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Erratum: Internal friction in enzyme reactions, IUBMB life, 2012, Jan;65(1):35-42. IUBMB Life 2013. [DOI: 10.1002/iub.1225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Rauscher A, Derényi I, Gráf L, Málnási-Csizmadia A. Internal friction in enzyme reactions. IUBMB Life 2013; 65:35-42. [PMID: 23281036 DOI: 10.1002/iub.1101] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Accepted: 09/21/2012] [Indexed: 11/11/2022]
Abstract
The empirical concept of internal friction was introduced 20 years ago. This review summarizes the results of experimental and theoretical studies that help to uncover the nature of internal friction. After the history of the concept, we describe the experimental challenges in measuring and interpreting internal friction based on the viscosity dependence of enzyme reactions. We also present speculations about the structural background of this viscosity dependence. Finally, some models about the relationship between the energy landscape and internal friction are outlined. Alternative concepts regarding the viscosity dependence of enzyme reactions are also discussed.
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Affiliation(s)
- Anna Rauscher
- Department of Biochemistry, Eötvös University, Budapest, Hungary
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Beauchamp DL, Khajehpour M. The effect of lithium ions on the hydrophobic effect: does lithium affect hydrophobicity differently than other ions? Biophys Chem 2012; 163-164:35-43. [DOI: 10.1016/j.bpc.2012.02.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2012] [Revised: 02/06/2012] [Accepted: 02/06/2012] [Indexed: 10/14/2022]
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Phosphate Assisted Proton Transfer in Water and Sugar Glasses: A Study Using Fluorescence of Pyrene-1-carboxylate and IR Spectroscopy. J Fluoresc 2008; 19:21-31. [DOI: 10.1007/s10895-008-0375-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2008] [Accepted: 04/10/2008] [Indexed: 10/22/2022]
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Nibbs J, Vinogradov SA, Vanderkool JM, Zelent B. Flexibility in Proteins: Tuning the Sensitivity to O2 Diffusion by Varying the Lifetime of a Phosphorescent Sensor in Horseradish Peroxidase¶. Photochem Photobiol 2007. [DOI: 10.1111/j.1751-1097.2004.tb00046.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Finkelstein IJ, Ishikawa H, Kim S, Massari AM, Fayer MD. Substrate binding and protein conformational dynamics measured by 2D-IR vibrational echo spectroscopy. Proc Natl Acad Sci U S A 2007; 104:2637-42. [PMID: 17296942 PMCID: PMC1815234 DOI: 10.1073/pnas.0610027104] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2006] [Indexed: 11/18/2022] Open
Abstract
Enzyme structural dynamics play a pivotal role in substrate binding and biological function, but the influence of substrate binding on enzyme dynamics has not been examined on fast time scales. In this work, picosecond dynamics of horseradish peroxidase (HRP) isoenzyme C in the free form and when ligated to a variety of small organic molecule substrates is studied by using 2D-IR vibrational echo spectroscopy. Carbon monoxide bound at the heme active site of HRP serves as a spectroscopic marker that is sensitive to the structural dynamics of the protein. In the free form, HRP assumes two distinct spectroscopic conformations that undergo fluctuations on a tens-of-picoseconds time scale. After substrate binding, HRP is locked into a single conformation that exhibits reduced amplitudes and slower time-scale structural dynamics. The decrease in carbon monoxide frequency fluctuations is attributed to reduced dynamic freedom of the distal histidine and the distal arginine, which are key residues in modulating substrate binding affinity. It is suggested that dynamic quenching caused by substrate binding can cause the protein to be locked into a conformation suitable for downstream steps in the enzymatic cycle of HRP.
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Affiliation(s)
| | - Haruto Ishikawa
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Seongheun Kim
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Aaron M. Massari
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - M. D. Fayer
- Department of Chemistry, Stanford University, Stanford, CA 94305
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Finkelstein IJ, Zheng J, Ishikawa H, Kim S, Kwak K, Fayer MD. Probing dynamics of complex molecular systems with ultrafast 2D IR vibrational echo spectroscopy. Phys Chem Chem Phys 2007; 9:1533-49. [PMID: 17429547 DOI: 10.1039/b618158a] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ultrafast 2D IR vibrational echo spectroscopy is described and a number of experimental examples are given. Details of the experimental method including the pulse sequence, heterodyne detection, and determination of the absorptive component of the 2D spectrum are outlined. As an initial example, the 2D spectrum of the stretching mode of CO bound to the protein myoglobin (MbCO) is presented. The time dependence of the 2D spectrum of MbCO, which is caused by protein structural evolution, is presented and its relationship to the frequency-frequency correlation function is described and used to make protein structural assignments based on comparisons to molecular dynamics simulations. The 2D vibrational echo experiments on the protein horseradish peroxidase are presented. The time dependence of the 2D spectra of the enzyme in the free form and with a substrate bound at the active site are compared and used to examine the influence of substrate binding on the protein's structural dynamics. The application of 2D vibrational echo spectroscopy to the study of chemical exchange under thermal equilibrium conditions is described. 2D vibrational echo chemical exchange spectroscopy is applied to the study of formation and dissociation of organic solute-solvent complexes and to the isomerization around a carbon-carbon single bond of an ethane derivative.
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Ohta Y, Mukouyama EB, Suzuki H. Kinetic Isotope Effect of the l-Phenylalanine Oxidase from Pseudomonas sp. P-501. ACTA ACUST UNITED AC 2006; 139:551-5. [PMID: 16567420 DOI: 10.1093/jb/mvj049] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Pseudomonas L-phenylalanine oxidase (deaminating and decarboxylating) mainly catalyzes oxygenation when L-phenylalanine is used as the substrate, but oxidation when L-methionine is used as the substrate. Using [C(alpha)-H]-DL-methionine and [C(alpha)-D]-DL-methionine as substrate, the reductive half reaction of FAD cofactor of enzyme has been studied by stopped-flow spectrophotometry. The rate of reduction of FAD cofactor has a kinetic isotope effect (KIE) of 5.4 and 4.1 in the absence and presence of 30% glycerol, respectively. The KIE is independent of temperature, but the rates of the reductive half reaction are dependent on temperature, indicating that thermally induced motion at the active site drives the H-transfer reaction by H-tunneling.
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Affiliation(s)
- Yui Ohta
- Division of Biosciences, Graduate School of Fundamental Life Science, Kitasato University, Sagamihara, Kanagawa
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Vanderkooi JM, Dashnau JL, Zelent B. Temperature excursion infrared (TEIR) spectroscopy used to study hydrogen bonding between water and biomolecules. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2005; 1749:214-33. [PMID: 15927875 DOI: 10.1016/j.bbapap.2005.03.008] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2004] [Revised: 02/15/2005] [Accepted: 03/09/2005] [Indexed: 11/22/2022]
Abstract
Water is a highly polar molecule that is capable of making four H-bonding linkages. Stability and specificity of folding of water-soluble protein macromolecules are determined by the interplay between water and functional groups of the protein. Yet, under some conditions, water can be replaced with sugar or other polar protic molecules with retention of protein structure. Infrared (IR) spectroscopy allows one to probe groups on the protein that interact with solvent, whether the solvent is water, sugar or glycerol. The basis of the measurement is that IR spectral lines of functional groups involved in H-bonding show characteristic spectral shifts with temperature excursion, reflecting the dipolar nature of the group and its ability to H-bond. For groups involved in H-bonding to water, the stretching mode absorption bands shift to lower frequency, whereas bending mode absorption bands shift to higher frequency as temperature decreases. The results indicate increasing H-bonding and decreasing entropy occurring as a function of temperature, even at cryogenic temperatures. The frequencies of the amide group modes are temperature dependent, showing that as temperature decreases, the amide group H-bonds to water strengthen. These results are relevant to protein stability as a function of temperature. The influence of solvent relaxation is demonstrated for tryptophan fluorescence over the same temperature range where the solvent was examined by infrared spectroscopy.
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Affiliation(s)
- Jane M Vanderkooi
- Johnson Research Foundation, Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, Philadelphia, 19104-6059, USA.
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Kaposi AD, Prabhu NV, Dalosto SD, Sharp KA, Wright WW, Stavrov SS, Vanderkooi JM. Solvent dependent and independent motions of CO-horseradish peroxidase examined by infrared spectroscopy and molecular dynamics calculations. Biophys Chem 2004; 106:1-14. [PMID: 14516907 DOI: 10.1016/s0301-4622(03)00122-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The role of the solvent matrix in affecting CO bound to ferrous horseradish peroxidase was examined by comparing band-widths of nu(CO) for the protein in aqueous solutions and in trehalose/sucrose glasses. We have previously observed that the optical absorption band and the CO stretching mode respond to the glass transition of glycerol/water in ways that depend upon the presence of substrate (Biochemistry 40 (2001) 3483). It is now demonstrated that the CO group band-width for the protein with bound inhibitor benzhydroxamic acid is relatively insensitive to temperature or the glass transition of the solvent. In contrast, in the absence of inhibitor, the band-width varies with the temperature that the glass is formed. The results show that solvent dependent and independent motions can be distinguished, and that the presence of substrate changes the protein such that the Fe[bond]CO site is occluded from the solvent conditions. Molecular dynamic calculations, based upon X-ray structures, showed that the presence of benzhydroxamic acid decreases the distance between His42 and Arg38 and this leads for closer distances to the O of the CO from these residues. These results are invoked to account for the observed line width changes of the CO band.
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Affiliation(s)
- Andras D Kaposi
- Department of Biophysics and Radiation Biology, Semmelweis University, Puskin u. 9, Budapest H-1088, Hungary
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Zelent B, Kaposi AD, Nucci NV, Sharp KA, Dalosto SD, Wright WW, Vanderkooi JM. Water Channel of Horseradish Peroxidase Studied by the Charge-Transfer Absorption Band of Ferric Heme. J Phys Chem B 2004. [DOI: 10.1021/jp037664q] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- B. Zelent
- Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, and Department of Biophysics and Radiation Biology, Semmelweis University of Medicine, H-1444 P.O.B. 263, Budapest, Hungary
| | - A. D. Kaposi
- Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, and Department of Biophysics and Radiation Biology, Semmelweis University of Medicine, H-1444 P.O.B. 263, Budapest, Hungary
| | - N. V. Nucci
- Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, and Department of Biophysics and Radiation Biology, Semmelweis University of Medicine, H-1444 P.O.B. 263, Budapest, Hungary
| | - K. A. Sharp
- Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, and Department of Biophysics and Radiation Biology, Semmelweis University of Medicine, H-1444 P.O.B. 263, Budapest, Hungary
| | - S. D. Dalosto
- Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, and Department of Biophysics and Radiation Biology, Semmelweis University of Medicine, H-1444 P.O.B. 263, Budapest, Hungary
| | - W. W. Wright
- Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, and Department of Biophysics and Radiation Biology, Semmelweis University of Medicine, H-1444 P.O.B. 263, Budapest, Hungary
| | - J. M. Vanderkooi
- Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, and Department of Biophysics and Radiation Biology, Semmelweis University of Medicine, H-1444 P.O.B. 263, Budapest, Hungary
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Nibbs J, Vinogradov SA, Vanderkooi JM, Zelent B. Flexibility in Proteins: Tuning the Sensitivity to O2 Diffusion by Varying the Lifetime of a Phosphorescent Sensor in Horseradish Peroxidase¶. Photochem Photobiol 2004; 80:36-40. [PMID: 15339214 DOI: 10.1562/2004-01-17-ra-046.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The heme in horseradish peroxidase (HRP) was replaced by phosphorescent Pt-mesoporphyrin IX (PtMP), which acted as a phosphorescent marker of oxygen quenching and allowed comparison with another probe, Pd-mesoporphyrin IX (Khajehpour et al. (2003) Proteins 53, 656-666). Benzohydroxamic acid (BHA), a competitive inhibitor of the enzyme, was also used to monitor its effects on phosphorescence quenching. With the addition of BHA, in the presence of oxygen, the phosphorescence intensity of the protein increased. In contrast, the addition of BHA, in the absence of oxygen, reduced the phosphorescence intensity of the protein. K(d) = 18 microM when BHA binds to PtMP-HRP. The effect of BHA can be explained by two factors: (1) BHA reduces the accessibility of O(2) to the protein interior and (2) BHA itself quenches the phosphorescence. Consistent with this, the oxygen quenching of the phosphorescence of PtMP-HRP gave a quenching constant of k(q) = 234 mm Hg(-1) s(-1) in the absence of BHA and k(q) = 28.7 mm Hg(-1) s(-1) in the presence of BHA. The quenching rate of BHA is 4000 s(-1). The relative quantum yield of the phosphorescence of the Pt derivative is about six times that of the Pd derivative, whereas the phosphorescence lifetime is approximately eight times shorter. The high quantum yield and suitable lifetime make Pt-porphyrins appropriate as sensors of O(2) diffusion and flexibility in heme proteins.
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Affiliation(s)
- Janna Nibbs
- Department of Biochemistry and Biophysics, Johnson Research Foundation, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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Khajehpour M, Rietveld I, Vinogradov S, Prabhu NV, Sharp KA, Vanderkooi JM. Accessibility of oxygen with respect to the heme pocket in horseradish peroxidase. Proteins 2003; 53:656-66. [PMID: 14579357 DOI: 10.1002/prot.10475] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Oxygen and other molecules of similar size take part in a variety of protein reactions. Therefore, it is critical to understand how these small molecules penetrate the protein matrix. The protein system studied in this case is horseradish peroxidase (HRP). We have converted the native HRP into a phosphorescent analog by replacing the heme prosthetic group by Pd-mesoporphyrin. Oxygen readily quenches the phosphorescence of Pd porphyrins, and this can be used to characterize oxygen diffusion through the protein matrix. Our measurements indicate that solvent viscosity and pH modulate the accessibility of the heme pocket relative to small molecules. The binding of the substrate benzohydroxamic acid (BHA) to the protein drastically impedes oxygen access to the heme pocket. These results indicate that, first, the penetration of small molecules through the protein matrix is a function of protein dynamics, and second, there are specific pathways for the diffusion of these molecules. The effect of substrate and pH on protein dynamics has been investigated with the use of molecular dynamics calculations. We demonstrate that the model of a "fluctuating entry point," as suggested by Zwanzig (J Chem Phys 1992;97:3587-3589), properly describes the diffusion of oxygen through the protein matrix.
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Affiliation(s)
- Mazdak Khajehpour
- Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
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Wright WW, Guffanti GT, Vanderkooi JM. Protein in sugar films and in glycerol/water as examined by infrared spectroscopy and by the fluorescence and phosphorescence of tryptophan. Biophys J 2003; 85:1980-95. [PMID: 12944311 PMCID: PMC1303370 DOI: 10.1016/s0006-3495(03)74626-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Sugars are known to stabilize proteins. This study addresses questions of the nature of sugar and proteins incorporated in solid sugar films. Infrared (IR) and Raman spectroscopy was used to examine trehalose and sucrose films and glycerol/water solvent. Proteins and indole-containing compounds that are imbedded in the sugar films were studied by IR and optical (absorption, fluorescence, and phosphorescence) spectroscopy. Water is able to move in the sugar films in the temperature range of 20-300 K as suggested by IR absorption bands of HOH bending and OH stretching modes that shift continuously with temperature. In glycerol/water these bands reflect the glass transition at approximately 160 K. The fluorescence of N-acetyl-L-tryptophanamide and tryptophan of melittin, Ca-free parvalbumin, and staphylococcal nuclease in dry trehalose/sucrose films remains broad and red-shifted over a temperature excursion of 20-300 K. In contrast, the fluorescence of these compounds in glycerol/water solvent shift to the blue as temperature decreases. The fluorescence of the buried tryptophan in Ca-bound parvalbumin in either sugar film or glycerol/water remains blue-shifted and has vibronic resolution over the entire temperature range. The red shift for fluorescence of indole groups exposed to solvent in the sugars is consistent with the motion of water molecules around the excited-state molecule that occurs even at low temperature, although the possibility of static complex formation between the excited-state molecule and water or other factors is discussed. The phosphorescence yield for protein and model indole compounds is sensitive to the matrix glass transition. Phosphorescence emission spectra are resolved and shift little in different solvents or temperature, as predicted by the small dipole moment of the excited triplet state molecule. The conclusion is that the sugar film maintains the environment present at the glass formation temperature for surface Trp and amide groups over a wide temperature excursion. In glycerol/water these groups reflect local changes in the environment as temperature changes.
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Affiliation(s)
- Wayne W Wright
- Johnson Research Foundation, Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, Philadelphia Pennsylvania 19104, USA
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