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Understanding of Structure-to-Function Relationships in Biological Macromolecules

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Macromolecules".

Deadline for manuscript submissions: closed (30 November 2023) | Viewed by 5418

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Special Issue Editor

Dr. Konstantin M. Boyko

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Guest Editor

Bach Institute of Biochemistry, Federal Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
Interests: structural biology; x-ray crystallography; cryoEM; protein fold; SAXS; XFEL; structure-guided drug design

Special Issue Information

Dear Colleagues,

Integrative structural biology (ISB), one of the key fields of modern life science, has become a powerful approach to determine the structural data of biological macromolecules. Elucidating such data for natural macromolecules contributes to solutions to biomedical and biotechnological tasks, such as structure-assisted drug design and the development and optimization of novel biocatalysts. ISB combines various modern complementary experimental techniques, including X-ray crystallography, NMR spectroscopy, electron microscopy, and SAXS/SANS, as well as computational methods, to generate complete structural models.

This Special Issue focuses on recent studies that aim to investigate macromolecular structures using a combination of structural biology methods. The special aim of this Special Issue is to address structure-to-function relationships among various biologically important molecules including relevant protein–protein and protein–ligand complexes. Original research studies providing such information are welcomed.

Dr. Konstantin M. Boyko
Guest Editor

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Keywords

structural biology
X-ray crystallography
cryoEM
NMR
SAXS
XFEL
structure–function relationships

Published Papers (4 papers)

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Research

22 pages, 4911 KiB

Open AccessArticle

Structure–Functional Examination of Novel Ribonucleoside Hydrolase C (RihC) from Limosilactobacillus reuteri LR1

by Leonid A. Shaposhnikov, Natalia Yu. Chikurova, Denis L. Atroshenko, Svyatoslav S. Savin, Sergei Yu. Kleymenov, Alla V. Chernobrovkina, Evgenii V. Pometun, Mikhail E. Minyaev, Ilya O. Matyuta, Dmitry M. Hushpulian, Konstantin M. Boyko, Vladimir I. Tishkov and Anastasia A. Pometun

Int. J. Mol. Sci. 2024, 25(1), 538; https://doi.org/10.3390/ijms25010538 - 30 Dec 2023

Viewed by 808

Abstract

Ribonucleoside hydrolase C (RihC, EC 3.2.2.1, 3.2.2.2, 3.2.2.3, 3.2.2.7, 3.2.2.8) belongs to the family of ribonucleoside hydrolases Rih and catalyzes the cleavage of ribonucleosides to nitrogenous bases and ribose. RihC is one of the enzymes that are synthesized by lactobacilli in response to the presence of Klebsiella. To characterize this protein from Limosilactobacillus reuteri LR1, we cloned and expressed it. The activity of the enzyme was studied towards a wide range of substrates, including ribonucleosides, deoxyribonucleosides as well as an arabinoside. It was shown that the enzyme is active only with ribonucleosides and arabinoside, with the best substrate being uridine. The thermal stability of this enzyme was studied, and its crystal structure was obtained, which demonstrated the tetrameric architecture of the enzyme and allowed to shed light on a correlation between its structure and enzymatic activity. Comprehensive comparisons of all known RihC structures, both existing crystal structures and computed model structures from various species, were made, allowing for the identification of structural motifs important for enzyme functioning. Full article

(This article belongs to the Special Issue Understanding of Structure-to-Function Relationships in Biological Macromolecules)

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30 pages, 5580 KiB

Open AccessArticle

by Jacob A. Lewis, Bixia Zhang, Rishi Harza, Nathan Palmer, Gautam Sarath, Scott E. Sattler, Paul Twigg, Wilfred Vermerris and ChulHee Kang

Int. J. Mol. Sci. 2023, 24(18), 13901; https://doi.org/10.3390/ijms241813901 - 9 Sep 2023

Cited by 2 | Viewed by 1620

Abstract

Flavonoids are potent antioxidants that play a role in defense against pathogens, UV-radiation, and the detoxification of reactive oxygen species. Dihydroflavonol 4-reductase (DFR) and flavanone 4-reductase (FNR) reduce dihydroflavonols and flavanones, respectively, using NAD(P)H to produce flavan-(3)-4-(di)ols in flavonoid biosynthesis. Anthocyanidin reductase (ANR) reduces anthocyanidins to flavan-3-ols. In addition to their sequences, the 3D structures of recombinant DFR, FNR and ANR from sorghum and switchgrass showed a high level of similarity. The catalytic mechanism, substrate-specificity and key residues of three reductases were deduced from crystal structures, site-directed mutagenesis, molecular docking, kinetics, and thermodynamic ana-lyses. Although DFR displayed its highest activity against dihydroflavonols, it also showed activity against flavanones and anthocyanidins. It was inhibited by the flavonol quercetin and high concentrations of dihydroflavonols/flavonones. SbFNR1 and SbFNR2 did not show any activity against dihydroflavonols. However, SbFNR1 displayed activity against flavanones and ANR activity against two anthocyanidins, cyanidin and pelargonidin. Therefore, SbFNR1 and SbFNR2 could be specific ANR isozymes without delphinidin activity. Sorghum has high concentrations of 3-deoxyanthocyanidins in vivo, supporting the observed high activity of SbDFR against flavonols. Mining of expression data indicated substantial induction of these three reductase genes in both switchgrass and sorghum in response to biotic stress. Key signature sequences for proper DFR/ANR classification are proposed and could form the basis for future metabolic engineering of flavonoid metabolism. Full article

(This article belongs to the Special Issue Understanding of Structure-to-Function Relationships in Biological Macromolecules)

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14 pages, 7290 KiB

Open AccessArticle

Oligomeric State of β-Coronavirus Non-Structural Protein 10 Stimulators Studied by Small Angle X-ray Scattering

by Wolfgang Knecht, S. Zoë Fisher, Jiaqi Lou, Céleste Sele, Shumeng Ma, Anna Andersson Rasmussen, Nikos Pinotsis and Frank Kozielski

Int. J. Mol. Sci. 2023, 24(17), 13649; https://doi.org/10.3390/ijms241713649 - 4 Sep 2023

Cited by 1 | Viewed by 1162

Abstract

The β-coronavirus family, encompassing Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), Severe Acute Respiratory Syndrome Coronavirus (SARS), and Middle East Respiratory Syndrome Coronavirus (MERS), has triggered pandemics within the last two decades. With the possibility of future pandemics, studying the coronavirus family members is necessary to improve knowledge and treatment. These viruses possess 16 non-structural proteins, many of which play crucial roles in viral replication and in other vital functions. One such vital protein is non-structural protein 10 (nsp10), acting as a pivotal stimulator of nsp14 and nsp16, thereby influencing RNA proofreading and viral RNA cap formation. Studying nsp10 of pathogenic coronaviruses is central to unraveling its multifunctional roles. Our study involves the biochemical and biophysical characterisation of full-length nsp10 from MERS, SARS and SARS-CoV-2. To elucidate their oligomeric state, we employed a combination of Multi-detection Size exclusion chromatography (Multi-detection SEC) with multi-angle static light scattering (MALS) and small angle X-ray scattering (SAXS) techniques. Our findings reveal that full-length nsp10s primarily exist as monomers in solution, while truncated versions tend to oligomerise. SAXS experiments reveal a globular shape for nsp10, a trait conserved in all three coronaviruses, although MERS nsp10, diverges most from SARS and SARS-CoV-2 nsp10s. In summary, unbound nsp10 proteins from SARS, MERS, and SARS-CoV-2 exhibit a globular and predominantly monomeric state in solution. Full article

(This article belongs to the Special Issue Understanding of Structure-to-Function Relationships in Biological Macromolecules)

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19 pages, 32536 KiB

Open AccessArticle

Structural Insights into Phosphorylation-Mediated Polymerase Function Loss for DNA Polymerase β Bound to Gapped DNA

by Amit Srivastava, Haitham Idriss and Dirar Homouz

Int. J. Mol. Sci. 2023, 24(10), 8988; https://doi.org/10.3390/ijms24108988 - 19 May 2023

Cited by 1 | Viewed by 1177

Abstract

DNA polymerase

β

is a member of the X-family of DNA polymerases, playing a critical role in the base excision repair (BER) pathway in mammalian cells by implementing the nucleotide gap-filling step. In vitro phosphorylation of DNA polymerase

β

with PKC on S44 [...] Read more.

DNA polymerase

β

β

with PKC on S44 causes loss in the enzyme’s DNA polymerase activity but not single-strand DNA binding. Although these studies have shown that single-stranded DNA binding is not affected by phosphorylation, the structural basis behind the mechanism underlying phosphorylation-induced activity loss remains poorly understood. Previous modeling studies suggested phosphorylation of S44 was sufficient to induce structural changes that impact the enzyme’s polymerase function. However, the S44 phosphorylated-enzyme/DNA complex has not been modeled so far. To address this knowledge gap, we conducted atomistic molecular dynamics simulations of pol

β

complexed with gapped DNA. Our simulations, which used explicit solvent and lasted for microseconds, revealed that phosphorylation at the S44 site, in the presence of Mg ions, induced significant conformational changes in the enzyme. Specifically, these changes led to the transformation of the enzyme from a closed to an open structure. Additionally, our simulations identified phosphorylation-induced allosteric coupling between the inter-domain region, suggesting the existence of a putative allosteric site. Taken together, our results provide a mechanistic understanding of the conformational transition observed due to phosphorylation in DNA polymerase

β

interactions with gapped DNA. Our simulations shed light on the mechanisms of phosphorylation-induced activity loss in DNA polymerase

β

and reveal potential targets for the development of novel therapeutics aimed at mitigating the effects of this post-translational modification. Full article

(This article belongs to the Special Issue Understanding of Structure-to-Function Relationships in Biological Macromolecules)

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