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Special Issue “Selected Papers from the 8th Asia-Pacific NMR (APNMR) Symposium: Recent Advances in NMR Spectroscopy”

by Surajit Bhattacharjya, Daiwen Yang and Ho Sup Yoon

Int. J. Mol. Sci. 2020, 21(12), 4419; https://doi.org/10.3390/ijms21124419 - 22 Jun 2020

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Abstract

Asia-Pacific NMR (APNMR) has been an important scientific event in the region, engaging a large number of NMR scientists from academia and industries [...] Full article

(This article belongs to the Special Issue Selected Papers from the 8th Asia-Pacific NMR Symposium (APNMR): Recent Advances in NMR Spectroscopy)

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17 pages, 2942 KiB

Open AccessArticle

Gadolinium Complexes as Contrast Agent for Cellular NMR Spectroscopy

by Nat Sakol, Ayako Egawa and Toshimichi Fujiwara

Int. J. Mol. Sci. 2020, 21(11), 4042; https://doi.org/10.3390/ijms21114042 - 5 Jun 2020

Cited by 11 | Viewed by 3504

Abstract

Aqua Gd³⁺ and Gd-DOTA (gadolinium-1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacete) complexes were studied as a contrast agent in cellular NMR (nuclear magnetic resonance) spectroscopy for distinguishing between intracellular and extracellular spaces. The contrast agents for this purpose should provide strong paramagnetic relaxation enhancement and localize in the [...] Read more.

Aqua Gd³⁺ and Gd-DOTA (gadolinium-1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacete) complexes were studied as a contrast agent in cellular NMR (nuclear magnetic resonance) spectroscopy for distinguishing between intracellular and extracellular spaces. The contrast agents for this purpose should provide strong paramagnetic relaxation enhancement and localize in the extracellular space without disturbing biological functions. Cell membrane permeability to Gd complexes was evaluated from the concentrations of gadolinium complexes in the inside and outside of E. coli cells measured by the ¹H-NMR relaxation. The site-specific binding of the complexes to E. coli cells was also analyzed by high-resolution solid-state ¹³C-NMR. The aqua Gd³⁺ complex did not enhance T₁ relaxation in proportion to the amount of added Gd³⁺. This Gd³⁺ concentration dependence and the ¹³C-NMR indicated that its strong cytotoxicity should be due to the binding of the paramagnetic ions to cellular components especially at the lipid membranes. In contrast, Gd-DOTA stayed in the solution states and enhanced relaxation in proportion to the added amount. This agent exhibited strong T₁ contrast between the intra- and extracellular spaces by a factor of ten at high concentrations under which the cells were viable over a long experimental time of days. These properties make Gd-DOTA suitable for selectively contrasting the living cellular space in NMR spectroscopy primarily owing to its weak interaction with cellular components. Full article

(This article belongs to the Special Issue Selected Papers from the 8th Asia-Pacific NMR Symposium (APNMR): Recent Advances in NMR Spectroscopy)

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16 pages, 949 KiB

Open AccessArticle

WT and A53T α-Synuclein Systems: Melting Diagram and Its New Interpretation

by Mónika Bokor, Ágnes Tantos, Péter Tompa, Kyou-Hoon Han and Kálmán Tompa

Int. J. Mol. Sci. 2020, 21(11), 3997; https://doi.org/10.3390/ijms21113997 - 3 Jun 2020

Cited by 8 | Viewed by 2365

Abstract

The potential barriers governing the motions of α-synuclein (αS) variants’ hydration water, especially energetics of them, is in the focus of the work. The thermodynamical approach yielded essential information about distributions and heights of the potential barriers. The proteins’ structural [...] Read more.

The potential barriers governing the motions of α-synuclein (αS) variants’ hydration water, especially energetics of them, is in the focus of the work. The thermodynamical approach yielded essential information about distributions and heights of the potential barriers. The proteins’ structural disorder was measured by ratios of heterogeneous water-binding interfaces. They showed the αS monomers, oligomers and amyloids to possess secondary structural elements, although monomers are intrinsically disordered. Despite their disordered nature, monomers have 33% secondary structure, and therefore they are more compact than a random coil. At the lowest potential barriers with mobile hydration water, monomers are already functional, a monolayer of mobile hydration water is surrounding them. Monomers realize all possible hydrogen bonds with the solvent water. αS oligomers and amyloids have half of the mobile hydration water amount than monomers because aggregation involves less mobile hydration. The solvent-accessible surface of the oligomers is ordered or homogenous in its interactions with water to 66%. As a contrast, αS amyloids are disordered or heterogeneous to 75% of their solvent accessible surface and both wild type and A53T amyloids show identical, low-level hydration. Mobile water molecules in the first hydration shell of amyloids are the weakest bound compared to other forms. Full article

(This article belongs to the Special Issue Selected Papers from the 8th Asia-Pacific NMR Symposium (APNMR): Recent Advances in NMR Spectroscopy)

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13 pages, 2262 KiB

Open AccessArticle

Signal Deconvolution and Noise Factor Analysis Based on a Combination of Time–Frequency Analysis and Probabilistic Sparse Matrix Factorization

by Shunji Yamada, Atsushi Kurotani, Eisuke Chikayama and Jun Kikuchi

Int. J. Mol. Sci. 2020, 21(8), 2978; https://doi.org/10.3390/ijms21082978 - 23 Apr 2020

Cited by 14 | Viewed by 3962

Abstract

Nuclear magnetic resonance (NMR) spectroscopy is commonly used to characterize molecular complexity because it produces informative atomic-resolution data on the chemical structure and molecular mobility of samples non-invasively by means of various acquisition parameters and pulse programs. However, analyzing the accumulated NMR data [...] Read more.

Nuclear magnetic resonance (NMR) spectroscopy is commonly used to characterize molecular complexity because it produces informative atomic-resolution data on the chemical structure and molecular mobility of samples non-invasively by means of various acquisition parameters and pulse programs. However, analyzing the accumulated NMR data of mixtures is challenging due to noise and signal overlap. Therefore, data-cleansing steps, such as quality checking, noise reduction, and signal deconvolution, are important processes before spectrum analysis. Here, we have developed an NMR measurement informatics tool for data cleansing that combines short-time Fourier transform (STFT; a time–frequency analytical method) and probabilistic sparse matrix factorization (PSMF) for signal deconvolution and noise factor analysis. Our tool can be applied to the original free induction decay (FID) signals of a one-dimensional NMR spectrum. We show that the signal deconvolution method reduces the noise of FID signals, increasing the signal-to-noise ratio (SNR) about tenfold, and its application to diffusion-edited spectra allows signals of macromolecules and unsuppressed small molecules to be separated by the length of the T₂* relaxation time. Noise factor analysis of NMR datasets identified correlations between SNR and acquisition parameters, identifying major experimental factors that can lower SNR. Full article

(This article belongs to the Special Issue Selected Papers from the 8th Asia-Pacific NMR Symposium (APNMR): Recent Advances in NMR Spectroscopy)

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15 pages, 4604 KiB

Open AccessArticle

Hydroxyapatite Formation Coexists with Amyloid-like Self-Assembly of Human Amelogenin

by Jing Zhang, Jian Wang, Chengwei Ma and Junxia Lu

Int. J. Mol. Sci. 2020, 21(8), 2946; https://doi.org/10.3390/ijms21082946 - 22 Apr 2020

Cited by 21 | Viewed by 3969

Abstract

Tooth enamel is formed in an extracellular environment. Amelogenin, the major component in the protein matrix of tooth enamel during the developing stage, could assemble into high molecular weight structures, regulating enamel formation. However, the molecular structure of amelogenin protein assembly at the [...] Read more.

Tooth enamel is formed in an extracellular environment. Amelogenin, the major component in the protein matrix of tooth enamel during the developing stage, could assemble into high molecular weight structures, regulating enamel formation. However, the molecular structure of amelogenin protein assembly at the functional state is still elusive. In this work, we found that amelogenin is able to induce calcium phosphate minerals into hydroxyapatite (HAP) structure in vitro at pH 6.0. Assessed using X-ray diffraction (XRD) and ³¹P solid-state NMR (SSNMR) evidence, the formed HAP mimics natural enamel closely. The structure of amelogenin protein assembly coexisting with the HAP was also studied using atomic force microscopy (AFM), transmission electron microscopy (TEM) and XRD, indicating the β-amyloid structure of the protein. SSNMR was proven to be an important tool in detecting both the rigid and dynamic components of the protein assembly in the sample, and the core sequence ¹⁸EVLTPLKWYQSI²⁹ was identified as the major segment contributing to the β-sheet secondary structure. Our research suggests an amyloid structure may be an important factor in controlling HAP formation at the right pH conditions with the help of other structural components in the protein assembly. Full article

(This article belongs to the Special Issue Selected Papers from the 8th Asia-Pacific NMR Symposium (APNMR): Recent Advances in NMR Spectroscopy)

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17 pages, 5636 KiB

Open AccessArticle

The Interactions between the Antimicrobial Peptide P-113 and Living Candida albicans Cells Shed Light on Mechanisms of Antifungal Activity and Resistance

by Kuang-Ting Cheng, Chih-Lung Wu, Bak-Sau Yip, Ya-Han Chih, Kuang-Li Peng, Su-Ya Hsu, Hui-Yuan Yu and Jya-Wei Cheng

Int. J. Mol. Sci. 2020, 21(7), 2654; https://doi.org/10.3390/ijms21072654 - 10 Apr 2020

Cited by 23 | Viewed by 4242

Abstract

In the absence of proper immunity, such as in the case of acquired immune deficiency syndrome (AIDS) patients, Candida albicans, the most common human fungal pathogen, may cause mucosal and even life-threatening systemic infections. P-113 (AKRHHGYKRKFH), an antimicrobial peptide (AMP) derived from [...] Read more.

In the absence of proper immunity, such as in the case of acquired immune deficiency syndrome (AIDS) patients, Candida albicans, the most common human fungal pathogen, may cause mucosal and even life-threatening systemic infections. P-113 (AKRHHGYKRKFH), an antimicrobial peptide (AMP) derived from the human salivary protein histatin 5, shows good safety and efficacy profiles in gingivitis and human immunodeficiency virus (HIV) patients with oral candidiasis. However, little is known about how P-113 interacts with Candida albicans or its degradation by Candida-secreted proteases that contribute to the fungi’s resistance. Here, we use solution nuclear magnetic resonance (NMR) methods to elucidate the molecular mechanism of interactions between P-113 and living Candida albicans cells. Furthermore, we found that proteolytic cleavage of the C-terminus prevents the entry of P-113 into cells and that increasing the hydrophobicity of the peptide can significantly increase its antifungal activity. These results could help in the design of novel antimicrobial peptides that have enhanced stability in vivo and that can have potential therapeutic applications. Full article

(This article belongs to the Special Issue Selected Papers from the 8th Asia-Pacific NMR Symposium (APNMR): Recent Advances in NMR Spectroscopy)

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20 pages, 3743 KiB

Open AccessArticle

Structural Characterization of an ACP from Thermotoga maritima: Insights into Hyperthermal Adaptation

by Yeongjoon Lee, Ahjin Jang, Min-Cheol Jeong, Nuri Park, Jungwoo Park, Woo Cheol Lee, Chaejoon Cheong and Yangmee Kim

Int. J. Mol. Sci. 2020, 21(7), 2600; https://doi.org/10.3390/ijms21072600 - 9 Apr 2020

Cited by 10 | Viewed by 3802

Abstract

Thermotoga maritima, a deep-branching hyperthermophilic bacterium, expresses an extraordinarily stable Thermotoga maritima acyl carrier protein (Tm-ACP) that functions as a carrier in the fatty acid synthesis system at near-boiling aqueous environments. Here, to understand the hyperthermal adaptation of Tm-ACP, [...] Read more.

Thermotoga maritima, a deep-branching hyperthermophilic bacterium, expresses an extraordinarily stable Thermotoga maritima acyl carrier protein (Tm-ACP) that functions as a carrier in the fatty acid synthesis system at near-boiling aqueous environments. Here, to understand the hyperthermal adaptation of Tm-ACP, we investigated the structure and dynamics of Tm-ACP by nuclear magnetic resonance (NMR) spectroscopy. The melting temperature of Tm-ACP (101.4 °C) far exceeds that of other ACPs, owing to extensive ionic interactions and tight hydrophobic packing. The D59 residue, which replaces Pro/Ser of other ACPs, mediates ionic clustering between helices III and IV. This creates a wide pocket entrance to facilitate the accommodation of long acyl chains required for hyperthermal adaptation of the T. maritima cell membrane. Tm-ACP is revealed to be the first ACP that harbor an amide proton hyperprotected against hydrogen/deuterium exchange for I15. The hydrophobic interactions mediated by I15 appear to be the key driving forces of the global folding process of Tm-ACP. Our findings provide insights into the structural basis of the hyperthermal adaptation of ACP, which might have allowed T. maritima to survive in hot ancient oceans. Full article

(This article belongs to the Special Issue Selected Papers from the 8th Asia-Pacific NMR Symposium (APNMR): Recent Advances in NMR Spectroscopy)

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19 pages, 5909 KiB

Open AccessArticle

A Coil-to-Helix Transition Serves as a Binding Motif for hSNF5 and BAF155 Interaction

by Jeongmin Han, Iktae Kim, Jae-Hyun Park, Ji-Hye Yun, Keehyoung Joo, Taehee Kim, Gye-Young Park, Kyoung-Seok Ryu, Yoon-Joo Ko, Kenji Mizutani, Sam-Young Park, Rho Hyun Seong, Jooyoung Lee, Jeong-Yong Suh and Weontae Lee

Int. J. Mol. Sci. 2020, 21(7), 2452; https://doi.org/10.3390/ijms21072452 - 1 Apr 2020

Cited by 5 | Viewed by 3240

Abstract

Human SNF5 and BAF155 constitute the core subunit of multi-protein SWI/SNF chromatin-remodeling complexes that are required for ATP-dependent nucleosome mobility and transcriptional control. Human SNF5 (hSNF5) utilizes its repeat 1 (RPT1) domain to associate with the SWIRM domain of BAF155. Here, we employed [...] Read more.

Human SNF5 and BAF155 constitute the core subunit of multi-protein SWI/SNF chromatin-remodeling complexes that are required for ATP-dependent nucleosome mobility and transcriptional control. Human SNF5 (hSNF5) utilizes its repeat 1 (RPT1) domain to associate with the SWIRM domain of BAF155. Here, we employed X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, and various biophysical methods in order to investigate the detailed binding mechanism between hSNF5 and BAF155. Multi-angle light scattering data clearly indicate that hSNF5^171–258 and BAF155^SWIRM are both monomeric in solution and they form a heterodimer. NMR data and crystal structure of the hSNF5^171–258/BAF155^SWIRM complex further reveal a unique binding interface, which involves a coil-to-helix transition upon protein binding. The newly formed α_N helix of hSNF5^171–258 interacts with the β2–α1 loop of hSNF5 via hydrogen bonds and it also displays a hydrophobic interaction with BAF155^SWIRM. Therefore, the N-terminal region of hSNF5^171–258 plays an important role in tumorigenesis and our data will provide a structural clue for the pathogenesis of Rhabdoid tumors and malignant melanomas that originate from mutations in the N-terminal loop region of hSNF5. Full article

(This article belongs to the Special Issue Selected Papers from the 8th Asia-Pacific NMR Symposium (APNMR): Recent Advances in NMR Spectroscopy)

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14 pages, 3476 KiB

Open AccessArticle

Musashi-1: An Example of How Polyalanine Tracts Contribute to Self-Association in the Intrinsically Disordered Regions of RNA-Binding Proteins

by Tsai-Chen Chen and Jie-rong Huang

Int. J. Mol. Sci. 2020, 21(7), 2289; https://doi.org/10.3390/ijms21072289 - 26 Mar 2020

Cited by 14 | Viewed by 3699

Abstract

RNA-binding proteins (RBPs) have intrinsically disordered regions (IDRs) whose biophysical properties have yet to be explored to the same extent as those of the folded RNA interacting domains. These IDRs are essential to the formation of biomolecular condensates, such as stress and RNA [...] Read more.

RNA-binding proteins (RBPs) have intrinsically disordered regions (IDRs) whose biophysical properties have yet to be explored to the same extent as those of the folded RNA interacting domains. These IDRs are essential to the formation of biomolecular condensates, such as stress and RNA granules, but dysregulated assembly can be pathological. Because of their structural heterogeneity, IDRs are best studied by NMR spectroscopy. In this study, we used NMR spectroscopy to investigate the structural propensity and self-association of the IDR of the RBP Musashi-1. We identified two transient α-helical regions (residues ~208–218 and ~270–284 in the IDR, the latter with a polyalanine tract). Strong NMR line broadening in these regions and circular dichroism and micrography data suggest that the two α-helical elements and the hydrophobic residues in between may contribute to the formation of oligomers found in stress granules and implicated in Alzheimer’s disease. Bioinformatics analysis suggests that polyalanine stretches in the IDRs of RBPs may have evolved to promote RBP assembly. Full article

(This article belongs to the Special Issue Selected Papers from the 8th Asia-Pacific NMR Symposium (APNMR): Recent Advances in NMR Spectroscopy)

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17 pages, 3174 KiB

Open AccessArticle

N-terminal Backbone Pairing Shifts in CCL5-¹²AAA¹⁴ Dimer Interface: Structural Significance of the FAY Sequence

by Jin-Ye Li, Yi-Chen Chen, Yi-Zong Lee, Chun-Hsiang Huang and Shih-Che Sue

Int. J. Mol. Sci. 2020, 21(5), 1689; https://doi.org/10.3390/ijms21051689 - 1 Mar 2020

Cited by 4 | Viewed by 2755

Abstract

CC-type chemokine ligand 5 (CCL5) has been known to regulate immune responses by mediating the chemotaxis of leukocytes. Depending on the environment, CCL5 forms different orders of oligomers to interact with targets and create functional diversity. A recent CCL5 trimer structure revealed that [...] Read more.

CC-type chemokine ligand 5 (CCL5) has been known to regulate immune responses by mediating the chemotaxis of leukocytes. Depending on the environment, CCL5 forms different orders of oligomers to interact with targets and create functional diversity. A recent CCL5 trimer structure revealed that the N-terminal conversed F12-A13-Y14 (¹²FAY¹⁴) sequence is involved in CCL5 aggregation. The CCL5-¹²AAA¹⁴ mutant with two mutations had a deficiency in the formation of high-order oligomers. In the study, we clarify the respective roles of F12 and Y14 through NMR analysis and structural determination of the CCL5-¹²AAA¹⁴ mutant where F12 is involved in the dimer assembly and Y14 is involved in aggregation. The CCL5-¹²AAA¹⁴ structure contains a unique dimer packing. The backbone pairing shifts for one-residue in the N-terminal interface, when compared to the native CCL5 dimer. This difference creates a new structural orientation and leads to the conclusion that F12 confines the native CCL5 dimer configuration. Without F12 anchoring in the position, the interfacial backbone pairing is permitted to slide. Structural plasticity occurs in the N-terminal interaction. This is the first case to report this structural rearrangement through mutagenesis. The study provides a new idea for chemokine engineering and complements the understanding of CCL5 oligomerization and the role of the ¹²FAY¹⁴ sequence. Full article

(This article belongs to the Special Issue Selected Papers from the 8th Asia-Pacific NMR Symposium (APNMR): Recent Advances in NMR Spectroscopy)

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22 pages, 4622 KiB

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Dynamics Studies of DNA with Non-canonical Structure Using NMR Spectroscopy

by Kwang-Im Oh, Jinwoo Kim, Chin-Ju Park and Joon-Hwa Lee

Int. J. Mol. Sci. 2020, 21(8), 2673; https://doi.org/10.3390/ijms21082673 - 11 Apr 2020

Cited by 14 | Viewed by 6386

Abstract

The non-canonical structures of nucleic acids are essential for their diverse functions during various biological processes. These non-canonical structures can undergo conformational exchange among multiple structural states. Data on their dynamics can illustrate conformational transitions that play important roles in folding, stability, and [...] Read more.

The non-canonical structures of nucleic acids are essential for their diverse functions during various biological processes. These non-canonical structures can undergo conformational exchange among multiple structural states. Data on their dynamics can illustrate conformational transitions that play important roles in folding, stability, and biological function. Here, we discuss several examples of the non-canonical structures of DNA focusing on their dynamic characterization by NMR spectroscopy: (1) G-quadruplex structures and their complexes with target proteins; (2) i-motif structures and their complexes with proteins; (3) triplex structures; (4) left-handed Z-DNAs and their complexes with various Z-DNA binding proteins. This review provides insight into how the dynamic features of non-canonical DNA structures contribute to essential biological processes. Full article

(This article belongs to the Special Issue Selected Papers from the 8th Asia-Pacific NMR Symposium (APNMR): Recent Advances in NMR Spectroscopy)

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16 pages, 2436 KiB

Open AccessReview

Insights into Structures and Dynamics of Flavivirus Proteases from NMR Studies

by Qingxin Li and CongBao Kang

Int. J. Mol. Sci. 2020, 21(7), 2527; https://doi.org/10.3390/ijms21072527 - 5 Apr 2020

Cited by 14 | Viewed by 3893

Abstract

Nuclear magnetic resonance (NMR) spectroscopy plays important roles in structural biology and drug discovery, as it is a powerful tool to understand protein structures, dynamics, and ligand binding under physiological conditions. The protease of flaviviruses is an attractive target for developing antivirals because [...] Read more.

Nuclear magnetic resonance (NMR) spectroscopy plays important roles in structural biology and drug discovery, as it is a powerful tool to understand protein structures, dynamics, and ligand binding under physiological conditions. The protease of flaviviruses is an attractive target for developing antivirals because it is essential for the maturation of viral proteins. High-resolution structures of the proteases in the absence and presence of ligands/inhibitors were determined using X-ray crystallography, providing structural information for rational drug design. Structural studies suggest that proteases from Dengue virus (DENV), West Nile virus (WNV), and Zika virus (ZIKV) exist in open and closed conformations. Solution NMR studies showed that the closed conformation is predominant in solution and should be utilized in structure-based drug design. Here, we reviewed solution NMR studies of the proteases from these viruses. The accumulated studies demonstrated that NMR spectroscopy provides additional information to understand conformational changes of these proteases in the absence and presence of substrates/inhibitors. In addition, NMR spectroscopy can be used for identifying fragment hits that can be further developed into potent protease inhibitors. Full article

(This article belongs to the Special Issue Selected Papers from the 8th Asia-Pacific NMR Symposium (APNMR): Recent Advances in NMR Spectroscopy)

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17 pages, 2013 KiB

Open AccessReview

Spotlight on the Ballet of Proteins: The Structural Dynamic Properties of Proteins Illuminated by Solution NMR

by Yuji Tokunaga, Thibault Viennet, Haribabu Arthanari and Koh Takeuchi

Int. J. Mol. Sci. 2020, 21(5), 1829; https://doi.org/10.3390/ijms21051829 - 6 Mar 2020

Cited by 7 | Viewed by 4187

Abstract

Solution NMR spectroscopy is a unique and powerful technique that has the ability to directly connect the structural dynamics of proteins in physiological conditions to their activity and function. Here, we summarize recent studies in which solution NMR contributed to the discovery of [...] Read more.

Solution NMR spectroscopy is a unique and powerful technique that has the ability to directly connect the structural dynamics of proteins in physiological conditions to their activity and function. Here, we summarize recent studies in which solution NMR contributed to the discovery of relationships between key dynamic properties of proteins and functional mechanisms in important biological systems. The capacity of NMR to quantify the dynamics of proteins over a range of time scales and to detect lowly populated protein conformations plays a critical role in its power to unveil functional protein dynamics. This analysis of dynamics is not only important for the understanding of biological function, but also in the design of specific ligands for pharmacologically important proteins. Thus, the dynamic view of structure provided by NMR is of importance in both basic and applied biology. Full article

(This article belongs to the Special Issue Selected Papers from the 8th Asia-Pacific NMR Symposium (APNMR): Recent Advances in NMR Spectroscopy)

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