Use of vibrational spectroscopy to study protein and DNA structure, hydration, and binding of biomolecules: A combined theoretical and experimental approach

Jalkanen, K. J.; Jürgensen, V. Würtz; Claussen, Anetta; Rahim, Abdur; Jensen, Greg; Wade, Rebecca C.; Nardi, F. De; Jung, Christiane; Degtyarenko, Ivan; Nieminen, Risto M.; Herrmann, Frank; Knapp-Mohammady, Michaela; Niehaus, Thomas A.; Frimand, Kenneth; Suhai, Sándor

doi:10.1002/qua.20863

Cited by 70 publications

(51 citation statements)

References 139 publications

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“…To obtain insights into the multicolor bioluminescence of the firefly, the polarized continuum model (PCM) [25,26] in the Gaussian 03 package [27] and the conductor-like screening model (COSMO) [28] in the Turbomole package [29] have been used to treat the effects due to the bulk water on the above two models. [17,18,[30][31][32] Explicit water molecules are often critical in predicting the absorption and emission spectra; for example, Nakatani [16] and Liu et al [33] proposed that explicit water molecules made the bioluminescence shift to red. Herein, we focus on the effects of three factors, namely, metal counter ion, the positively charged Nterminal amino acid, and the possible chemiluminescence by protonation on the emission of the active site molecules, keto(À1), and the resonance structure, keto(À1)', in bulk water.…”

Section: Introductionmentioning

confidence: 99%

“…[16] Moreover, to make the system neutral, the counter ions were often added to charged biological systems. [17,18] Since NaOH and HCl were used to alter the pH in aqueous solution, [19] here we have added sodium cations to study the effects of the counter ions. Nakatani et al also evaluated the interaction energy as the classical Coulombic charge interaction between OxyLH 2 and the surrounding molecules.…”

Section: Introductionmentioning

confidence: 99%

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A Time‐Dependent Density Functional Theory Investigation on the Origin of Red Chemiluminescence

et al. 2010

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Is the resonance-based anionic keto form of oxyluciferin the chemical origin of multicolor bioluminescence? Can it modulate green into red luminescence? There is as yet no definitive answer from experiment or theory. The resonance-based anionic keto forms of oxyluciferin have been proposed as a cause of multicolor bioluminescence in the firefly. We model the possible structures by adding sodium or ammonium cations and investigating the ground- and excited-state geometries as well as the electronic absorption and emission spectra. A role for the resonance structures is obvious in the gas phase. The absorption and emission spectra of the two structures are quite different--one in the blue and another in the red. The differences in the spectra of the models are small in aqueous solution, with all the absorption and emission spectra in the yellow-green region. The resonance-based anionic keto form of oxyluciferin may be one origin of the red-shifted luminescence but is not the exclusive explanation for the variation from green (approximately 530 nm) to red (approximately 635 nm). We study the geometries, absorption, and emission spectra of the possible protonated compounds of keto(-1) in the excited states. A new emitter keto(-1)'-H is considered.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

A Time‐Dependent Density Functional Theory Investigation on the Origin of Red Chemiluminescence

et al. 2010

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“…The later biological repair process of DNA is initiated by the absorption of a photon of light. Hence the process starts on the excited state energy in a very complex environment and evolves in time [247,248]. Clearly all of the tools and methods discussed in this review and covered in this special focus issue are needed to attack such problems.…”

Section: Discussion Conclusion and Perspectivesmentioning

confidence: 99%

Role of quantum chemical calculations in molecular biophysics with a historical perspective

Kukushkin

Jalkanen

2009

Theor Chem Acc

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We discuss how the basic principles of quantum chemistry and quantum mechanics can be and have been applied to a variety of problems in molecular biophysics. First, the historical development of quantum concepts in biophysics is discussed. Next, we describe a series of interesting applications of quantum chemical methods for studying biologically active molecules, molecular structures and some of the important processes which play a role in living organisms. We discuss the application of quantum chemistry to such processes as energy storage and transformation, and the transmission of genetic information. Quantum chemical approaches are essential to comprehend and understand the molecular nature of these processes. To conclude our work, we present a short discussion of the perspectives of quantum chemical methods in modern biophysics, the field of experimental and theoretical chiral vibrational and electronic spectroscopy.

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“…In 2006 Jalkanen et al published complex, combined computational research on IR, vCd, Raman, RoA, and SERS spectroscopy of L-alanine, L-tryptophan, L-histidine, some model peptides, and a variety of small molecules of relevance to protein systems [154]. A variety of computational methods including molecular mechanics, SCC-dFtB (self-consistent charge density functional tight binding) [155], RhF, mP2, and dFt methods were combined with continuous and discrete solvation by several water molecules.…”

Section: Vibrational Chiroptical Studies On Common Amino Acid Charactmentioning

confidence: 99%

α-Amino Acids In Water: A Review Of VCD And ROA Spectra

Dobrowolski

Lipiński

Rode

et al. 2013

Challenges and Advances in Computational Chemistry and Physics

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An up-to-date perspective on the capability of vibrational Circular dichroism (vCd) and Raman optical Activity (RoA) spectroscopy of the 20 encoded α-amino acids to solve the structural problems appearing in water is provided in this review. VCD and ROA spectroscopy of the α-amino acid molecules reviewed in this chapter refer only to free and single amino acids in water at various ph levels. to well understand the implications of such studies for biology and medicine, we devote one subchapter to the role of free amino acids in an organism's metabolism and physiology. A variety of side chains that modify the α-amino acids character from acidic to basic and from hydrophilic to hydrophobic makes the possible dissociation equilibria in water very complex and dependent on several factors. therefore, information on dissociation constants, isoelectric points, and hydrophobicity parameters of α-amino acids is summarised in the next subchapter. The conformational variety, complexity of interactions, and entanglement of equilibria makes considering the influence of these factors on vCd and RoA spectra with quantum chemical analysis absolutely necessary. the elements of the theory of chiroptical vibrational spectra and methods enabling solvent simulations are provided in the subsequent subchapter. We report on experimental methods, techniques and tricks for measuring and simulating the vCd and RoA spectra in water at different ph levels. the review is concluded by listing the not-yet-measured amino acids, a presentation of the main challenges for computational methods, and suggestions for the most promising experimental techniques that may be used in future studies. Keywords

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Use of vibrational spectroscopy to study protein and DNA structure, hydration, and binding of biomolecules: A combined theoretical and experimental approach

Cited by 70 publications

References 139 publications

A Time‐Dependent Density Functional Theory Investigation on the Origin of Red Chemiluminescence

A Time‐Dependent Density Functional Theory Investigation on the Origin of Red Chemiluminescence

Role of quantum chemical calculations in molecular biophysics with a historical perspective

α-Amino Acids In Water: A Review Of VCD And ROA Spectra

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