å resolution shows that its surface is strongly enriched in acidic amino acids. The structural comparison of these two models is the first direct observation of the relative impact of acidic surface enrichment on the water structure organization between a halophilic protein and its non-adapted counterpart. The data show that surface acidic amino acids disrupt pentagonal water networks in the hydration shell. These crystallographic observations are discussed with respect to halophilic protein behaviors in solution
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Affiliation(s)
- Romain Talon
- Institut de Biologie Structurale, Université Grenoble Alpes Grenoble, France ; CEA, DSV, Institut de Biologie Structurale Grenoble, France ; Institut de Biologie Structurale, Centre National de la Recherche Scientifique Grenoble, France
| | - Nicolas Coquelle
- Institut de Biologie Structurale, Université Grenoble Alpes Grenoble, France ; CEA, DSV, Institut de Biologie Structurale Grenoble, France ; Institut de Biologie Structurale, Centre National de la Recherche Scientifique Grenoble, France
| | - Dominique Madern
- Institut de Biologie Structurale, Université Grenoble Alpes Grenoble, France ; CEA, DSV, Institut de Biologie Structurale Grenoble, France ; Institut de Biologie Structurale, Centre National de la Recherche Scientifique Grenoble, France
| | - Eric Girard
- Institut de Biologie Structurale, Université Grenoble Alpes Grenoble, France ; CEA, DSV, Institut de Biologie Structurale Grenoble, France ; Institut de Biologie Structurale, Centre National de la Recherche Scientifique Grenoble, France
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63
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Song J, Franck J, Pincus P, Kim MW, Han S. Specific ions modulate diffusion dynamics of hydration water on lipid membrane surfaces. J Am Chem Soc 2014; 136:2642-9. [PMID: 24456096 PMCID: PMC3985948 DOI: 10.1021/ja4121692] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
![]()
Effects
of specific ions on the local translational diffusion of
water near large hydrophilic lipid vesicle surfaces were measured
by Overhauser dynamic nuclear polarization (ODNP). ODNP relies on
an unpaired electron spin-containing probe located at molecular or
surface sites to report on the dynamics of water protons within ∼10
Å from the spin probe, which give rise to spectral densities
for electron–proton cross-relaxation processes in the 10 GHz
regime. This pushes nuclear magnetic resonance relaxometry to more
than an order of magnitude higher frequencies than conventionally
feasible, permitting the measurement of water moving with picosecond
to subnanosecond correlation times. Diffusion of water within ∼10
Å of, i.e., up to ∼3 water layers around the spin probes
located on hydrophilic lipid vesicle surfaces is ∼5 times retarded
compared to the bulk water translational diffusion. This directly
reflects on the activation barrier for surface water diffusion, i.e.,
how tightly water is bound to the hydrophilic surface and surrounding
waters. We find this value to be modulated by the presence of specific
ions in solution, with its order following the known Hofmeister series.
While a molecular description of how ions affect the hydration structure
at the hydrophilic surface remains to be answered, the finding that
Hofmeister ions directly modulate the surface water diffusivity implies
that the strength of the hydrogen bond network of surface hydration
water is directly modulated on hydrophilic surfaces.
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Affiliation(s)
- Jinsuk Song
- Department of Chemistry and Biochemistry and ‡Materials and Physics Department, University of California, Santa Barbara , Santa Barbara, California 93106, United States
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64
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Nakagawa H, Kataoka M. Investigation of Hydration and Glass Transition of Food Protein by Inelastic Neutron Scattering. J JPN SOC FOOD SCI 2014. [DOI: 10.3136/nskkk.61.323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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65
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Fischer T, Riedl R. Strategic targeting of multiple water-mediated interactions: a concise and rational structure-based design approach to potent and selective MMP-13 inhibitors. ChemMedChem 2013; 8:1457-61, 1572. [PMID: 23894097 PMCID: PMC4281860 DOI: 10.1002/cmdc.201300278] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Indexed: 11/09/2022]
Affiliation(s)
- Thomas Fischer
- Institute for Chemistry and Biological Chemistry, Zurich University of Applied Sciences (ZHAW), Einsiedlerstrasse 31, 8820 Wädenswil (Switzerland) www.icbc.zhaw.ch/organic‐chemistry
| | - Rainer Riedl
- Institute for Chemistry and Biological Chemistry, Zurich University of Applied Sciences (ZHAW), Einsiedlerstrasse 31, 8820 Wädenswil (Switzerland) www.icbc.zhaw.ch/organic‐chemistry
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Nakasako M, Takayama Y, Oroguchi T, Sekiguchi Y, Kobayashi A, Shirahama K, Yamamoto M, Hikima T, Yonekura K, Maki-Yonekura S, Kohmura Y, Inubushi Y, Takahashi Y, Suzuki A, Matsunaga S, Inui Y, Tono K, Kameshima T, Joti Y, Hoshi T. KOTOBUKI-1 apparatus for cryogenic coherent X-ray diffraction imaging. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2013; 84:093705. [PMID: 24089834 DOI: 10.1063/1.4822123] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
We have developed an experimental apparatus named KOTOBUKI-1 for use in coherent X-ray diffraction imaging experiments of frozen-hydrated non-crystalline particles at cryogenic temperature. For cryogenic specimen stage with small positional fluctuation for a long exposure time of more than several minutes, we here use a cryogenic pot cooled by the evaporation cooling effect for liquid nitrogen. In addition, a loading device is developed to bring specimens stored in liquid nitrogen to the specimen stage in vacuum. The apparatus allows diffraction data collection for frozen-hydrated specimens at 66 K with a positional fluctuation of less than 0.4 μm and provides an experimental environment to easily exchange specimens from liquid nitrogen storage to the specimen stage. The apparatus was developed and utilized in diffraction data collection of non-crystalline particles with dimensions of μm from material and biological sciences, such as metal colloid particles and chloroplast, at BL29XU of SPring-8. Recently, it has been applied for single-shot diffraction data collection of non-crystalline particles with dimensions of sub-μm using X-ray free electron laser at BL3 of SACLA.
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Affiliation(s)
- Masayoshi Nakasako
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
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67
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Matsuoka D, Nakasako M. Application of empirical hydration distribution functions around polar atoms for assessing hydration structures of proteins. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2012.12.040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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68
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Oliete R, Pous J, Rodríguez-Puente S, Abad-Zapatero C, Guasch A. Elastic and inelastic diffraction changes upon variation of the relative humidity environment of PurE crystals. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:194-212. [DOI: 10.1107/s090744491204454x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Accepted: 10/27/2012] [Indexed: 11/11/2022]
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69
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Miyashita Y, Wazawa T, Mogami G, Takahashi S, Sambongi Y, Suzuki M. Hydration-state change of horse heart cytochrome c corresponding to trifluoroacetic-acid-induced unfolding. Biophys J 2013; 104:163-72. [PMID: 23332069 DOI: 10.1016/j.bpj.2012.11.3825] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2012] [Revised: 11/07/2012] [Accepted: 11/29/2012] [Indexed: 12/14/2022] Open
Abstract
We investigate the hydration state of horse-heart cytochrome c (hh cyt c) in the unfolding process induced by trifluoroacetic acid (TFA). The conformation of hh cyt c changes from the native (N) state (2.9 < pH < 6.0) to the acid-unfolded (U(A)) state (1.7 < pH < 2.0) to the acid-induced molten globule (A) state (pH ∼1.2). Hydration properties of hh cyt c during this process are measured at 20°C by high-resolution dielectric relaxation (DR) spectroscopy, UV-vis absorbance, and circular dichroism spectroscopy. Constrained water of hh cyt c is observed at every pH as an ∼5-GHz Debye component (DC) (DR time, τ(D) ∼30 ps) and its DR amplitude (DRA) is increased by 77% upon N-to-U(A) transition, when pH changes from 6.0 to 2.0. Even in the N state, the DRA of the constrained-water component is found to be increased by 22% with decreasing pH from 6.0 to 2.9, suggesting an increase in the accessible surface area of native hh cyt c. Moreover, hypermobile water around native hh cyt c is detected at pH 6.0 as a 19-GHz DC (τ(D) ∼ 8.4 ps <τ(DW) = 9.4 ps), but is not found at other pH values. The DRA signal of constrained water is found to return to the pH 2.9 (N-state) level upon U(A)-to-A transition. Fast-response water (slightly slower than bulk) around A-state hh cyt c is detected at pH 1.2, and this suggests some accumulation of TFA(-) ions around the peptide chain. Thus, this high-resolution DR spectroscopy study reveals that hh cyt c exhibits significant hydration-state change in the TFA-unfolding process.
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Affiliation(s)
- Yusuke Miyashita
- Department of Materials Processing, Graduate School of Engineering, Tohoku University, Sendai, Miyagi, Japan
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70
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Biela A, Nasief NN, Betz M, Heine A, Hangauer D, Klebe G. Zerlegung des hydrophoben Effekts auf molekularer Ebene: Die Rolle von Wasser, Enthalpie und Entropie bei der Ligandenbindung an Thermolysin. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201208561] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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71
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Biela A, Nasief NN, Betz M, Heine A, Hangauer D, Klebe G. Dissecting the hydrophobic effect on the molecular level: the role of water, enthalpy, and entropy in ligand binding to thermolysin. Angew Chem Int Ed Engl 2013; 52:1822-8. [PMID: 23283700 DOI: 10.1002/anie.201208561] [Citation(s) in RCA: 116] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Indexed: 11/07/2022]
Affiliation(s)
- Adam Biela
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35032 Marburg, Germany
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72
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Biela A, Betz M, Heine A, Klebe G. Water makes the difference: rearrangement of water solvation layer triggers non-additivity of functional group contributions in protein-ligand binding. ChemMedChem 2012; 7:1423-34. [PMID: 22733601 DOI: 10.1002/cmdc.201200206] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2012] [Revised: 05/21/2012] [Indexed: 12/18/2022]
Abstract
The binding of four congeneric peptide-like thermolysin inhibitors has been studied by high-resolution crystal structure analysis and isothermal titration calorimetry. The ligands differ only by a terminal carboxylate and/or methyl group. A surprising non-additivity of functional group contributions for the carboxylate and/or methyl groups is detected. Adding the methyl first and then the carboxylate group results in a small Gibbs free energy increase and minor enthalpy/entropy partitioning for the first modification, whereas the second involves a strong affinity increase combined with large enthalpy/entropy changes. However, first adding the carboxylate and then the methyl group yields reverse effects: the acidic group attachment now causes minor effects, whereas the added methyl group provokes large changes. As all crystal structures show virtually identical binding modes, affinity changes are related to rearrangements of the first solvation layer next to the S(2)' pocket. About 20-25 water molecules are visible next to the studied complexes. The added COO(-) groups perturb the local water network in both carboxylated complexes, and the attached methyl groups provide favorable interaction sites for water molecules. Apart from one example, a contiguously connected water network between protein and ligand functional groups is observed in all complexes. In the complex with the carboxylated ligand, which still lacks the terminal methyl group, the water network is unfavorably ruptured. This results in a surprising thermodynamic signature showing only a minor affinity increase upon COO(-) group attachment. Because the further added methyl group provides a favorable interaction site for water, the network can be reestablished, and a strong affinity increase with a large enthalpy/entropy signature is then detected.
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Affiliation(s)
- Adam Biela
- Department of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, 35032 Marburg, Germany
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73
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Takayama Y, Nakasako M. Humidity-controlled preparation of frozen-hydrated biological samples for cryogenic coherent x-ray diffraction microscopy. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2012; 83:054301. [PMID: 22667634 DOI: 10.1063/1.4718359] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Coherent x-ray diffraction microscopy (CXDM) has the potential to visualize the structures of micro- to sub-micrometer-sized biological particles, such as cells and organelles, at high resolution. Toward advancing structural studies on the functional states of such particles, here, we developed a system for the preparation of frozen-hydrated biological samples for cryogenic CXDM experiments. The system, which comprised a moist air generator, microscope, micro-injector mounted on a micromanipulator, custom-made sample preparation chamber, and flash-cooling device, allowed for the manipulation of sample particles in the relative humidity range of 20%-94%rh at 293 K to maintain their hydrated and functional states. Here, we report the details of the system and the operation procedure, including its application to the preparation of a frozen-hydrated chloroplast sample. Sample quality was evaluated through a cryogenic CXDM experiment conducted at BL29XUL of SPring-8. Taking the performance of the system and the quality of the sample, the system was suitable to prepare frozen-hydrated biological samples for cryogenic CXDM experiments.
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Affiliation(s)
- Yuki Takayama
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kanagawa 223-8522, Japan
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74
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Li Z, He Y, Wong L, Li J. Progressive dry-core-wet-rim hydration trend in a nested-ring topology of protein binding interfaces. BMC Bioinformatics 2012; 13:51. [PMID: 22452998 PMCID: PMC3373366 DOI: 10.1186/1471-2105-13-51] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2011] [Accepted: 03/27/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Water is an integral part of protein complexes. It shapes protein binding sites by filling cavities and it bridges local contacts by hydrogen bonds. However, water molecules are usually not included in protein interface models in the past, and few distribution profiles of water molecules in protein binding interfaces are known. RESULTS In this work, we use a tripartite protein-water-protein interface model and a nested-ring atom re-organization method to detect hydration trends and patterns from an interface data set which involves immobilized interfacial water molecules. This data set consists of 206 obligate interfaces, 160 non-obligate interfaces, and 522 crystal packing contacts. The two types of biological interfaces are found to be drier than the crystal packing interfaces in our data, agreeable to a hydration pattern reported earlier although the previous definition of immobilized water is pure distance-based. The biological interfaces in our data set are also found to be subject to stronger water exclusion in their formation. To study the overall hydration trend in protein binding interfaces, atoms at the same burial level in each tripartite protein-water-protein interface are organized into a ring. The rings of an interface are then ordered with the core atoms placed at the middle of the structure to form a nested-ring topology. We find that water molecules on the rings of an interface are generally configured in a dry-core-wet-rim pattern with a progressive level-wise solvation towards to the rim of the interface. This solvation trend becomes even sharper when counterexamples are separated. CONCLUSIONS Immobilized water molecules are regularly organized in protein binding interfaces and they should be carefully considered in the studies of protein hydration mechanisms.
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Affiliation(s)
- Zhenhua Li
- Bioinformatics Research Center at the School of Computer Engineering, Nanyang Technological University, Singapore 639798, Singapore
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75
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Lim VI, Curran JF, Garber MB. Hydration shells of molecules in molecular association: A mechanism for biomolecular recognition. J Theor Biol 2012; 301:42-8. [PMID: 22365908 DOI: 10.1016/j.jtbi.2012.02.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2011] [Revised: 01/24/2012] [Accepted: 02/08/2012] [Indexed: 10/28/2022]
Abstract
It has become clear that water should not be treated as an inert environment, but rather as an integral and active component of molecules. Here, we consider molecules and their hydration shells together as single entities. We show that: (1) the rate of association of molecules should be determined by the energetic barriers arising from interactions between their hydration shells; (2) replacing non-polar atoms of molecular surfaces with polar atoms increases these barriers; (3) reduction of the hydration shells during molecular association is the driving force for association not only of non-polar, but of polar molecules as well; (4) in most cases the dehydration of polar atoms during molecular association thermodynamically counteracts association; (5) on balance the thermodynamic stability of associated complexes is basically determined by the action of these two opposing factors: reduction of the hydration shells and dehydration of polar atoms; (6) molecular crowding reduces the energetic barriers counteracting association and changes the thermodynamic stability of associated complexes. These results lead to a mechanism for biomolecular recognition in the context of which the formation of unique structures is provided by rapidly forming kinetic traps with a biologically necessary lifetime but with a marginal thermodynamic stability. The mechanism gives definitive answers to questions concerning the heart of specific interactions between biomolecules, their folding and intracellular organization. Predictions are given that can be subjected to direct experimental tests.
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Affiliation(s)
- Valery I Lim
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov str. 32, 119991 Moscow, Russia
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76
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Zeng G, Shou JJ, Li KK, Zhang YH. In-situ confocal Raman observation of structural changes of insulin crystals in sequential dehydration process. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:1631-40. [DOI: 10.1016/j.bbapap.2011.09.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2011] [Revised: 09/01/2011] [Accepted: 09/02/2011] [Indexed: 11/25/2022]
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77
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Malferrari M, Francia F, Venturoli G. Coupling between Electron Transfer and Protein–Solvent Dynamics: FTIR and Laser-Flash Spectroscopy Studies in Photosynthetic Reaction Center Films at Different Hydration Levels. J Phys Chem B 2011; 115:14732-50. [DOI: 10.1021/jp2057767] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Marco Malferrari
- Laboratorio di Biochimica e Biofisica, Dipartimento di Biologia, Università di Bologna, 40126 Bologna, Italy
| | - Francesco Francia
- Laboratorio di Biochimica e Biofisica, Dipartimento di Biologia, Università di Bologna, 40126 Bologna, Italy
| | - Giovanni Venturoli
- Laboratorio di Biochimica e Biofisica, Dipartimento di Biologia, Università di Bologna, 40126 Bologna, Italy
- Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia, c/o Dipartimento di Fisica, Università di Bologna, 40127 Bologna, Italy
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78
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Idris A, Bukhari A. Immobilized Candida antarctica lipase B: Hydration, stripping off and application in ring opening polyester synthesis. Biotechnol Adv 2011; 30:550-63. [PMID: 22041165 DOI: 10.1016/j.biotechadv.2011.10.002] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Revised: 09/09/2011] [Accepted: 10/04/2011] [Indexed: 10/16/2022]
Abstract
This work reviews the stripping off, role of water molecules in activity, and flexibility of immobilized Candida antarctica lipase B (CALB). Employment of CALB in ring opening polyester synthesis emphasizing on a polylactide is discussed in detail. Execution of enzymes in place of inorganic catalysts is the most green alternative for sustainable and environment friendly synthesis of products on an industrial scale. Robust immobilization and consequently performance of enzyme is the essential objective of enzyme application in industry. Water bound to the surface of an enzyme (contact class of water molecules) is inevitable for enzyme performance; it controls enzyme dynamics via flexibility changes and has intensive influence on enzyme activity. The value of pH during immobilization of CALB plays a critical role in fixing the active conformation of an enzyme. Comprehensive selection of support and protocol can develop a robust immobilized enzyme thus enhancing its performance. Organic solvents with a log P value higher than four are more suitable for enzymatic catalysis as these solvents tend to strip away very little of the enzyme surface bound water molecules. Alternatively ionic liquid can work as a more promising reaction media. Covalent immobilization is an exclusively reliable technique to circumvent the leaching of enzymes and to enhance stability. Activated polystyrene nanoparticles can prove to be a practical and economical support for chemical immobilization of CALB. In order to reduce the E-factor for the synthesis of biodegradable polymers; enzymatic ring opening polyester synthesis (eROPS) of cyclic monomers is a more sensible route for polyester synthesis. Synergies obtained from ionic liquids and immobilized enzyme can be much effective eROPS.
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Affiliation(s)
- Ani Idris
- Department of Bioprocess Engineering, Faculty of Chemical Engineering, Universiti Teknologi Malaysia, 81310 UTM Skudai, Johor, Malaysia.
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79
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Lee AG. Biological membranes: the importance of molecular detail. Trends Biochem Sci 2011; 36:493-500. [PMID: 21855348 DOI: 10.1016/j.tibs.2011.06.007] [Citation(s) in RCA: 145] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Revised: 06/21/2011] [Accepted: 06/24/2011] [Indexed: 10/17/2022]
Abstract
Are lipid interactions with membrane proteins best described in terms of the physical properties of the lipid bilayer or in terms of direct molecular interactions between particular lipid molecules and particular sites on a protein? A molecular interpretation is more challenging because it requires detailed knowledge of the 3D structure of a membrane protein, but recent studies have suggested that a molecular interpretation is necessary. Here, the idea is explored that lipid molecules modify the ways that transmembrane α-helices pack into bundles, by penetrating between the helices and by binding into clefts between the helices, and that these effects on helix packing will modulate the activity of a membrane protein.
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Affiliation(s)
- Anthony G Lee
- School of Biological Sciences, Life Sciences Building 85, University of Southampton, Southampton, SO17 1BJ, UK.
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80
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Kodama W, Nakasako M. Application of a real-space three-dimensional image reconstruction method in the structural analysis of noncrystalline biological macromolecules enveloped by water in coherent x-ray diffraction microscopy. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011; 84:021902. [PMID: 21929015 DOI: 10.1103/physreve.84.021902] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2010] [Revised: 03/08/2011] [Indexed: 05/31/2023]
Abstract
Coherent x-ray diffraction microscopy is a novel technique in the structural analyses of particles that are difficult to crystallize, such as the biological particles composing living cells. As water is indispensable for maintaining particles in functional structures, sufficient hydration of targeted particles is required during sample preparation for diffraction microscopy experiments. However, the water enveloping particles also contributes significantly to the diffraction patterns and reduces the electron-density contrast of the sample particles. In this study, we propose a protocol for the structural analyses of particles in water by applying a three-dimensional reconstruction method in real space for the projection images phase-retrieved from diffraction patterns, together with a developed density modification technique. We examined the feasibility of the protocol through three simulations involving a protein molecule in a vacuum, and enveloped in either a droplet or a cube-shaped water. The simulations were carried out for the diffraction patterns in the reciprocal planes normal to the incident x-ray beam. This assumption and the simulation conditions corresponded to experiments using x-ray wavelengths of shorter than 0.03 Å. The analyses demonstrated that our protocol provided an interpretable electron-density map. Based on the results, we discuss the advantages and limitations of the proposed protocol and its practical application for experimental data. In particular, we examined the influence of Poisson noise in diffraction patterns on the reconstructed three-dimensional electron density in the proposed protocol.
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Affiliation(s)
- Wataru Kodama
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
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81
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Takayama Y, Nakasako M. A few low-frequency normal modes predominantly contribute to conformational responses of hen egg white lysozyme in the tetragonal crystal to variations of molecular packing controlled by environmental humidity. Biophys Chem 2011; 159:237-46. [PMID: 21802827 DOI: 10.1016/j.bpc.2011.07.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Revised: 07/03/2011] [Accepted: 07/03/2011] [Indexed: 10/18/2022]
Abstract
The structures of proteins in crystals are fixed by molecular interactions with neighboring molecules, except in non-contacting flexible regions. Thus, it is difficult to imagine what conformational changes occur in solution. However, if molecular interactions can be changed by manipulating molecular packing in crystals, it may be possible to visualize conformational responses of proteins at atomic resolution by diffraction experiments. For this purpose, it is suitable to control the molecular packing in protein crystals by changing the volume of solvent channels through variation of the environmental relative humidity. Here, we studied conformational responses of hen egg white lysozyme (HEWL) in the tetragonal crystal by X-ray diffraction experiments using a humidity-control apparatus, which provided air flow of 20-98%rh at 298 K. First, we monitored the lattice parameters and crystalline order during dehydration and rehydration of HEWL crystal between 61 and 94%rh at 300 K. Then two crystal structures at a resolution of 2.1 Å using diffraction data obtained at 84.2 and 71.9%rh were determined to discuss the conformational responses of HEWL against the external perturbation induced by changes in molecular packing. The structure at 71.9%rh displayed a closure movement that was likely induced by the molecular contacts formed during dehydration and could be approximated by ten low-frequency normal modes for the crystal structure obtained at 84.2%rh. In addition, we observed reorganization of hydration structures at the molecular interfaces between symmetry neighbors. These findings suggest that humidity-controlled X-ray crystallography is an effective tool to investigate the responses of inherent intramolecular motions of proteins to external perturbations.
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Affiliation(s)
- Yuki Takayama
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kanagawa 223-8522, Japan
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82
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Efficient synthesis of optically pure alcohols by asymmetric hydrogen-transfer biocatalysis: application of engineered enzymes in a 2-propanol-water medium. Appl Microbiol Biotechnol 2011; 93:1075-85. [PMID: 21739266 DOI: 10.1007/s00253-011-3447-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2011] [Revised: 06/13/2011] [Accepted: 06/15/2011] [Indexed: 10/18/2022]
Abstract
We describe an efficient method for producing both enantiomers of chiral alcohols by asymmetric hydrogen-transfer bioreduction of ketones in a 2-propanol (IPA)-water medium with E. coli biocatalysts expressing phenylacetaldehyde reductase (PAR: wild-type and mutant enzymes) from Rhodococcus sp. ST-10 and alcohol dehydrogenase from Leifsonia sp. S749 (LSADH). We also describe the detailed properties of mutant PARs, Sar268, and HAR1, which were engineered to have high activity and productivity in media composed of polar organic solvent and water, and the construction of three-dimensional structure of PAR by homology modeling. The K(m) and V(max) values for some substrates and the substrate specificity of mutant PARs were quite different from those of wild-type PAR. The results well explained the increased productivity of engineered PARs in IPA-water medium.
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83
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Structural characteristics of hydration sites in lysozyme. Biophys Chem 2011; 156:31-42. [DOI: 10.1016/j.bpc.2011.02.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Revised: 02/17/2011] [Accepted: 02/17/2011] [Indexed: 11/17/2022]
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84
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85
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Nucci NV, Pometun MS, Wand AJ. Site-resolved measurement of water-protein interactions by solution NMR. Nat Struct Mol Biol 2011; 18:245-9. [PMID: 21196937 PMCID: PMC3058360 DOI: 10.1038/nsmb.1955] [Citation(s) in RCA: 188] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2010] [Accepted: 10/18/2010] [Indexed: 11/09/2022]
Abstract
The interactions of biological macromolecules with water are fundamental to their structure, dynamics and function. Historically, characterization of the location and residence times of hydration waters of proteins in solution has been quite difficult. Confining proteins within the nanoscale interior of a reverse micelle slows water dynamics, allowing global protein-water interactions to be detected using nuclear magnetic resonance techniques. Complications that normally arise from hydrogen exchange and long-range dipolar coupling are overcome by the nature of the reverse micelle medium. Characterization of the hydration of ubiquitin demonstrates that encapsulation within a reverse micelle allows detection of dozens of hydration waters. Comparison of nuclear Overhauser effects obtained in the laboratory and rotating frames indicate a considerable range of hydration water dynamics is present on the protein surface. In addition, an unprecedented clustering of different hydration-dynamics classes of sites is evident.
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Affiliation(s)
- Nathaniel V Nucci
- Johnson Research Foundation, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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86
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Wazawa T, Miyazaki T, Sambongi Y, Suzuki M. Hydration analysis of Pseudomonas aeruginosa cytochrome c551 upon acid unfolding by dielectric relaxation spectroscopy. Biophys Chem 2010; 151:160-9. [DOI: 10.1016/j.bpc.2010.06.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2010] [Revised: 06/21/2010] [Accepted: 06/22/2010] [Indexed: 10/19/2022]
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87
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Willenbring D, Xu Y, Tang P. The role of structured water in mediating general anesthetic action on alpha4beta2 nAChR. Phys Chem Chem Phys 2010; 12:10263-9. [PMID: 20661501 PMCID: PMC3265171 DOI: 10.1039/c003573d] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Water is an essential component for many biological processes. Pauling proposed that water might play a critical role in general anesthesia by forming water clathrates around anesthetic molecules. To examine potential involvement of water in general anesthesia, we analyzed water within alpha4beta2 nAChR, a putative protein target hypersensitive to volatile anesthetics. Experimental structure-derived closed- and open-channel nAChR systems in a fully hydrated lipid bilayer were examined using all-atom molecular dynamics simulations. At the majority of binding sites in alpha4beta2 nAChR, halothane replaced the slow-exchanging water molecules and caused a regional water population decrease. Only two binding sites had an increased quantity of water in the presence of halothane, where water arrangements resemble clathrate-like structures. The small number of such clathrate-like water clusters suggests that the formation of water clathrates is unlikely to be a primary cause for anesthesia. Despite the decrease in water population at most of the halothane binding sites, the number of sites that can be occupied transiently by water is actually increased in the presence of halothane. Many of these water sites were located between two subunits or in regions containing agonist binding sites or critical structural elements for transducing agonist binding to channel gating. Changes in water sites in the presence of halothane affected water-mediated protein-protein interactions and the protein dynamics, which can have direct impact on protein function. Collectively, water contributes to the action of anesthetics in proteins by mediating interactions between protein subunits and altering protein dynamics, instead of forming water clathrates around anesthetics.
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Affiliation(s)
- Dan Willenbring
- Department of Anesthesiology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
| | - Yan Xu
- Department of Anesthesiology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
| | - Pei Tang
- Department of Anesthesiology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
- Department of Computational Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
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88
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Nakasako M, Maeno A, Kurimoto E, Harada T, Yamaguchi Y, Oka T, Takayama Y, Iwata A, Kato K. Redox-Dependent Domain Rearrangement of Protein Disulfide Isomerase from a Thermophilic Fungus. Biochemistry 2010; 49:6953-62. [DOI: 10.1021/bi1006089] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Masayoshi Nakasako
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kouho-ku, Yokohama 223-8522, Japan
- The RIKEN Harima Institute/SPring-8, Sayo, Hyogo 679-5148, Japan
| | - Aya Maeno
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan
| | - Eiji Kurimoto
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan
- Faculty of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya 468-8503, Japan
| | - Takushi Harada
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan
| | - Yoshiki Yamaguchi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan
- Structural Glycobiology Team, Systems Glycobiology Research Group, Chemical Biology Department, Advanced Research Institute, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Toshihiko Oka
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kouho-ku, Yokohama 223-8522, Japan
| | - Yuki Takayama
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kouho-ku, Yokohama 223-8522, Japan
- The RIKEN Harima Institute/SPring-8, Sayo, Hyogo 679-5148, Japan
| | - Aya Iwata
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kouho-ku, Yokohama 223-8522, Japan
- The RIKEN Harima Institute/SPring-8, Sayo, Hyogo 679-5148, Japan
| | - Koichi Kato
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan
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89
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Matsuoka D, Nakasako M. Prediction of Hydration Structures around Hydrophilic Surfaces of Proteins by Using the Empirical Hydration Distribution Functions from a Database Analysis. J Phys Chem B 2010; 114:4652-63. [DOI: 10.1021/jp9100224] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Daisuke Matsuoka
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan, and RIKEN Harima Institute, 1-1-1 Kouto, Mikaduki, Sayo, Hyogo, Japan
| | - Masayoshi Nakasako
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan, and RIKEN Harima Institute, 1-1-1 Kouto, Mikaduki, Sayo, Hyogo, Japan
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90
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Glass DC, Krishnan M, Nutt DR, Smith JC. Temperature Dependence of Protein Dynamics Simulated with Three Different Water Models. J Chem Theory Comput 2010. [DOI: 10.1021/ct9006508] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dennis C. Glass
- University of Tennessee/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, and Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, United Kingdom
| | - Marimuthu Krishnan
- University of Tennessee/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, and Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, United Kingdom
| | - David R. Nutt
- University of Tennessee/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, and Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, United Kingdom
| | - Jeremy C. Smith
- University of Tennessee/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, and Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, United Kingdom
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91
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Branco RJF, Graber M, Denis V, Pleiss JÃ. Molecular Mechanism of the Hydration ofCandida antarcticaLipase B in the Gas Phase: Water Adsorption Isotherms and Molecular Dynamics Simulations. Chembiochem 2009; 10:2913-9. [DOI: 10.1002/cbic.200900544] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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92
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Matsuoka D, Nakasako M. Probability distributions of hydration water molecules around polar protein atoms obtained by a database analysis. J Phys Chem B 2009; 113:11274-92. [PMID: 19621908 DOI: 10.1021/jp902459n] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Hydration structures on protein surfaces are visualized by high-resolution cryogenic X-ray crystallography. We calculated the probability distributions of 4,831,570 hydration water molecules found around the 4,214,227 polar atoms in main chains and hydrophilic side chains from the 17,984 crystal structures in the Protein Data Bank. The structures are refined using the diffraction data collected below 150 K and at resolutions of better than 2.2 A. The calculated distributions were nonrandom but condensed into a few clusters. The clusters were decomposed into the distance and angular distributions by viewing from the polar coordinate system. The major peaks in the clusters were almost located along the directions of the N-H and O-H bonds or the lone pairs of oxygen atoms. The Gaussian fitting method was applied for the distribution profiles to evaluate quantitatively the peak positions and the widths. The parameters characterizing the distributions apparently depended on the hydrogen-bond partners of water molecules and on the modes whether the water molecules acted as donors or acceptors of protons. This led to propose the different roles of NH(n) (n = 1, 3), OH, and CO groups in protein hydration and possible in protein-ligand and protein-protein interaction: While C horizontal lineO groups appear to control the H-bond distances, NH(n) groups likely limit the angular range of H-bonds. The OH groups have both characteristics. In addition, it was also demonstrated that polar protein atoms were arranged to satisfy the tetrahedral hydrogen-bond geometry of water molecules, suggesting essential roles of water molecules in the folding process and in the stabilization of protein structures. These probability distributions are probably one of fundamental data to better understand the roles of hydration water molecules in the folding process and the stability of proteins in solution.
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Affiliation(s)
- Daisuke Matsuoka
- Department of Physics, Faculty of Science and Technology, Keio University, Yokohama, Kanagawa 223-8522, Japan
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93
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Guo F, Friedman JM. Charge density-dependent modifications of hydration shell waters by Hofmeister ions. J Am Chem Soc 2009; 131:11010-8. [PMID: 19603752 PMCID: PMC2745343 DOI: 10.1021/ja902240j] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Gadolinium (Gd(3+)) vibronic sideband luminescence spectroscopy (GVSBLS) is used to probe, as a function of added Hofmeister series salts, changes in the OH stretching frequency derived from first-shell waters of aqueous Gd(3+) and of Gd(3+) coordinated to three different types of molecules: (i) a chelate (EDTA), (ii) structured peptides (mSE3/SE2) of the lanthanide-binding tags (LBTs) family with a single high-affinity binding site, and (iii) a calcium-binding protein (calmodulin) with four binding sites. The vibronic sideband (VSB) corresponding to the OH stretching mode of waters coordinated to Gd(3+), whose frequency is inversely correlated with the strength of the hydrogen bonding to neighboring waters, exhibits an increase in frequency when Gd(3+) becomes coordinated to either EDTA, calmodulin, or mSE3 peptide. In all of these cases, the addition of cation chloride or acetate salts to the solution increases the frequency of the vibronic band originating from the OH stretching mode of the coordinated waters in a cation- and concentration-dependent fashion. The cation dependence of the frequency increase scales with charge density of the cations, giving rise to an ordering consistent with the Hofmeister ordering. On the other hand, water Raman spectroscopy shows no significant change upon addition of these salts. Additionally, it is shown that the cation effect is modulated by the specific anion used. The results indicate a mechanism of action for Hofmeister series ions in which hydrogen bonding among hydration shell waters is modulated by several factors. High charge density cations sequester waters in a configuration that precludes strong hydrogen bonding to neighboring waters. Under such conditions, anion effects emerge as anions compete for hydrogen-bonding sites with the remaining free waters on the surface of the hydration shell. The magnitude of the anion effect is both cation and Gd(3+)-binding site specific.
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Affiliation(s)
- Feng Guo
- Department of Biophysics and Physiology, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, New York, U.S.A. 10461
| | - Joel M. Friedman
- Department of Biophysics and Physiology, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, New York, U.S.A. 10461
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94
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Lee J, Kim SH. Water polygons in high-resolution protein crystal structures. Protein Sci 2009; 18:1370-6. [PMID: 19551896 PMCID: PMC2775207 DOI: 10.1002/pro.162] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2009] [Accepted: 04/29/2009] [Indexed: 11/05/2022]
Abstract
We have analyzed the interstitial water (ISW) structures in 1500 protein crystal structures deposited in the Protein Data Bank that have greater than 1.5 A resolution with less than 90% sequence similarity with each other. We observed varieties of polygonal water structures composed of three to eight water molecules. These polygons may represent the time- and space-averaged structures of "stable" water oligomers present in liquid water, and their presence as well as relative population may be relevant in understanding physical properties of liquid water at a given temperature. On an average, 13% of ISWs are localized enough to be visible by X-ray diffraction. Of those, averages of 78% are water molecules in the first water layer on the protein surface. Of the localized ISWs beyond the first layer, almost half of them form water polygons such as trigons, tetragons, as well as expected pentagons, hexagons, higher polygons, partial dodecahedrons, and disordered networks. Most of the octagons and nanogons are formed by fusion of smaller polygons. The trigons are most commonly observed. We suggest that our observation provides an experimental basis for including these water polygon structures in correlating and predicting various water properties in liquid state.
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Affiliation(s)
- Jonas Lee
- Department of Chemistry, University of CaliforniaBerkeley, California 94720-5230
- Physical Biosciences Division, Lawrence Berkeley National LaboratoryBerkeley, California 94720
| | - Sung-Hou Kim
- Department of Chemistry, University of CaliforniaBerkeley, California 94720-5230
- Physical Biosciences Division, Lawrence Berkeley National LaboratoryBerkeley, California 94720
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95
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Yang PK, Lim C. Strategies to model the near-solute solvent molecular density/polarization. J Comput Chem 2009; 30:700-9. [PMID: 18711719 DOI: 10.1002/jcc.21089] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The solvent molecular distribution significantly affects the behavior of the solute molecules and is thus important in studying many biological phenomena. It can be described by the solvent molecular density distribution, g, and the solvent electric dipole distribution, p. The g and p can be computed directly by counting the number of solvent molecules/dipoles in a microscopic volume centered at r during a simulation or indirectly from the mean force F and electrostatic field E acting on the solvent molecule at r, respectively. However, it is not clear how the g and p derived from simulations depend on the solvent molecular center or the solute charge and if the g(F) and p(E) computed from the mean force and electric field acting on the solvent molecule, respectively, could reproduce the corresponding g and p obtained by direct counting. Hence, we have computed g, p, g(F), and p(E) using different water centers from simulations of a solute atom of varying charge solvated in TIP3P water. The results show that g(F) and p(E) can reproduce the g and p obtained using a given count center. This implies that rather than solving the coordinates of each water molecule by MD simulations, the distribution of water molecules could be indirectly obtained from analytical formulas for the mean force F and electrostatic field E acting on the solvent molecule at r. Furthermore, the dependence of the g and p distributions on the solute charge revealed provides an estimate of the change in g and p surrounding a biomolecule upon a change in its conformation.
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Affiliation(s)
- Pei-Kun Yang
- The Institute of Biomedical Sciences, Academia Sinica, Taipei 115
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96
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Yoshida N, Imai T, Phongphanphanee S, Kovalenko A, Hirata F. Molecular recognition in biomolecules studied by statistical-mechanical integral-equation theory of liquids. J Phys Chem B 2009; 113:873-86. [PMID: 19105732 DOI: 10.1021/jp807068k] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Recent progress in the theory of molecular recognition in biomolecules is reviewed, which has been made based on the statistical mechanics of liquids or the RISM/3D-RISM theory during the last five years in the authors' group. The method requires just the structure of protein and the potential energy parameters for the biomolecules and solutions as inputs. The calculation is carried out in two steps. The first step is to obtain the pair correlation functions for solutions consisting of water and ligands based on the RISM theory. Then, given the pair correlation functions prepared in the first step, we calculate the 3D-distribution functions of water and ligands around and inside protein based on the 3D-RISM theory. The molecular recognition of a ligand by the protein is realized by the 3D-distribution functions: if one finds some conspicuous peaks in the distribution of a ligand inside protein, then the ligand is regarded as "recognized" by the protein. Some biochemical processes are investigated, which are intimately related to the molecular recognition of small ligands including water, noble gases, and ions by a protein.
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Affiliation(s)
- Norio Yoshida
- Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Okazaki 444-8585, Japan
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97
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Róg T, Murzyn K, Milhaud J, Karttunen M, Pasenkiewicz-Gierula M. Water Isotope Effect on the Phosphatidylcholine Bilayer Properties: A Molecular Dynamics Simulation Study. J Phys Chem B 2009; 113:2378-87. [DOI: 10.1021/jp8048235] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Tomasz Róg
- Department of Physics, Tampere University of Technology, Tampere, Finland; Department of Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland; Laboratoire de Biophysique Moléculaire, Cellulaire et Tissulaire, UFR SMBH Université Paris 13, Paris, France; and Department of Applied Mathematics, The University of Western Ontario, London, Ontario, Canada
| | - Krzysztof Murzyn
- Department of Physics, Tampere University of Technology, Tampere, Finland; Department of Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland; Laboratoire de Biophysique Moléculaire, Cellulaire et Tissulaire, UFR SMBH Université Paris 13, Paris, France; and Department of Applied Mathematics, The University of Western Ontario, London, Ontario, Canada
| | - Jeannine Milhaud
- Department of Physics, Tampere University of Technology, Tampere, Finland; Department of Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland; Laboratoire de Biophysique Moléculaire, Cellulaire et Tissulaire, UFR SMBH Université Paris 13, Paris, France; and Department of Applied Mathematics, The University of Western Ontario, London, Ontario, Canada
| | - Mikko Karttunen
- Department of Physics, Tampere University of Technology, Tampere, Finland; Department of Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland; Laboratoire de Biophysique Moléculaire, Cellulaire et Tissulaire, UFR SMBH Université Paris 13, Paris, France; and Department of Applied Mathematics, The University of Western Ontario, London, Ontario, Canada
| | - Marta Pasenkiewicz-Gierula
- Department of Physics, Tampere University of Technology, Tampere, Finland; Department of Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland; Laboratoire de Biophysique Moléculaire, Cellulaire et Tissulaire, UFR SMBH Université Paris 13, Paris, France; and Department of Applied Mathematics, The University of Western Ontario, London, Ontario, Canada
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98
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Azuara C, Orland H, Bon M, Koehl P, Delarue M. Incorporating dipolar solvents with variable density in Poisson-Boltzmann electrostatics. Biophys J 2008; 95:5587-605. [PMID: 18820239 PMCID: PMC2599837 DOI: 10.1529/biophysj.108.131649] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2008] [Accepted: 09/03/2008] [Indexed: 11/18/2022] Open
Abstract
We describe a new way to calculate the electrostatic properties of macromolecules that goes beyond the classical Poisson-Boltzmann treatment with only a small extra CPU cost. The solvent region is no longer modeled as a homogeneous dielectric media but rather as an assembly of self-orienting interacting dipoles of variable density. The method effectively unifies both the Poisson-centric view and the Langevin Dipole model. The model results in a variable dielectric constant epsilon(r) in the solvent region and also in a variable solvent density rho(r) that depends on the nature of the closest exposed solute atoms. The model was calibrated using small molecules and ions solvation data with only two adjustable parameters, namely the size and dipolar moment of the solvent. Hydrophobicity scales derived from the solvent density profiles agree very well with independently derived hydrophobicity scales, both at the atomic or residue level. Dimerization interfaces in homodimeric proteins or lipid-binding regions in membrane proteins clearly appear as poorly solvated patches on the solute accessible surface. Comparison of the thermally averaged solvent density of this model with the one derived from molecular dynamics simulations shows qualitative agreement on a coarse-grained level. Because this calculation is much more rapid than that from molecular dynamics, applications of a density-profile-based solvation energy to the identification of the true structure among a set of decoys become computationally feasible. Various possible improvements of the model are discussed, as well as extensions of the formalism to treat mixtures of dipolar solvents of different sizes.
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Affiliation(s)
- Cyril Azuara
- Unité de Dynamique Structurale des Macromolécules, URA 2185 du Centre National de la Recherche Scientifique, Institut Pasteur, Paris, France
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99
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Valiaev A, Lim DW, Schmidler S, Clark RL, Chilkoti A, Zauscher S. Hydration and conformational mechanics of single, end-tethered elastin-like polypeptides. J Am Chem Soc 2008; 130:10939-46. [PMID: 18646848 PMCID: PMC2736882 DOI: 10.1021/ja800502h] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We investigated the effect of temperature, ionic strength, solvent polarity, and type of guest residue on the force-extension behavior of single, end-tethered elastin-like polypeptides (ELPs), using single molecule force spectroscopy (SMFS). ELPs are stimulus-responsive polypeptides that contain repeats of the five amino acids Val-Pro-Gly-Xaa-Gly (VPGXG), where Xaa is a guest residue that can be any amino acid with the exception of proline. We fitted the force-extension data with a freely jointed chain (FJC) model which allowed us to resolve small differences in the effective Kuhn segment length distributions that largely arise from differences in the hydrophobic hydration behavior of ELP. Our results agree qualitatively with predictions from recent molecular dynamics simulations and demonstrate that hydrophobic hydration modulates the molecular elasticity for ELPs. Furthermore, our results show that SMFS, when combined with our approach for data analysis, can be used to study the subtleties of polypeptide-water interactions and thus provides a basis for the study of hydrophobic hydration in intrinsically unstructured biomacromolecules.
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Affiliation(s)
- Alexei Valiaev
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708
- Center for Biologically Inspired Materials and Materials Systems, Duke University, Durham, North Carolina 27708
| | - Dong Woo Lim
- Center for Biologically Inspired Materials and Materials Systems, Duke University, Durham, North Carolina 27708
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708
| | - Scott Schmidler
- Institute of Statistics and Decision Sciences, Duke University, Durham, North Carolina 27708
| | - Robert L. Clark
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708
- Center for Biologically Inspired Materials and Materials Systems, Duke University, Durham, North Carolina 27708
| | - Ashutosh Chilkoti
- Center for Biologically Inspired Materials and Materials Systems, Duke University, Durham, North Carolina 27708
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708
| | - Stefan Zauscher
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708
- Center for Biologically Inspired Materials and Materials Systems, Duke University, Durham, North Carolina 27708
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100
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Nakakido M, Tanaka Y, Mitsuhori M, Kudou M, Ejima D, Arakawa T, Tsumoto K. Structure-based analysis reveals hydration changes induced by arginine hydrochloride. Biophys Chem 2008; 137:105-9. [PMID: 18725174 DOI: 10.1016/j.bpc.2008.07.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2008] [Revised: 07/28/2008] [Accepted: 07/30/2008] [Indexed: 11/29/2022]
Abstract
Arginine hydrochloride has been used to suppress protein aggregation during refolding and in various other applications. We investigated the structure of hen egg-white lysozyme (HEL) and solvent molecules in arginine hydrochloride solution by X-ray crystallography. Neither the backbone nor side-chain structure of HEL was altered by the presence of arginine hydrochloride. In addition, no stably bound arginine molecules were observed. The number of hydration water molecules, however, changed with the arginine hydrochloride concentration. We suggest that arginine hydrochloride suppresses protein aggregation by altering the hydration structure and the transient binding of arginine molecules that could not be observed.
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Affiliation(s)
- Makoto Nakakido
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8562, Japan
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