Protein dynamics from time resolved UV Raman spectroscopy

Balakrishnan, Gurusamy; Weeks, Colin L.; Ibrahim, Mohammed; Soldatova, Alexandra; Spiro, Thomas G.

doi:10.1016/j.sbi.2008.06.001

Cited by 69 publications

(64 citation statements)

References 40 publications

(48 reference statements)

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“…This view has been most prominently propagated in the works of the Frauenfelder, Freire, Nussinov, and Wolynes groups (6,(36)(37)(38)(39). The experimental hints in support of this new paradigm, were provided over the years by a variety of different techniques (40,41), in particular by NMR (19) and other spectroscopic methods (42). Recently, single-molecule studies allowed us to glimpse into the distribution itself (ion channel opening, kinesins walking on tubulin).…”

Section: Discussionmentioning

confidence: 99%

Global distribution of conformational states derived from redundant models in the PDB points to non-uniqueness of the protein structure

Burra¹,

Zhang

Godzik

et al. 2009

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

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Section: Discussionmentioning

confidence: 99%

Global distribution of conformational states derived from redundant models in the PDB points to non-uniqueness of the protein structure

Burra¹,

Zhang

Godzik

et al. 2009

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

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“…The instrument response is rapid. For example, structural changes of proteins occurring within a picosecond-to-millisecond range have been successfully monitored by using UV Raman spectroscopy (75). Other important protein conformational changes, such as alpha-helix peptide folding and unfolding, can be monitored by using UV resonance Raman spectroscopy on a nanosecond time scale (68).…”

Section: Discussionmentioning

confidence: 99%

Detection of Receptor-Induced Glycoprotein Conformational Changes on Enveloped Virions by Using Confocal Micro-Raman Spectroscopy

Liu

Benavides-Montaño

et al. 2013

J Virol

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Conformational changes in the glycoproteins of enveloped viruses are essential for membrane fusion, a critical step during both viral entry and the pathognomonic cell-cell fusion (syncytia) associated with many viral infections, such as those of the paramyxoviruses. However, technologies that detect glycoprotein conformational changes on actual enveloped virions are difficult and time-consuming for those viruses for which such detection is possible (1-6). Additionally, there is a great need for rapid identification and characterization of virions in medical, veterinary, or food samples. Having a method with these capabilities would advance the fields of virus diagnosis and analysis.Our model, Nipah virus (NiV), is an enveloped virus in the important Paramyxoviridae family, which comprises human and veterinary enveloped viruses such as measles virus, mumps virus, Newcastle disease virus, respiratory syncytial virus, canine distemper virus, the metapneumoviruses, the human parainfluenza viruses, Hendra virus (HeV), and NiV (6-8). NiV is an emerging zoonotic virus in the Henipavirus genus that causes severe illness in humans, characterized by encephalitis and respiratory disease associated with syncytium formation (7, 9). Although NiV causes 40 to 75% mortality in humans, there is no approved treatment; thus, NiV is classified as a biosafety level 4 agent and a priority pathogen in the NIH/NIAID agenda. Additionally, because paramyxoviruses are relatively stable in aerosols and NiV is capable of animal-to-animal, animal-to-human, and human-to-human transmission, NiV is considered a potential agro-and/or bioterrorism agent (7).Conformational changes of the viral glycoproteins are required for viral entry and cell-cell fusion. However, it is difficult to obtain X-ray crystal structural information from intact full-length glycoproteins because their hydrophobic transmembrane regions are embedded in a lipid membrane. Therefore, structural studies have been skewed toward ectodomain glycoprotein forms because it is relatively more straightforward to obtain structural information for them. Viral glycoprotein conformational changes have typically been observed either by analysis of viral glycoprotein soluble ectodomain forms (e.g., see references 10-12) or by analysis of full-length wild-type glycoproteins expressed on cell surfaces (e.g., see reference 13). Although soluble ectodomains normally bind their respective cell receptors, it is often not possible to assess how accurately their structures and structural changes compare with those of their membrane-bound full-length wild-type counterparts. Moreover, the tendency of soluble glycoprotein ectodomains to adopt postfusion conformations in many cases limits our ability to detect and characterize essential glycoprotein receptorinduced conformational changes (12,14). Analysis of receptorinduced conformational changes of full-length wild-type glycoproteins embedded in cellular or viral membranes is preferred, and even for such analyses, there may be differences in the role...

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“…To obtain more information about the structure and function of quinones, Raman spectroscopy is an incisive technique for studying aqueous biological samples giving fingerprint information on the chemical bond vibrations of target molecules [9,10]. Previous Raman investigations of benzoquinone (BQ), BQ anion radicals, and benzoquinols have shown that the C-O associated vibrations of these three species are distinguishable [11][12][13].…”

Section: Introductionmentioning

confidence: 99%

Directly probing redox-linked quinones in photosystem II membrane fragments via UV resonance Raman scattering

Chen

Yao

Pagba

et al. 2015

Biochimica et Biophysica Acta (BBA) - Bioenergetics

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In photosynthesis, photosystem II (PSII) harvests sunlight with bound pigments to oxidize water and reduce quinone to quinol, which serves as electron and proton mediators for solar-to-chemical energy conversion. At least two types of quinone cofactors in PSII are redox-linked: QA, and QB. Here, we for the first time apply 257-nm ultraviolet resonance Raman (UVRR) spectroscopy to acquire the molecular vibrations of plastoquinone (PQ) in PSII membranes. Owing to the resonance enhancement effect, the vibrational signal of PQ in PSII membranes is prominent. A strong band at 1661 cm(-1) is assigned to ring CC/CO symmetric stretch mode (ν8a mode) of PQ, and a weak band at 469 cm(-1) to ring stretch mode. By using a pump-probe difference UVRR method and a sample jet technique, the signals of QA and QB can be distinguished. A frequency difference of 1.4 cm(-1) in ν8a vibrational mode between QA and QB is observed, corresponding to ~86 mV redox potential difference imposed by their protein environment. In addition, there are other PQs in the PSII membranes. A negligible anharmonicity effect on their combination band at 2130 cm(-1) suggests that the 'other PQs' are situated in a hydrophobic environment. The detection of the 'other PQs' might be consistent with the view that another functional PQ cofactor (not QA or QB) exists in PSII. This UVRR approach will be useful to the study of quinone molecules in photosynthesis or other biological systems.

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Protein dynamics from time resolved UV Raman spectroscopy

Cited by 69 publications

References 40 publications

Global distribution of conformational states derived from redundant models in the PDB points to non-uniqueness of the protein structure

Global distribution of conformational states derived from redundant models in the PDB points to non-uniqueness of the protein structure

Detection of Receptor-Induced Glycoprotein Conformational Changes on Enveloped Virions by Using Confocal Micro-Raman Spectroscopy

Directly probing redox-linked quinones in photosystem II membrane fragments via UV resonance Raman scattering

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