Clarification of the thermally-induced pretransition of ribonuclease A in solution by principal component analysis and two-dimensional correlation infrared spectroscopy

Wang, Lixu; Wu, Yuqing; Meersman, Filip

doi:10.1016/j.vibspec.2006.05.010

Cited by 15 publications

(24 citation statements)

References 22 publications

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“…In fact, the simulated conformations containing nonnative helix might provide an indication of the pathway to the N-terminal domain-swapped dimer. In earlier MD simulations (34), α1 became completely detached from the main core of the protein at both neutral and low pH, leading to conformations similar to the N-terminal domain-swapped dimer with the same transient nonnative helix (residues [15][16][17][18][19][20][21][22]. At neutral pH, nonnative helix formation was linked to a further movement of the N-terminus away from the core.…”

Section: Temperature-induced Conformational Changes Of Rnase A-secondmentioning

confidence: 99%

“…The structure consists of two lobes, each containing a β-sheet and a helix that packs against it, with the N-terminal helix (α1) partially filling the cleft between the two lobes ( Figure 1A). This cleft contains the active site.The thermal unfolding of RNase A has been studied by differential scanning calorimetry (8-12), nonspecific photochemical surface labeling (13), circular dichroism (14) (and references in 15), Fourier transform infrared (FTIR) (9,(15)(16)(17)(18)(19), Raman (20), and UV spectroscopy (14, 21), NMR (22,23), and limited proteolysis (14,15,21). All of these techniques identify the major unfolding transition of RNase A to be in the range 334-337 K near neutral pH.…”

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confidence: 99%

“…However, principal component analysis of their FTIR and far-UV CD data can detect it (9). Similarly, 2D FTIR correlation techniques (16)(17)(18)(19) also detect the pretransition. The pretransition temperature coincides with the onset of the loss of enzymatic activity (21).…”

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Conformational Changes below the T_m: Molecular Dynamics Studies of the Thermal Pretransition of Ribonuclease A

2007

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Recent work suggests that some native conformations of proteins can vary with temperature. To obtain an atomic-level description of this structural and conformational variation, we have performed all-atom, explicit-solvent molecular dynamics simulations of bovine pancreatic ribonuclease A (RNase A) up to its melting temperature (T m ≈ 337 K). RNase A has a thermal pretransition near 320 K [Stelea, S.D, Pancoska, P., Benight, A.S., Keiderling, T.A. (2001) Prot. Sci. 10, 970-978]. Our simulations identify a conformational change that coincides with this pretransition. Between 310 and 320 K, there is a small but significant decrease in the number of native contacts, β-sheet hydrogen bonding, and deviation of backbone conformation from the starting structure, and an increase in nonnative contacts. Native contacts are lost in β-sheet regions and in α1, partially due to movement of α1 away from the β-sheet core. At 330 and 340 K, a nonnative helical segment forms at residues 15-20, corresponding to a helix observed in the N-terminal domain-swapped dimer [Liu Y.S., Hart, P.J., Schulnegger, M.P., Eisenberg, D. (1998) Proc. Natl. Acad. Sci. USA, 95, 3437-3432]. The conformations observed at the higher temperatures possess native-like topology and overall conformation, with many native contacts, but they have a disrupted active site. We propose that these conformations may represent the native state at elevated temperature, or the N′ state. These simulations show that subtle, functionally important changes in protein conformation can occur below the T m .A typical free-energy diagram for protein folding shows stable macrostates (native, denatured and intermediates, if any) as approximately harmonic energy wells along a global reaction coordinate. A more complete picture considers macrostates composed of ensembles of microstates with similar, but not identical, energies and conformations. Expressed differently, the energy landscape is rugged. Simulation studies, alternative conformations in crystal and solution structures, the inactivation of enzymes under folded conditions, and single molecule enzymology (1) demonstrate that the native state is heterogeneous. Microstates are populated according to the Boltzmann distribution. Changing the temperature changes the relative population of conformational microstates with the macrostate. If the average molecular conformation varies with temperature, the observable properties of the native state will also † This research was supported by National Institutes of Health grant GM50789 (to VD) and a Molecular Biophysics Training Grant 5 T32 GM008268-19 (to EM) *To whom correspondence should be addressed. Email: daggett@u.washington.edu, 206.685.1510 (T), 206.685.3300 (F). 1 RNase A, bovine pancreatic ribonuclease A; MD, molecular dynamics; FTIR, Fourier transform infrared spectroscopy; 2D FTIR, twodimensional Fourier transform infrared correlation spectroscopy; CD, circular dichroism spectroscopy; NMR, nuclear magnetic resonance spectroscopy; UV, ultraviolet; F3C, flexible thr...

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Section: Temperature-induced Conformational Changes Of Rnase A-secondmentioning

confidence: 99%

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Conformational Changes below the T_m: Molecular Dynamics Studies of the Thermal Pretransition of Ribonuclease A

2007

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“…When temperature increases, 2D correlation IR spectra, which is based on thermal perturbation, reveals characteristic behaviors of individual molecular constituents. This method was successfully applied in study of influence of thermally induced perturbation of other biological molecules such as: phospholipid membranes, 21 ribonuclease A, 22 b-purothionin, 23 etc.…”

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Structural analysis of some soluble elastins by means of FT‐IR and 2D IR correlation spectroscopy

Popescu¹,

Vasile²,

Crăciunescu

2010

Biopolymers

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Fourier transform infrared (FT‐IR) spectroscopy combined with 2D correlation spectroscopy has been used to offer some information about stability and structure of some soluble elastins. Temperature has been chosen as the perturbation to monitor the infrared behavior of various soluble elastins, namely, α‐elastin p, α‐elastin, and k‐elastin. In the 3800–2700 cm−1 region, the H‐containing groups were analyzed. The bonded hydroxyls are found to decrease prior to the NH‐related hydrogen bonds and also to the conformational reorganization of hydrocarbon chains. The transition temperatures were evaluated and they were found to agree with those obtained from DSC data. The FTIR spectra and their 2nd derivatives denote that α‐ elastins exhibited amide‐I, ‐II and ‐III bands at 1656, 1539 and 1236 cm−1, respectively, while in k‐elastin these bands were found at 1652 cm−1 for amide I, 1540 cm−1 for amide II and 1248 cm−1 for amide III. The macroscopic IR finger‐print method, which combines: general IR spectra, secondary derivative spectra, and 2D‐IR correlation spectra, is useful to discriminate different elastins. Thus using the differences of the position and intensity of the bands from “fingerprint region” of studied elastins, which include the peaks assigned to CO, CC groups from α‐helix, β‐turn, and the peaks assigned to the amide groups, it is possible to identify and discriminate elastins from each others. Furthermore, the pattern of 2D‐IR correlation spectra under thermal perturbation, allow their direct identification and discrimination. © 2010 Wiley Periodicals, Inc. Biopolymers 93: 1072–1084, 2010.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com

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“…To address such question, one needs tools capable of resolving different elements and revealing minor structural changes. The principal component analysis (PCA) in combination with two-dimensional (2D) infrared correlation spectroscopy can provide answers to this question [4,5]. PCA is a well-established technique in statistics and chemometrics that gives a precise mathematical estimation of changes along the object and variable vectors [6,7].…”

Section: Introductionmentioning

confidence: 99%

Thermally induced early events of ribonuclease A under reducing conditions: Evidenced by principal component analysis and two-dimensional correlation infrared spectroscopy

Wang

Zhang

2009

Vibrational Spectroscopy

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Clarification of the thermally-induced pretransition of ribonuclease A in solution by principal component analysis and two-dimensional correlation infrared spectroscopy

Cited by 15 publications

References 22 publications

Conformational Changes below the T_m: Molecular Dynamics Studies of the Thermal Pretransition of Ribonuclease A

Conformational Changes below the T_m: Molecular Dynamics Studies of the Thermal Pretransition of Ribonuclease A

Structural analysis of some soluble elastins by means of FT‐IR and 2D IR correlation spectroscopy

Thermally induced early events of ribonuclease A under reducing conditions: Evidenced by principal component analysis and two-dimensional correlation infrared spectroscopy

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Clarification of the thermally-induced pretransition of ribonuclease A in solution by principal component analysis and two-dimensional correlation infrared spectroscopy

Cited by 15 publications

References 22 publications

Conformational Changes below the Tm: Molecular Dynamics Studies of the Thermal Pretransition of Ribonuclease A

Conformational Changes below the Tm: Molecular Dynamics Studies of the Thermal Pretransition of Ribonuclease A

Structural analysis of some soluble elastins by means of FT‐IR and 2D IR correlation spectroscopy

Thermally induced early events of ribonuclease A under reducing conditions: Evidenced by principal component analysis and two-dimensional correlation infrared spectroscopy

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Conformational Changes below the T_m: Molecular Dynamics Studies of the Thermal Pretransition of Ribonuclease A

Conformational Changes below the T_m: Molecular Dynamics Studies of the Thermal Pretransition of Ribonuclease A