Jin Hae Kim

Bio: Jin Hae Kim is an academic researcher from Daegu Gyeongbuk Institute of Science and Technology. The author has contributed to research in topics: Familial amyloid cardiomyopathy & Nuclear magnetic resonance spectroscopy. The author has co-authored 3 publications.

17O NMR Spectroscopy: A Novel Probe for Characterizing Protein Structure and Folding.

Abstract: Oxygen is a key atom that maintains biomolecular structures, regulates various physiological processes, and mediates various biomolecular interactions. Oxygen-17 (17O), therefore, has been proposed as a useful probe that can provide detailed information about various physicochemical features of proteins. This is attributed to the facts that (1) 17O is an active isotope for nuclear magnetic resonance (NMR) spectroscopic approaches; (2) NMR spectroscopy is one of the most suitable tools for characterizing the structural and dynamical features of biomolecules under native-like conditions; and (3) oxygen atoms are frequently involved in essential hydrogen bonds for the structural and functional integrity of proteins or related biomolecules. Although 17O NMR spectroscopic investigations of biomolecules have been considerably hampered due to low natural abundance and the quadruple characteristics of the 17O nucleus, recent theoretical and technical developments have revolutionized this methodology to be optimally poised as a unique and widely applicable tool for determining protein structure and dynamics. In this review, we recapitulate recent developments in 17O NMR spectroscopy to characterize protein structure and folding. In addition, we discuss the highly promising advantages of this methodology over other techniques and explain why further technical and experimental advancements are highly desired.

Exploring ensemble structures of Alzheimer’s amyloid β (1-42) monomer using linear regression for the MD simulation and NMR chemical shift

Abstract: Aggregation of intrinsically disordered amyloid β (Aβ) is a hallmark of Alzheimer9s disease. Although complex aggregation mechanisms have been increasingly revealed, structural ensembles of Aβ monomers with heterogeneous and transient properties still hamper detailed experimental accesses to early events of amyloidogenesis. We herein developed a new mathematical tool based on multiple linear regression to obtain the reasonable ensemble structures of Aβ monomer by using the solution nuclear magnetic resonance (NMR) and molecular dynamics simulation data. Our approach provided the best-fit ensemble to two-dimensional NMR chemical shifts, also consistent with circular dichroism and dynamic light scattering analyses. The major monomeric structures of Aβ including β-sheets in both terminal and central hydrophobic core regions and the minor partially-helical structures suggested initial structure-based explanation on possible mechanisms of early molecular association and nucleation for amyloid generation. A wide-spectrum application of the current approach was also indicated by showing a successful utilization for ensemble structures of folded proteins. We propose that multiple linear regression in combination to experimental results will be highly promising for studies on protein misfolding diseases and functions by providing a convincing template structure.

Aggregation-Prone Structural Ensembles of Transthyretin Collected With Regression Analysis for NMR Chemical Shift.

Abstract: Monomer dissociation and subsequent misfolding of the transthyretin (TTR) is one of the most critical causative factors of TTR amyloidosis. TTR amyloidosis causes several human diseases, such as senile systemic amyloidosis and familial amyloid cardiomyopathy/polyneuropathy; therefore, it is important to understand the molecular details of the structural deformation and aggregation mechanisms of TTR. However, such molecular characteristics are still elusive because of the complicated structural heterogeneity of TTR and its highly sensitive nature to various environmental factors. Several nuclear magnetic resonance (NMR) spectroscopy and molecular dynamics (MD) studies of TTR variants have recently reported evidence of transient aggregation-prone structural states of TTR. According to these studies, the stability of the DAGH β-sheet, one of the two main β-sheets in TTR, is a crucial determinant of the TTR amyloidosis mechanism. In addition, its conformational perturbation and possible involvement of nearby structural motifs facilitates TTR aggregation. This study proposes aggregation-prone structural ensembles of TTR obtained by MD simulation with enhanced sampling and a multiple linear regression approach. This method provides plausible structural models that are composed of ensemble structures consistent with NMR chemical shift data. This study validated the ensemble models with experimental data obtained from circular dichroism (CD) spectroscopy and NMR order parameter analysis. In addition, our results suggest that the structural deformation of the DAGH β-sheet and the AB loop regions may correlate with the manifestation of the aggregation-prone conformational states of TTR. In summary, our method employing MD techniques to extend the structural ensembles from NMR experimental data analysis may provide new opportunities to investigate various transient yet important structural states of amyloidogenic proteins.

Solid-State NMR Dipolar and Chemical Shift Anisotropy Recoupling Techniques for Structural and Dynamical Studies in Biological Systems

Abstract: With the development of NMR methodology and technology during the past decades, solid-state NMR (ssNMR) has become a particularly important tool for investigating structure and dynamics at atomic scale in biological systems, where the recoupling techniques play pivotal roles in modern high-resolution MAS NMR. In this review, following a brief introduction on the basic theory of recoupling in ssNMR, we highlight the recent advances in dipolar and chemical shift anisotropy recoupling methods, as well as their applications in structural determination and dynamical characterization at multiple time scales (i.e., fast-, intermediate-, and slow-motion). The performances of these prevalent recoupling techniques are compared and discussed in multiple aspects, together with the representative applications in biomolecules. Given the recent emerging advances in NMR technology, new challenges for recoupling methodology development and potential opportunities for biological systems are also discussed.

Atomic Mechanisms of Transthyretin Tetramer Dissociation Studied by Molecular Dynamics Simulations

Abstract: The dissociation of the transthyretin (TTR) tetramer into a monomer is closely related to various TTR amyloidoses in humans. While the tetramer dissociation has been reported to be the rate-limiting step for TTR aggregation, few details are known about the mechanism. Here, molecular dynamics (MD) simulations were performed by combining conventional MD and biased metadynamics to investigate the mechanism for the wild-type (WT) and mutant (T119M) structures. Both were found to have a great deal in common. Conventional MD simulations reveal that interfacial hydrophobic interactions contribute significantly to stabilize the tetramer. Interfacial residues including L17, V20, L110, and V121 with close contacts form a hydrophobic channel. Metadynamics simulations indicate that the mouth opening of the hydrophobic channel is the first and the most difficult step for dissociation. Interactions of V20 between opposing dimers lock four monomers into the tetramer, and disruption of the interactions is found to be involved in the final step. During the dissociation, an increasing extent of solvation was observed by calculating the radial distribution functions of water around interfacial hydrophobic residues, suggesting that water plays a role in driving the tetramer dissociation. Moreover, compared to T119, residue M119 has a longer side chain that extends into the hydrophobic channel, making solvation more difficult, consistent with a higher energy barrier for dissociation of the T119M tetramer. This result provides a good explanation for the protective role of the T119M mutation. Overall, this study can provide atomic-level insights to better understand the pathogenesis of TTR amyloidosis and guide rational drug design in the future.

Magnetically aligned nanodiscs enable direct measurement of 17O residual quadrupolar coupling for small molecules.

Abstract: The use of 17O in NMR spectroscopy for structural studies has been limited due to its low natural abundance, low gyromagnetic ratio, and quadrupolar relaxation. Previous solution 17O work has primarily focused on studies of liquids where the 17O quadrupolar coupling is averaged to zero by isotropic molecular tumbling, and therefore has ignored the structural information contained in this parameter. Here, we use magnetically aligned polymer nanodiscs as an alignment medium to measure residual quadrupolar couplings (RQCs) for 17O-labelled benzoic acid in the aqueous phase. We show that increasing the magnetic field strength improves spectral sensitivity and resolution and that each satellite peak of the expected pentet pattern resolves clearly at 18.8 T. We observed no significant dependence of the RQC magnitudes on the magnetic field strength. However, changing the orientation of the alignment medium alters the RQC by a consistent factor, suggesting that 17O RQCs measured in this way can provide reliable orientational information for elucidations of molecular structures.

Fast and Cost-Efficient 17O-Isotopic Labeling of Carboxylic Groups in Biomolecules: from Free Amino Acids to Peptide Chains.

Abstract: 17 O NMR spectroscopy is a powerful technique, which can provide unique information regarding the structure and reactivity of biomolecules. However, the low natural abundance of 17 O (0.04%) generally requires working with enriched samples, which are not easily accessible. Here, we present simple, fast and cost-efficient 17 O-enrichment strategies for amino acids and peptides, using mechanochemistry. First, five unprotected amino acids were enriched under ambient conditions, consuming only microliter amounts of costly labeled water, and producing pure molecules with enrichment levels up to ~ 40%, yields ~ 60-85%, and no loss of optical purity. Subsequently, 17 O-enriched Fmoc/ t Bu-protected amino acids were produced on a 1g/day scale with high enrichment levels. Lastly, a site-selective 17 O-labeling of carboxylic functions in peptide side-chains was achieved for RGD and GRGDS peptides, with ~ 28% enrichment level. For all molecules, 17 O ssNMR spectra were recorded at 14.1T in reasonable times, making this an important step forward for future NMR studies of biomolecules.

The expanding frontier between mechanochemistry & solid state NMR: Special focus on inorganic components of materials

Abstract: While the research fields of mechanochemistry and solid state NMR (ssNMR) have been developing in independent ways for many years, there are an increasing number of studies in which both topics meet. On one hand, ssNMR can be used to perform advanced characterizations of the structure, morphology and also properties of materials prepared by mechanochemistry. On the other, syntheses performed using mechanochemistry can help push forward the current frontiers of solid state NMR, for example through the development of new phases enriched in NMR-active isotopes. Lastly, studies at the interface between mechanochemistry and ssNMR are increasingly being carried out, notably to help elucidate reaction mechanisms in ball-milling (BM). In this chapter, illustrations of investigations along these lines will be provided, focusing on the synthesis and characterization of materials with an inorganic component, such as oxides, metal-organic frameworks, and zeolites, just to name a few.