C−D Modes of Deuterated Side Chain of Leucine as Structural Reporters via Dual-frequency Two-dimensional Infrared Spectroscopy

Abstract

Perdeuteration of the side chains of amino acids such as leucine results in appearance of reasonably strong absorption peaks around 2050-2220 cm(-1) that belong to the CD stretching modes and exhibit extinction coefficients of up to 120 M(-1) cm(-1). The properties of the CD stretching transitions in leucine-d(10) as structural labels are studied via the methods of two-dimensional infrared (2DIR) spectroscopy. The cross peaks caused by interactions of the CD stretching modes with amide I (Am-I), CO, and amide II (Am-II) modes are obtained by the dual-frequency 2DIR method. The CD stretching peaks in leucine-d(10) are characterized using DFT computational modeling as well as relaxation-assisted 2DIR (RA 2DIR) measurements. The RA 2DIR measurements showed different enhancements and different energy transport times (arrival times) for different CD/Am-II and CD/CO cross peaks; a correlation between the intermode distance, the arrival time, and the amplification factor is reported. We demonstrated that the CD transitions of leucine-d(10) amino acid can serve as convenient structural reporters via the dual-frequency 2DIR methods and discussed the potential of leucine-d(10) and other amino acids with deuterium-labeled side chains as probes of protein structure and dynamics.

Transition from IVR limited vibrational energy transport to bulk heat transport

“…In our experiments [19][20][21][22], the amount of vibrational energy in the vicinity of a peptide unit is measured by probing the transient IR frequency shift of a localized C=O mode. The same mechanism has been used in the context of other IR reporter groups like C−D [6] and NO 2 -vibrations [7]. The physical origin of that thermometer is the well-known Dunham expansion of the vibrational energy…”

“…Heat transport in nanoscale objects [1] has reached considerable interest, both in low-dimensional structures like nanotube thermal rectifiers [2], anharmonic molecular junctions [3], longchain hydrocarbon molecules [4] and bridged azulene-anthracene compounds [5], but also in more complicated structures reaching from single amino acids [6,7], small molecules in solution [8], phospholipid bilayer liposomes [9], reverse micelles [10] to real proteins [11][12][13][14]. In all cases, large temperature gradients are generated over length scales of a few chemical bonds and vibrational excess energy is dissipated on a few picosecond timescale.…”

Vibrational Energy Transport through a Capping Layer of Appropriately Designed Peptide Helices over Gold Nanoparticles

“…In a similar manner, vibrational sum-frequency generation from molecular chains on a bulk gold surface has been studied by Dlott and coworkers [19,20]. Also 2-dimensional IR spectroscopy is a versatile tool to study energy transport processes [21,22].…”

Two-dimensional IR spectroscopy and segmental 13 C labeling reveals the domain structure of human γD-crystallin amyloid fibrils

“…Even if longer sequences could be synthesized, a single 13 C ¼ 18 O label would eventually be obscured by Glu, Asp, and Arg side chains, as well as natural abundance 13 C ¼ 16 O bonds, all of which absorb in the same frequency range (18). Nonnatural amino acids and deuterium labels are well-resolved in protein IR spectra, but only report on local environment not structure (19)(20)(21). In this article, we describe an alternative approach in which we isotope label an entire section of a protein rather than a single C═O bond.…”