Low frequency vibrations of amino acid homopolymers observed by synchrotron far-ir absorption spectroscopy: Excited state effects dominate the temperature dependence of the spectra

Xie, Aihua; He, Qin; Miller, Lisa M.; Sclavi, Bianca; Chance, Mark R.

doi:10.1002/(sici)1097-0282(199906)49:7<591::aid-bip5>3.0.co;2-q

Cited by 41 publications

(32 citation statements)

References 31 publications

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“…If fact, experimental measurements for the helical structure of bacteriorhodopsin produced conformational transition times of ca. 65 and 400 ns, which give the oscillation frequencies of 15.4 and 2.5 MHz, respectively [39][40][41][42]. These secondary-structure conformational vibrations are already close to our frequency range, while those of the tertiary structure should have still lower frequencies, due to larger effective masses and lower effective force constants.…”

Section: Acoustic Wave Interaction With the Biopolymer Moleculesupporting

confidence: 52%

Dynamics of secondary and tertiary structure relaxation of a cyclic penta-peptide: Time-resolved FTIR studies

Makarov¹,

Khmelinskii²

2006

Chemical Physics

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Section: Acoustic Wave Interaction With the Biopolymer Moleculesupporting

confidence: 52%

Dynamics of secondary and tertiary structure relaxation of a cyclic penta-peptide: Time-resolved FTIR studies

Makarov¹,

Khmelinskii²

2006

Chemical Physics

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“…The excitation and relaxation of these collective modes are generally achieved via anharmonic interactions with other normal modes for energy exchange. It is believed that low frequency collective modes are responsible for the directed flow of conformational energy for a variety of vital biological processes ranging from electron transfer [1][2][3] to enzyme action [4,5]. However, without the knowledge of the actual lifetimes of these states it is extremely difficult to connect theory and experiment.…”

Section: Introductionmentioning

confidence: 99%

Excited-State Lifetimes of Far-Infrared Collective Modes in Proteins

2001

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Abstract. Vibrational excitations of low frequency collective modes are essential for functionally important conformational transitions in proteins. Here we report the first direct measurement on the lifetime of vibrational excitations of the collective modes at 87 pm (115 cm −1 ) in bacteriorhodopsin, a transmembrane protein. The data show that these modes have extremely long lifetime of vibrational excitations, over 500 picoseconds, accommodating 1500 vibrations. We suggest that there is a connection between this relatively slow anharmonic relaxation rate of approximately 10 g sec −1 and the similar observed rate of conformational transitions in proteins, which require require multi-level vibrational excitations and energy exchanges with other vibrational modes and collisional motions of solvent molecules.

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“…Conventional IR spectromicroscopy examination of biological tissues has limitations (10)(11)(12) including an insufficient spatial resolution of only ~20-25 μm. These problems are overcome by synchrotron IR light by virtue of its brightness, which is 100-1000 times greater than that from a conventional source (13).…”

Section: Discussionmentioning

confidence: 99%

Fourier transform infrared spectromicroscopy and hierarchical cluster analysis of human meningiomas

Ali

Lu²,

Christensen³

et al. 2008

Int J Mol Med

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Abstract. Limitations of conventional light microscopy in pathological diagnosis of brain tumors include subjective bias in interpretation and discordance of nomenclature. A study using mid-infrared (IR) spectromicroscopy was undertaken to determine whether meningiomas, a group of brain tumors prone to recurrence, could be identified by the unique spectral 'fingerprints' of their chemical composition. Paired, thin (5-μm) cryosections of snap-frozen human meningioma tumor samples removed at elective surgery were mounted on glass (hematoxylin and eosin-stained tissue section) and infrared (unstained tissue section) reflectance slides, respectively. Concordance of the tumor-bearing areas identified in the stained section by a pathologist with the unstained IR tissue section was ensured using a novel digital grid and tumor-mapping system developed in our laboratory. Compared with the normal control, tumor samples from four meningioma patients revealed a marked decrease in bands associated with unsaturated fatty acids, particularly in the bands at 3010, 2920, 2850, and 1735 cm -1 . Spectral datasets were subjected to hierarchical cluster analyses (HCA) using Ward's algorithm for comparison and grouping of similar data groups, and were converted into color-coded digital maps for matching spectra with their respective clusters. False color images of 5 and 6 clusters obtained by HCA identified dominant clusters corresponding to tumor tissue. Corroboration of these findings in a larger number of meningiomas may allow for more precise identification of these and other types of brain tumors.

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Low frequency vibrations of amino acid homopolymers observed by synchrotron far-ir absorption spectroscopy: Excited state effects dominate the temperature dependence of the spectra

Cited by 41 publications

References 31 publications

Dynamics of secondary and tertiary structure relaxation of a cyclic penta-peptide: Time-resolved FTIR studies

Dynamics of secondary and tertiary structure relaxation of a cyclic penta-peptide: Time-resolved FTIR studies

Excited-State Lifetimes of Far-Infrared Collective Modes in Proteins

Fourier transform infrared spectromicroscopy and hierarchical cluster analysis of human meningiomas

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