Coupled vibrations in peptides and proteins: Structural information using 2D-IR spectroscopy

We describe experimental evidence of how detecting the coupling between vibrations can give access to structural information of proteins and peptides at the molecular level. We focus on the investigation of the folded and unfolded states of proteins and peptides in equilibrium. We investigate two types of vibrations: those involved in salt bridges, and backbone amide I vibrations, and the size of the systems than we study ranges from a dimer formed by a few atoms to proteins formed by several hundreds of atoms. The first three chapters are introductory. In Chapter 4 we present the characterization of the 2D-IR response of salt bridges in solution formed by guanidinium and acetate. Chapter 5 is closely related, and we show how the 2D-IR response of a salt bridge between arginine and glutamic acid can be detected in peptides in solution. In Chapter 6 we study the amide I vibrations of tripeptides, and discuss the conformational changes upon variation in the charges of the side groups and C-terminus. The next two chapters contain a study of the chemical-denaturation mechanism of guanidinium, which is a powerful denaturant. In Chapter 7 we investigate the guanidinium-induced denaturation of two well-known proteins, lysozyme and α-chymotrypsin. In Chapter 8 we study how guanidinium affects the stability of a designed mini-protein, a zinc-finger mutant, which has structural properties that differ from most natural proteins. Finally, in Chapter 9 we introduce the topic of amyloid-fibril formation, and show how the appearance of fibrils in lysozyme can be induced with a ‘temperature-shock’

Protein Denaturation with Guanidinium: A 2D-IR Study

[Image: see text] Guanidinium (Gdm(+)) is a widely used denaturant, but it is still largely unknown how it operates at the molecular level. In particular, the effect of guanidinium on the different types of secondary structure motifs of proteins is at present not clear. Here, we use two-dimensional infrared spectroscopy (2D-IR) to investigate changes in the secondary structure of two proteins with mainly α-helical or β-sheet content upon addition of Gdm-(13)C(15)N(3)·Cl. We find that upon denaturation, the β-sheet protein shows a complete loss of β-sheet structure, whereas the α-helical protein maintains most of its secondary structure. These results suggest that Gdm(+) disrupts β-sheets much more efficiently than α-helices, possibly because in the former, hydrophobic interactions are more important and the number of dangling hydrogen bonds is larger

The structure of salt bridges between Arg+ and Glu- in peptides investigated with 2D-IR spectroscopy: Evidence for two distinct hydrogen-bond geometries

Salt bridges play an important role in protein folding and in supramolecular chemistry, but they are difficult to detect and characterize in solution. Here, we investigate salt bridges between glutamate (Glu−) and arginine (Arg+) using two-dimensional infrared (2D-IR) spectroscopy. The 2D-IR spectrum of a salt-bridged dimer shows cross peaks between the vibrational modes of Glu− and Arg+, which provide a sensitive structural probe of Glu−⋯Arg+ salt bridges. We use this probe to investigate a β-turn locked by a salt bridge, an α-helical peptide whose structure is stabilized by salt bridges, and a coiled coil that is stabilized by intra- and intermolecular salt bridges. We detect a bidentate salt bridge in the β-turn, a monodentate one in the α-helical peptide, and both salt-bridge geometries in the coiled coil. To our knowledge, this is the first time 2D-IR has been used to probe tertiary side chain interactions in peptides, and our results show that 2D-IR spectroscopy is a powerful method for investigating salt bridges in solution

Solvent-Exposed Salt Bridges Influence the Kinetics of α-Helix Folding and Unfolding

Salt bridges are known to play an essential role in the thermodynamic stability of the folded conformation of many proteins, but their influence on the kinetics of folding remains largely unknown. Here, we investigate the effect of Glu-Arg salt bridges on the kinetics of α-helix folding using temperature-jump transient-infrared spectroscopy and steady-state UV circular dichroism. We find that geometrically optimized salt bridges (Glu- and Arg+ are spaced four peptide units apart, and the Glu/Arg order is such that the side-chain rotameric preferences favor salt-bridge formation) significantly speed up folding and slow down unfolding, whereas salt bridges with unfavorable geometry slow down folding and slightly speed up unfolding. Our observations suggest a possible explanation for the surprising fact that many biologically active proteins contain salt bridges that do not stabilize the native conformation: these salt bridges might have a kinetic rather than a thermodynamic function

Folding Dynamics of the Trp-Cage Miniprotein: Evidence for a Native-Like Intermediate from Combined Time-Resolved Vibrational Spectroscopy and Molecular Dynamics Simulations

Trp-cage is a synthetic 20-residue miniprotein which folds rapidly and spontaneously to a well-defined globular structure more typical of larger proteins. Due to its small size and fast folding, it is an ideal model system for experimental and theoretical investigations of protein folding mechanisms. However, Trp-cage's exact folding mechanism is still a matter of debate.,Here we investigate Trp-cage's relaxation dynamics in the amide I' spectral region (1530- 1700 cm(-1)) using time-resolved infrared spectroscopy. Residue-specific information was obtained by incorporating an isotopic label (C-13=O-18) into the amide carbonyl group of residue Gly11, thereby spectrally isolating an individual 3(10)-helical residue. The folding unfolding equilibrium is perturbed using a nanosecond temperature jump (T jump), and the subsequent re-equilibration is probed by observing the time dependent vibrational response in the amide I' region. We observe bimodal relaxation kinetics with time constants of 100 +/- 10 and 770 +/- 40 ns at 322 K, suggesting that the folding involves an intermediate state, the character of which can be determined from the time and frequency resolved data We find that the relaxation dynamics close to the melting temperature involve fast fluctuations in the polyproline II region, whereas the slower process can be attributed to conformational rearrangements due to the global (un)folding transition of the protein. Combined analysis of our T-jump data and molecular dynamics simulations indicates that the formation of a well-defined alpha-helix precedes the rapid formation of the hydrophobic cage structure, implying a native like folding intermediate, that Mainly differs from the folded conformation in the orientation of the C-terminal polyproline II helix relative to the N-terminal part of the backbone., We find that the main free energy barrier is positioned between the folding intermediate and the unfolded state ensemble, and that it involves the formation of the alpha-helix, the 3(10)-helix, and the Asp9- Arg16 salt bridge. Our results suggest that at low temperature (T << T-m) a folding path via formation of alpha-helical contacts followed by hydrophobic clustering becomes more important