A novel method for detection of selenomethionine incorporation in protein crystals<i>via</i>Raman microscopy

Vergara, Alessandro; Merlino, Antonello; Pizzo, Elio; D’Alessio, Giuseppe; Mazzarella, L.

doi:10.1107/s0907444907058416

Cited by 23 publications

(52 citation statements)

References 21 publications

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“…Particularly, the melting temperature associated to the trimer disassembly is around 40 °C [2]. The low-resolution picture of (PPG) 10 shows a cylinder with length and diameter of 8.6 and 1.5 nm, respectively. The high resolution (1.3 Å) crystallographic structure of (PPG) 10 (Protein Data Bank code 1K6F) revealed accurate φ and ψ angles, and an alignment between chains driven by the charged extremity (N and C terminals) [1].…”

Section: Introductionmentioning

confidence: 99%

“…(Pro-Pro-Gly) 10 , (PPG) 10 , is a collagen model peptide, whose structure is known at high resolution. Herein, Raman microscopy data of (PPG) 10 powders and single crystals are reported.…”

Section: Introductionmentioning

confidence: 99%

“…Two of these collagen models, (Pro-Pro-Gly) 10 , referred to as (PPG) 10 , and (Pro-Hyp-Gly) 10 (POG) adopt a structural motif typical of a triple helix. (PPG) 10 is well characterized both from a structural [1] and a thermodynamic [2] point of view.…”

Section: Introductionmentioning

confidence: 99%

“…(PPG) 10 is well characterized both from a structural [1] and a thermodynamic [2] point of view. Particularly, the melting temperature associated to the trimer disassembly is around 40 °C [2].…”

Section: Introductionmentioning

confidence: 99%

“…The high resolution (1.3 Å) crystallographic structure of (PPG) 10 (Protein Data Bank code 1K6F) revealed accurate φ and ψ angles, and an alignment between chains driven by the charged extremity (N and C terminals) [1]. Based on high resolution structural information of (PPG) 10 [1], generalized as (X-Y-G) 10 , a new hypothesis was proposed for the extra stabilization induced by Hyp in Y [3]. This hypothesis is based on intrinsic conformational propensities of pyrrolidine rings within the triple helix of (X-Y-Gly) 10 .…”

Section: Introductionmentioning

confidence: 99%

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Correlation between Raman and X-ray crystallography data of (Pro-Pro-Gly)10

Merlino¹,

Sica²,

Mazzarella³

et al. 2008

Biophysical Chemistry

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Model biopolymers are powerful tools to guide the interpretation of physical properties in complex systems. (Pro-Pro-Gly) 10 , (PPG) 10 , is a collagen model peptide, whose structure is known at high resolution. Herein, Raman microscopy data of (PPG) 10 powders and single crystals are reported. The spectra interpretation leads to an accurate assignment of three well-resolved amide bands corresponding to the three peptide bonds (PP, PG and GP) present in the (PPG) 10 structure.These data together with the availability of torsional angles φ and ψ derived from the highresolution crystal structure, provide the opportunity to test the validity of theoretical equations for the calculation of non canonical amide III bands and represent a reference for theoretical calculations of vibrational spectra and for polyproline II detection in complex proteins.Spectroscopic data do not support the indication of two distinct and equally populated up and down conformations of the pyrrolidin rings observed in the (PPG) 10 crystal structure.

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Section: Introductionmentioning

confidence: 99%

“…(Pro-Pro-Gly) 10 , (PPG) 10 , is a collagen model peptide, whose structure is known at high resolution. Herein, Raman microscopy data of (PPG) 10 powders and single crystals are reported.…”

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Correlation between Raman and X-ray crystallography data of (Pro-Pro-Gly)10

Merlino¹,

Sica²,

Mazzarella³

et al. 2008

Biophysical Chemistry

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Combined crystallographic and spectroscopic analysis of Trematomus bernacchii hemoglobin highlights analogies and differences in the peculiar oxidation pathway of Antarctic fish hemoglobins

et al. 2009

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Recent studies have demonstrated that hemoglobins isolated from Antarctic fish undergo peculiar oxidation processes. Here we show, by combining crystallographic and spectroscopic data, that the oxidation pathway of Trematomus bernacchii hemoglobin (HbTb) is distinct from that observed for the major component of Trematomus newnesi (Hb1Tn), despite the high sequence identity of the two proteins and structural similarity of their ferrous and fully oxidized states. Resonance Raman analysis of HbTb autoxidation upon air-exposure reveals the absence of the oxidized pentacoordinated state that was observed for Hb1Tn. The HbTb oxidation pathway is characterized by two ferric species: an aquo hexacoordinated high spin state and a bis-histidyl hexacoordinated low spin form, which appear in the early stages of the oxidation process. The high resolution structure of an intermediate along the oxidation pathway has been determined at 1.4 A resolution. The analysis of the electron density of the heme pocket shows, for both the alpha and the beta iron, the coexistence of multiple binding states. In this partially oxidized form, HbTb exhibits significant deviations from the canonical R state both at the local and global level. The analysis of these modifications highlights the structural correlation between key functional regions of the protein.

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Raman scattering investigation of selenomethionine replacement in protein SOUL crystals

Rossi

Mariotto

Ambrosi

et al. 2009

J Raman Spectroscopy

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The vibrational properties of both wild-type and selenomethionine (SeMet)-substituted protein SOUL crystals have been investigated here by Raman spectroscopy. Several Raman peaks observed in the spectra of methionine and SeMet were identified as specific markers. The unambiguous assignment of these peaks has been inferred by comparing the experimental Raman spectra of the pure amino acids, recorded in solid state and in aqueous solution, and the Raman intensities computed using quantum chemical calculations. Moreover, a quantitative evaluation of the relative amount of SeMet replacement in the crystals of protein SOUL labelled with SeMet has been estimated through the ratio between the Raman intensities of marker peaks. These results offer evidence of the potential of Raman microscopy as a reliable and non-invasive tool for novel in-depth structural investigations in biocrystallography.

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A novel method for detection of selenomethionine incorporation in protein crystalsviaRaman microscopy

Cited by 23 publications

References 21 publications

Correlation between Raman and X-ray crystallography data of (Pro-Pro-Gly)10

Correlation between Raman and X-ray crystallography data of (Pro-Pro-Gly)10

Combined crystallographic and spectroscopic analysis of Trematomus bernacchii hemoglobin highlights analogies and differences in the peculiar oxidation pathway of Antarctic fish hemoglobins

Raman scattering investigation of selenomethionine replacement in protein SOUL crystals

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