Proteins and pressure

Frauenfelder, Hans; Alberding, N.; Ansari, Anjum; Braunstein, D.; Cowen, B. R.; Hong, Mineui; Iben, Icko; Johnson, Jerald B.; Luck, Stanley; Marden, Michael C.; Mourant, Judith R.; Ormos, Pál; Reinisch, Lou; Scholl, Reinhard; Schulte, Alfons; Erramilli, Shyamsunder; Sorensen, L. B.; Steinbach, Peter; Xie, Aihua; Young, Robert D.; Yue, Kwok To

doi:10.1021/j100366a002

Cited by 284 publications

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“…The basic idea of this study is that pressure would allow us to discriminate between close but distinct protein-fluctuation modes associated to distinct solvent or ligand conditions. Frauenfelder and coworkers [24] have published a study of pressure (up to 400 MPa) and temperature (230-330 K) effects on the Fe-CO bond at the binding site. Their data are discussed in terms of conformational substates.…”

Section: Discussionmentioning

confidence: 99%

An infrared study of ²H‐bond variation in myoglobin revealed by high pressure

Tilly

Sire

Alpert

et al. 1992

European Journal of Biochemistry

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A high-pressure Fourier-transform infrared technique was used to probe the evolution of 'H bonds inside the helical segments of myoglobin in relation to p2H, Tris concentration in the medium and iron-ligand nature. The analysis was focused on changes in the conformation-sensitive amide-I' band, reflecting the peptide C = 0 group stretching vibrations coupled to the in-plane N-2H bending and C = N stretching modes. From data obtained under high pressure, the strength of 2H bonds, inside the a-helical segments of the protein at atmospheric pressure, is not simply a function of p2H and salt concentration. At low Tris concentration (50 mM), the strength of these 2H bonds increases with p'H, whereas for a higher Tris concentration (100 mM) this strength is lower at p2H 7 than at p'H 6.0 or 8.5. It is also observed that the azidometmyoglobin molecule exhibits tighter intrahelical interactions and lower sensitivity to pressure than aquametmyoglobin. Information is also presented regarding interhelical interactions in relation to the solvent.Hydrogen bonds play a key role in protein stability [l] and protein dynamics [2, 31. However, in comparison with current knowledge about hydrogen bonds in gases, liquids or crystal lattices, little is known about hydrogen bonds inside proteins. The problem of assignment of collective modes of hydrogen bonds in proteins [4], the factors determining the intra-helical structure with weak or strong hydrogen bonds [5] are difficult to classify. Notable successes among the few high-pressure Fourier-transform infrared studies were performed using the conformation-sensitive amide-I' band [6 -81. This hand represents the C = 0-stretching vibration of the amide groups coupled to the in-plane N-H bending and C = N-stretching modes [9]. The energy of the C = O stretching vibration is primarily determined by the particular structure adopted by the peptide chains. In the case of the myoglobin molecule, the amide-I' band comprises a main helix band near 1650 cm-'and minor bands at 1627-1638 cm-' and 1671 -1675 cmreflecting the interhelical interactions [4].Since H bonds are basically dipoles, it is interesting to study whether or not the H bonds, inside a monomeric molecule such as myoglobin, are an invariant parameter not affected by the pH of the solvent. Investigating the hydrogen-bond network in this protein in solution is of importance, since most of our knowledge about such interactions derives from the crystallized protein. changes in the heme macrocycle [ l l , 121, whereas the crystal structure remains unaltered [13]. Possible 'H-bond-strength variation could accompany ligand binding, whereas the protein conformation would remain roughly unaltered. Extreme pressure, by reducing intermolecular distance, allows the estimation of variation in 'H-bond strength and emphasizes the relationships between protein residues and solvent molecules [7, 141. The relative strength of the 'H-bond interactions in the helical protein segments at atmospheric pressure can be estimated from the relative magni...

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Section: Discussionmentioning

confidence: 99%

An infrared study of ²H‐bond variation in myoglobin revealed by high pressure

Tilly

Sire

Alpert

et al. 1992

European Journal of Biochemistry

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“…Experimental techniques such as optical spectroscopy, Raman scattering, and NMR have been used to observe pressure effects on proteins (Weber & Drickamer, 1983;Frauenfelder et al, 1990;Jaenicke, 1991;Silva & Weber, 1993;Gross & Jaenicke, 1994 . The pressure denaturation of monomeric proteins, the dissociation of oligomers, and the effects of pressure on macromolecular assemblages have provided insights into the microscopic mechanism of protein folding and the role of solvent in this process (Zipp & Kauzmann, 1973;Li et al, 1976;Chryssomallis et al, 1981;Weber & Drickamer, 1983;Silva et al, 1986;Silva & Weber, 1993;Weber, 1993;Dufour et al, 1994;Peng et al, 1994;Schulte et al, 1995;Silva et al, 1996).…”

Section: Introductionmentioning

confidence: 99%

Effects of pressure on the structure of metmyoglobin: Molecular dynamics predictions for pressure unfolding through a molten globule intermediate

et al. 1998

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We investigated the pathway for pressure unfolding of metmyoglobin using molecular dynamics (MD) for a range of pressures (0.1 MPa to 1.2 GPa) and a temperature of 300 K. We find that the unfolding of metmyoglobin proceeds via a two-step mechanism native + molten globule intermediate + unfolded, where the molten globule forms at 700 MPa. The simulation describes qualitatively the experimental behavior of metmyoglobin under pressure. We find that unfolding of the alpha-helices follows the sequence of migrating hydrogen bonds (i,i + 4) + (i,i + 2).Keywords: molecular dynamics; molten globule; myoglobin; pressure; unfolding The effect of pressure on chemical and biological systems can lead to improved understanding of the fundamental interactions and to improved processes. Thus, high pressure has been used in food sterilization, extraction procedures, bioconversion using barophilic microorganisms, and enzymology under supercritical conditions (Balny et al., 1992). In addition, microbiology under deep-sea high pressure conditions offers biotechnological opportunities and may provide insights into the origin of life. Microorganisms in the deep-sea live at high pressures (1 10 MPa at 10,660 m) at both low and high temperature and in darkness (Yayanos, 1995).Experimental techniques such as optical spectroscopy, Raman scattering, and NMR have been used to observe pressure effects on proteins (Weber & Drickamer, 1983;Frauenfelder et al., 1990;Jaenicke, 1991;Silva & Weber, 1993;Gross & Jaenicke, 1994 . The pressure denaturation of monomeric proteins, the dissociation of oligomers, and the effects of pressure on macromolecular assemblages have provided insights into the microscopic mechanism of protein folding and the role of solvent in this process (Zipp & Kauzmann, 1973;Li et al., 1976;Chryssomallis et al., 1981;Weber & Drickamer, 1983;Silva et al., 1986;Silva & Weber, 1993;Weber, 1993;Dufour et al., 1994;Peng et al., 1994;Schulte et al., 1995;Silva et al., 1996). These effects are often reversible but can show different degrees of hysteresis.Despite this progress, the detailed atomistic changes involved in pressure transformations have not been well characterized. To provide such information we carried out molecular dynamics (MD) simulations on metmyoglobin as a function of applied external pressure. We selected myoglobin since its folding mechanism and protein folding intermediates have been studied experimentally by many techniques. We find that the applied pressure perturbs the native structure of the protein, eventually destabilizing to denature the molecule. By examining the conformation of the intermediates from the MD, we determined the pathway for unfolding. The results are in agreement with the experiment. 2301

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“…G lobular proteins are characterized by a funnel-like energy landscape with a deep minimum associated with the native state (1)(2)(3)(4)(5)(6). The native state is somewhat degenerate and possesses a rugged energy landscape as a result of residual frustration between subtle competing structural conformations (1,(4)(5)(6)(7).…”

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“…This frustration may arise in part from the competition of possible interresidue contacts that are explored during the protein's dynamics and can be paralleled with residual entropy in spin glasses (4)(5)(6). Under physiological conditions, much of the native landscape is thermally accessible, resulting in incessant fluctuations between available states (1,(3)(4)(5)(6). Hence, understanding the organization of the local minima in the native state energy landscape is vital to our understanding of protein function, such as in allosteric proteins and enzymes (8)(9)(10).…”

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“…Revealing the organization of the energy landscape of eglin c is the first goal to be accomplished in this work. The native state energy landscape is best thought of in terms of a hierarchy of similar conformational states, arranged in a tiered fashion (2)(3)(4)(5)(6)26). Significant work has been done to characterize the energy landscape for peptides, by using, for example, disconnectivity graphs (DGs) (27)(28)(29).…”

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Hierarchical organization of eglin c native state dynamics is shaped by competing direct and water-mediated interactions

Materese

Goldmon²,

Papoian

2008

Proc. Natl. Acad. Sci. U.S.A.

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The native state dynamics of the small globular serine protease inhibitor eglin c has been studied in a long 336 ns computer simulation in explicit solvent. We have elucidated the energy landscape explored during the course of the simulation by using Principal Component Analysis. We observe several basins in the energy landscape in which the system lingers for extended periods. Through an iterative process we have generated a tree-like hierarchy of states describing the observed dynamics. We observe a range of divergent contact types including salt bridges, hydrogen bonds, hydrophilic interactions, and hydrophobic interactions, pointing to the frustration between competing interactions. Additionally, we find evidence of competing water-mediated interactions. Divergence in water-mediated interactions may be found to supplement existing direct contacts, but they are also found to be independent of such changes. Water-mediated contacts facilitate interactions between residues of like charge as observed in the simulation. Our results provide insight into the complexity of the dynamic native state of a globular protein and directly probe the residual frustration in the native state.principal component analysis ͉ protein dynamics ͉ protein energy landscape ͉ tree-like hierarchy of states

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Proteins and pressure

Cited by 284 publications

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An infrared study of ²H‐bond variation in myoglobin revealed by high pressure

An infrared study of ²H‐bond variation in myoglobin revealed by high pressure

Effects of pressure on the structure of metmyoglobin: Molecular dynamics predictions for pressure unfolding through a molten globule intermediate

Hierarchical organization of eglin c native state dynamics is shaped by competing direct and water-mediated interactions

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Proteins and pressure

Cited by 284 publications

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An infrared study of 2H‐bond variation in myoglobin revealed by high pressure

An infrared study of 2H‐bond variation in myoglobin revealed by high pressure

Effects of pressure on the structure of metmyoglobin: Molecular dynamics predictions for pressure unfolding through a molten globule intermediate

Hierarchical organization of eglin c native state dynamics is shaped by competing direct and water-mediated interactions

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An infrared study of ²H‐bond variation in myoglobin revealed by high pressure

An infrared study of ²H‐bond variation in myoglobin revealed by high pressure