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Sgarbossa A, Monti S, Lenci F, Bramanti E, Bizzarri R, Barone V. The effects of ferulic acid on β-amyloid fibrillar structures investigated through experimental and computational techniques. Biochim Biophys Acta Gen Subj 2013; 1830:2924-37. [PMID: 23291428 DOI: 10.1016/j.bbagen.2012.12.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2012] [Revised: 11/29/2012] [Accepted: 12/21/2012] [Indexed: 01/01/2023]
Abstract
BACKGROUND Current research has indicated that small natural compounds could interfere with β-amyloid fibril growth and have the ability to disassemble preformed folded structures. Ferulic acid (FA), which possesses both hydrophilic and hydrophobic moieties and binds to peptides/proteins, is a potential candidate against amyloidogenesis. The molecular mechanisms connected to this action have not been elucidated in detail yet. METHODS Here the effects of FA on preformed fibrils are investigated by means of a concerted experimental-computational approach. Spectroscopic techniques, such as FTIR, fluorescence, size exclusion chromatography and confocal microscopy in combination with molecular dynamics simulations are used to identify those features which play a key role in the destabilization of the aggregates. RESULTS Experimental findings highlight that FA has disruptive effects on the fibrils. The computational analysis suggests that dissociation of peptides from the amyloid superstructures could take place along the fibril axis and be primarily determined by the cooperative rupture of the backbone hydrogen bonds and of the Asp-Lys salt bridges. CONCLUSION FA clusters could induce a sort of stabilization and tightening of the fibril structure in the short term and its disruption in the long term, inhibiting further fibril re-assembly through FA screening effects. GENERAL SIGNIFICANCE The combination of experimental and computational techniques could be successfully used to identify the disrupting action of FA on preformed Aβ fibrils in water solution.
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Affiliation(s)
- Antonella Sgarbossa
- Biophysics Institute, National Research Council, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
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Chirgadze YN, Larionova EA, Ivanov VV. Novel Recognition Sign of DNA-binding α-Helix in Complexes of Transcription Factors from Different Families with Operator DNA. J Biomol Struct Dyn 2009; 27:83-96. [DOI: 10.1080/07391102.2009.10507298] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Rialdi G, Battistel E. Thermodynamics of proteins in unusual environments. Biophys Chem 2006; 126:65-79. [PMID: 16814921 DOI: 10.1016/j.bpc.2006.05.029] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2006] [Revised: 05/26/2006] [Accepted: 05/26/2006] [Indexed: 11/19/2022]
Abstract
Some aspects of protein thermodynamics in unconventional environments are addressed and discussed. Aqueous medium, especially dilute solution is the 'usual' ambient, which mediates all the interactions between protein and nearby molecules. When the water content is low, the surroundings may be considered 'unusual', exerting new stresses on the protein molecule and demanding different responses and property changes. The unusual systems considered in this article are low-water protein environments, including nearly dry state powders, organic solvent dispersions and reverse micelles' inclusions. The changes of hydration experienced by the protein after immobilization on solid supports are emphasized with respect to the free bulk solution state. Finally, the aqueous medium altered by water connectivity perturbing agents (polysaccharides) or in macromolecular crowding conditions (in the presence of polyols) is also considered as highly not ideal protein environments. The different responses elicited by the protein under the stress induced by drastic surrounding alterations may give insights for the controlled exploitation of the protein's biological and thermodynamic properties.
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Noinville S, Revault M, Quiquampoix H, Baron MH. Structural effects of drying and rehydration for enzymes in soils: a kinetics-FTIR analysis of α-chymotrypsin adsorbed on montmorillonite. J Colloid Interface Sci 2004; 273:414-25. [PMID: 15082376 DOI: 10.1016/j.jcis.2004.01.067] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2003] [Accepted: 01/30/2004] [Indexed: 10/26/2022]
Abstract
The effects of desiccation and rehydration cycles encountered by extracellular enzymes in soils are studied on -chymotrypsin adsorbed on montmorillonite. The controlled hygrometric FTIR cell used in this study enables to monitor drying and rehydration steps undergone by the -chymotrypsin-montmorillonite suspension or by the enzyme alone. Relative humidity (RH) determines the amount of deuterated water in the FTIR cell atmosphere. The molar water/protein ratio (W/P) as well as the conformational and solvation states of the enzyme have been determined using H/D exchange monitored by FTIR-transmission spectroscopy. When the W/P ratio decreases from 3500 to approximately 400, unfolding of beta-secondary structure in three different domains involves about 8% of the polypeptide backbone with respect to the most solvated states. Desiccation induces beta-unfolding, which opens channels allowing free vapor water molecules to diffuse into the enzyme at 15% RH. On drying to 0% RH, displacements of internal water (H2O) in the enzyme are demonstrated by reverse peptide isotopic exchanges (COND ==> CONH). Specific beta-structures, only formed in highly solvated states, sequester around 20 internal H2O molecules. Indeed, most of the unfolded secondary structures during the drying step are refolded at W/P approximately 1000 during rehydration. However, self-association hinders the recovery of the initial closed tertiary structure. The pD-dependent structural changes controlling inward and outward water diffusion are suppressed, whether the protein is initially in an adsorbed state or in solution. Changes in secondary structures encountered during desiccation/rehydration cycle are similar for the protein either free or in the adsorbed state. Thus domains that are unfolded by adsorption are not concerned by the desiccation/rehydration cycle.
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Affiliation(s)
- S Noinville
- Laboratoire de Dynamique, Interactions et Réactivité CNRS-Université Paris 6, UMR 7075, 2 rue Henri Dunant, 94320 Thiais, France.
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Ciocchetti A, Bizzarri AR, Cannistraro S. Long-term molecular dynamics simulation of copper plastocyanin in water. Biophys Chem 1997; 69:185-98. [PMID: 17029927 DOI: 10.1016/s0301-4622(97)00089-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/1997] [Revised: 06/12/1997] [Accepted: 06/12/1997] [Indexed: 10/16/2022]
Abstract
A long molecular dynamics simulation (1.1 ns) of fully hydrated plastocyanin has been performed and analysed to relate protein dynamics to structural elements and functional properties. The solvated structure is described in detail by the analysis of H-bond network. During all the simulation, the crystal H-bond network is maintained in the beta-sheet regions, while several H-bonds are broken or formed on the external surface of the protein. To evaluate whether such changes could be due to conformational rearrangements or to solvent competition, we have examined the average number of H-bonds between protein atoms and water molecules, and the root mean square deviations from crystal structure as a function of protein residues. Protein mobility and flexibility have been examined by positional and dihedral angle rms fluctuations. Finally, cross-correlation maps have revealed the existence of correlated motions among residues connected by hydrogen bonds.
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Affiliation(s)
- A Ciocchetti
- Unità INFM, Dipartimento di Fisica dell'Università, Perugia I-06100, Italy; Dipartimento di Scienze Ambientali, Università della Tuscia, Viterbo I-01100, Italy
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Steinbach PJ, Brooks BR. Hydrated myoglobin's anharmonic fluctuations are not primarily due to dihedral transitions. Proc Natl Acad Sci U S A 1996; 93:55-9. [PMID: 8552674 PMCID: PMC40177 DOI: 10.1073/pnas.93.1.55] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
To characterize the functionally important anharmonic motions of proteins, simulations of carboxymyoglobin (MbCO) dynamics have been performed during which dihedral transitions were prohibited. Comparison of torsionally restrained and unrestrained protein dynamics simulated at three levels of hydration and at temperatures ranging from 100 to 400 K suggests that hydration "catalyzes" protein mobility by facilitating collective anharmonic motions that do not require dihedral transitions. When dihedral transitions were prohibited, dehydrated MbCO, to a good approximation, exhibited only harmonic fluctuations, whereas hydrated MbCO exhibited both harmonic and anharmonic motions. The fluctuation of helix centers of mass also remained highly anharmonic in the torsionally restrained hydrated system. Atomic mean-square fluctuation at 300 K was reduced upon prohibition of dihedral transitions by only 28% and 10% for MbCO hydrated by 350 and 3830 water molecules, respectively.
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Affiliation(s)
- P J Steinbach
- Laboratory of Structural Biology, National Institutes of Health, Bethesda, MD 20892, USA
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Poole P. The role of hydration in lysozyme structure and activity: Relevance in protein engineering and design. J FOOD ENG 1994. [DOI: 10.1016/0260-8774(94)90039-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Steinbach PJ, Brooks BR. Protein hydration elucidated by molecular dynamics simulation. Proc Natl Acad Sci U S A 1993; 90:9135-9. [PMID: 8415667 PMCID: PMC47516 DOI: 10.1073/pnas.90.19.9135] [Citation(s) in RCA: 214] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Molecular dynamics (MD) simulation covering a wide range of hydration indicate that myoglobin is fully hydrated by 350 water molecules, in agreement with experiment. These waters, originally placed uniformly about the protein, form clusters that hydrate every charged group throughout the entire simulation. Some atoms in charged groups are hydrated by two water layers while 37% of the protein surface remains uncovered. The locations of the 350 waters are consistent with those of crystallographic waters resolved by x-ray and neutron diffraction. Hydration by 350 waters at 300 K stabilizes the conformation of carboxymyoglobin measured by x-ray diffraction throughout the entire protein, halves the rate of torsional transitions, and promotes alternative conformations for surface atoms. The glass transition observed experimentally in hydrated myoglobin near 220 K is also seen in the simulations and correlates with an increase in the number of dihedral angles undergoing transitions. The anharmonic protein motion above 220 K is enhanced by protein hydration.
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Affiliation(s)
- P J Steinbach
- Laboratory of Structural Biology, National Institutes of Health, Betheda, MD 20892
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Almagor A, Yedgar S, Gavish B. Viscous cosolvent effect on the ultrasonic absorption of bovine serum albumin. Biophys J 1992; 61:480-6. [PMID: 1547333 PMCID: PMC1260262 DOI: 10.1016/s0006-3495(92)81852-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Protein-ligand binding and enzyme activity have been shown to be regulated by solvent viscosity, induced by the addition of viscous cosolvents. This was indirectly interpreted as an effect on protein dynamics. However, viscous cosolvents might affect dynamic, e.g., viscosity, as well as thermodynamic properties of the solution, e.g., activity of solution components. This work was undertaken to examine the effect of viscous cosolvent on the structural dynamics of proteins and its correlation with dynamic and thermodynamic solution properties. For this purpose we studied the effect of viscous cosolvent on the specific ultrasonic absorption, delta mu, of bovine serum albumin, at pH = 7.0 and at 21 degrees C, and frequency range of 3-4 MHz. Ultrasonic absorption (UA) directly probes protein dynamics related to energy dissipation processes. It was found that the addition of sucrose, glycerol, or ethylene glycol increased the BSA delta mu. This increase correlates well with the solvent viscosity, but not with the cosolvent mass concentration, activity of the solvent components, dielectric constant, or the hydration of charged groups. On the grounds of these results and previously reported findings, as well as theoretical considerations, we propose the following mechanism for the solvent viscosity effect on the protein structural fluctuations, reflected in the UA: increased solvent viscosity alters the frequency spectrum of the polypeptide chain movements; attenuating the fast (small amplitude) movements, and enhancing the slow (large amplitude) ones. This modulates the interaction strength between the polypeptide and water species that "lubricates" the chain's movements, leading to larger protein-volume fluctuation and higher ultrasonic absorption. This study demonstrates that solvent viscosity is a regulator of protein structural fluctuations.
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Affiliation(s)
- A Almagor
- Department of Biochemistry, Hebrew University-Hadassah Medical School, Jerusalem, Israel
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Affiliation(s)
- J A Rupley
- Department of Biochemistry, University of Arizona, Tucson 85716
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Jakobsen RJ, Wasacz FM, Brasch JW, Smith KB. The relationship of bound water to the IR amide I bandwidth of albumin. Biopolymers 1986; 25:639-54. [PMID: 3708108 DOI: 10.1002/bip.360250409] [Citation(s) in RCA: 35] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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12
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Kimura N, Umemura J, Hayashi S, Takenaka T. Polarized FT—IR spectra of oriented water molecules in a liquid crystal. J Mol Struct 1984. [DOI: 10.1016/0022-2860(84)80191-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Poole P, Finney J. Hydration-induced conformational and flexibility changes in lysozyme at low water content. Int J Biol Macromol 1983. [DOI: 10.1016/0141-8130(83)90047-8] [Citation(s) in RCA: 80] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Gavish B. Proteins main-chain atomic displacements and density of stabilizing interactions. ACTA ACUST UNITED AC 1983. [DOI: 10.1007/bf00535540] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Lüscher-mattli M, Rüegg M. Thermodynamic functions of biopolymer hydration. I. Their determination by vapor pressure studies, discussed in an analysis of the primary hydration process. Biopolymers 1982. [DOI: 10.1002/bip.360210212] [Citation(s) in RCA: 59] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Proton transfer in and polarizability of hydrogen bonds in proteins. Tyrosine-lysine and glutamic acid-lysine hydrogen bonds ? IR investigations. ACTA ACUST UNITED AC 1980. [DOI: 10.1007/bf00537294] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Brazhnikov EV, Chirgadze YN. The use of deuterium exchange for the study of the distortion of alpha-helices in proteins. J Mol Biol 1978; 122:127-35. [PMID: 682187 DOI: 10.1016/0022-2836(78)90030-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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18
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Chirgadze YN, Brazhnikov EV, Nevskaya NA. Intramolecular distortion of the alpha-helical structure of polypeptides. J Mol Biol 1976; 102:781-92. [PMID: 940155 DOI: 10.1016/0022-2836(76)90291-6] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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21
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Hiltner A, Baer E. Mechanical properties of polymers at cryogenic temperatures: relationships between relaxation, yield and fracture processes. POLYMER 1974. [DOI: 10.1016/0032-3861(74)90142-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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