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Protein Structure and Function in Microorganisms

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

Deadline for manuscript submissions: closed (31 May 2023) | Viewed by 20932

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Prof. Dr. Chun-Hua Hsu

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1. Department of Agricultural Chemistry, National Taiwan University, Taipei 10617, Taiwan
2. Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan
3. Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 115024, Taiwan
Interests: structural biochemistry; X-ray crystallography; NMR spectroscopy; biophysics; chemical biology; molecular enzymology; post-translational modification; protein engineering and biotechnology
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Dear Colleagues,

Microorganisms comprise a large community, consisting of species considered pathogenic to humans, animals and plants, or even beneficial species that interact with other organisms and being utilized as useful bioresources. Therefore, proteins and enzymes from microorganisms are attractive targets for the study of structural and functional relationship due to the unique fundamental biological problem as well as the potential agricultural, industrial and pharmaceutical applications. The progress with structural tools, genome mining, protein engineering, and modern molecular biology has led to a deep understanding of the most aspects of these important biomolecules.

This special issue "Protein structure and function in microorganisms" gathering original research and review articles aims to present a tribune to broad range advanced structural studies via X-ray, NMR, Cryo-EM, molecular simulation and biophysical methods, or their synergetic combination for understanding protein structural-functional relationships in their very broad context. The topics would be listed below but not limited, such as proteins in cell division or cell cycle, proteins in infectious or defense systems, enzymes for post-translational modifications, enzymes involved in natural product biosynthesis, proteins from extremophiles, druggable protein targets, metabolic enzymes, industrial and food processing enzymes, plastic and pollutant degradating enzymes, as well as diagnostic and therapeutic proteins.

Prof. Dr. Chun-Hua Hsu
Guest Editor

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Keywords

protein structures
X-ray crystallography
NMR spectroscopy
cryo-electron microscopy
molecular simulation
protein modification
protein engineering
enzyme applications
drug targets
natural product biosynthesis
diagnosis
plastic and pollutant degradation
therapeutic proteins
industrial enzymes

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Related Special Issue

Protein Structure and Function in Microorganisms 2.0 in International Journal of Molecular Sciences

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Research

12 pages, 1810 KiB

Open AccessArticle

Mesophiles vs. Thermophiles: Untangling the Hot Mess of Intrinsically Disordered Proteins and Growth Temperature of Bacteria

by Alibek Kruglikov and Xuhua Xia

Int. J. Mol. Sci. 2024, 25(4), 2000; https://doi.org/10.3390/ijms25042000 - 7 Feb 2024

Viewed by 1381

Abstract

The dynamic structures and varying functions of intrinsically disordered proteins (IDPs) have made them fascinating subjects in molecular biology. Investigating IDP abundance in different bacterial species is crucial for understanding adaptive strategies in diverse environments. Notably, thermophilic bacteria have lower IDP abundance than mesophiles, and a negative correlation with optimal growth temperature (OGT) has been observed. However, the factors driving these trends are yet to be fully understood. We examined the types of IDPs present in both mesophiles and thermophiles alongside those unique to just mesophiles. The shared group of IDPs exhibits similar disorder levels in the two groups of species, suggesting that certain IDPs unique to mesophiles may contribute to the observed decrease in IDP abundance as OGT increases. Subsequently, we used quasi-independent contrasts to explore the relationship between OGT and IDP abundance evolution. Interestingly, we found no significant relationship between OGT and IDP abundance contrasts, suggesting that the evolution of lower IDP abundance in thermophiles may not be solely linked to OGT. This study provides a foundation for future research into the intricate relationship between IDP evolution and environmental adaptation. Our findings support further research on the adaptive significance of intrinsic disorder in bacterial species. Full article

(This article belongs to the Special Issue Protein Structure and Function in Microorganisms)

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21 pages, 4276 KiB

Open AccessArticle

Characterization of GEXP15 as a Potential Regulator of Protein Phosphatase 1 in Plasmodium falciparum

by Hala Mansour, Alejandro Cabezas-Cruz, Véronique Peucelle, Amaury Farce, Sophie Salomé-Desnoulez, Ines Metatla, Ida Chiara Guerrera, Thomas Hollin and Jamal Khalife

Int. J. Mol. Sci. 2023, 24(16), 12647; https://doi.org/10.3390/ijms241612647 - 10 Aug 2023

Viewed by 1543

Abstract

The Protein Phosphatase type 1 catalytic subunit (PP1c) (PF3D7_1414400) operates in combination with various regulatory proteins to specifically direct and control its phosphatase activity. However, there is little information about this phosphatase and its regulators in the human malaria parasite, Plasmodium falciparum. To address this knowledge gap, we conducted a comprehensive investigation into the structural and functional characteristics of a conserved Plasmodium-specific regulator called Gametocyte EXported Protein 15, GEXP15 (PF3D7_1031600). Through in silico analysis, we identified three significant regions of interest in GEXP15: an N-terminal region housing a PP1-interacting RVxF motif, a conserved domain whose function is unknown, and a GYF-like domain that potentially facilitates specific protein–protein interactions. To further elucidate the role of GEXP15, we conducted in vitro interaction studies that demonstrated a direct interaction between GEXP15 and PP1 via the RVxF-binding motif. This interaction was found to enhance the phosphatase activity of PP1. Additionally, utilizing a transgenic GEXP15-tagged line and live microscopy, we observed high expression of GEXP15 in late asexual stages of the parasite, with localization predominantly in the nucleus. Immunoprecipitation assays followed by mass spectrometry analyses revealed the interaction of GEXP15 with ribosomal- and RNA-binding proteins. Furthermore, through pull-down analyses of recombinant functional domains of His-tagged GEXP15, we confirmed its binding to the ribosomal complex via the GYF domain. Collectively, our study sheds light on the PfGEXP15–PP1–ribosome interaction, which plays a crucial role in protein translation. These findings suggest that PfGEXP15 could serve as a potential target for the development of malaria drugs. Full article

(This article belongs to the Special Issue Protein Structure and Function in Microorganisms)

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11 pages, 2809 KiB

Open AccessArticle

In Silico Screening and Molecular Dynamics Simulation Studies in the Identification of Natural Compound Inhibitors Targeting the Human Norovirus RdRp Protein to Fight Gastroenteritis

by Rami J. Obaid, Alaa Shafie, M. Shaheer Malik, Munirah M. Al-Rooqi, Ziad Moussa, Osama Abdulaziz, Abdulelah Aljuaid, Mamdouh Allahyani, Mazen Almehmadi, Farah Anjum and Saleh A. Ahmed

Int. J. Mol. Sci. 2023, 24(5), 5003; https://doi.org/10.3390/ijms24055003 - 5 Mar 2023

Cited by 4 | Viewed by 2745

Abstract

Norovirus (HNoV) is a leading cause of gastroenteritis globally, and there are currently no treatment options or vaccines available to combat it. RNA-dependent RNA polymerase (RdRp), one of the viral proteins that direct viral replication, is a feasible target for therapeutic development. Despite the discovery of a small number of HNoV RdRp inhibitors, the majority of them have been found to possess a little effect on viral replication, owing to low cell penetrability and drug-likeness. Therefore, antiviral agents that target RdRp are in high demand. For this purpose, we used in silico screening of a library of 473 natural compounds targeting the RdRp active site. The top two compounds, ZINC66112069 and ZINC69481850, were chosen based on their binding energy (BE), physicochemical and drug-likeness properties, and molecular interactions. ZINC66112069 and ZINC69481850 interacted with key residues of RdRp with BEs of −9.7, and −9.4 kcal/mol, respectively, while the positive control had a BE of −9.0 kcal/mol with RdRp. In addition, hits interacted with key residues of RdRp and shared several residues with the PPNDS, the positive control. Furthermore, the docked complexes showed good stability during the molecular dynamic simulation of 100 ns. ZINC66112069 and ZINC69481850 could be proven as potential inhibitors of the HNoV RdRp in future antiviral medication development investigations. Full article

(This article belongs to the Special Issue Protein Structure and Function in Microorganisms)

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18 pages, 3547 KiB

Open AccessArticle

Virus-like Particles of Nodavirus Displaying the Receptor Binding Domain of SARS-CoV-2 Spike Protein: A Potential VLP-Based COVID-19 Vaccine

by Kiven Kumar, Wen Siang Tan, Siti Suri Arshad and Kok Lian Ho

Int. J. Mol. Sci. 2023, 24(5), 4398; https://doi.org/10.3390/ijms24054398 - 23 Feb 2023

Cited by 1 | Viewed by 3015

Abstract

Since the outbreak of the coronavirus disease 2019 (COVID-19), various vaccines have been developed for emergency use. The efficacy of the initial vaccines based on the ancestral strain of severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) has become a point of contention due to the emergence of new variants of concern (VOCs). Therefore, continuous innovation of new vaccines is required to target upcoming VOCs. The receptor binding domain (RBD) of the virus spike (S) glycoprotein has been extensively used in vaccine development due to its role in host cell attachment and penetration. In this study, the RBDs of the Beta (β) and Delta (δ) variants were fused to the truncated Macrobrachium rosenbergii nodavirus capsid protein without the protruding domain (CΔ116-MrNV-CP). Immunization of BALB/c mice with the virus-like particles (VLPs) self-assembled from the recombinant CP showed that, with AddaVax as an adjuvant, a significantly high level of humoral response was elicited. Specifically, mice injected with equimolar of adjuvanted CΔ116-MrNV-CP fused with the RBD of the β- and δ-variants increased T helper (Th) cell production with a CD8⁺/CD4⁺ ratio of 0.42. This formulation also induced proliferation of macrophages and lymphocytes. Overall, this study demonstrated that the nodavirus truncated CP fused with the SARS-CoV-2 RBD has potential to be developed as a VLP-based COVID-19 vaccine. Full article

(This article belongs to the Special Issue Protein Structure and Function in Microorganisms)

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17 pages, 3965 KiB

Open AccessArticle

Identification of the Actin-Binding Region and Binding to Host Plant Apple Actin of Immunodominant Transmembrane Protein of ‘Candidatus Phytoplasma mali’

by Kajohn Boonrod, Linda Kuaguim, Mario Braun, Christine Müller-Renno, Christiane Ziegler and Gabi Krczal

Int. J. Mol. Sci. 2023, 24(2), 968; https://doi.org/10.3390/ijms24020968 - 4 Jan 2023

Cited by 4 | Viewed by 1635

Abstract

‘Candidatus Phytoplasma mali’ (‘Ca. P. mali’) has only one major membrane protein, the immunodominant membrane protein (Imp), which is regarded as being close to the ancestor of all phytoplasma immunodominant membrane proteins. Imp binds to actin and possibly facilitates its movement in the plant or insect host cells. However, protein sequences of Imp are quite diverse among phytoplasma species, thus resulting in difficulties in identifying conserved domains across species. In this work, we compare Imp protein sequences of ‘Ca. P. mali’ strain PM19 (Imp-PM19) with Imp of different strains of ‘Ca. P. mali’ and identify its actin-binding domain. Moreover, we show that Imp binds to the actin of apple (Malus x domestica), which is the host plant of ‘Ca. P. mali’. Using molecular and scanning force spectroscopy analysis, we find that the actin-binding domain of Imp-PM19 contains a highly positively charged amino acid cluster. Our result could allow investigating a possible correlation between Imp variants and the infectivity of the corresponding ‘Ca. P. mali’ isolates. Full article

(This article belongs to the Special Issue Protein Structure and Function in Microorganisms)

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17 pages, 2906 KiB

Open AccessArticle

Reovirus μ2 Protein Impairs Translation to Reduce U5 snRNP Protein Levels

by Simon Boudreault, Carole-Anne Martineau, Laurence Faucher-Giguère, Sherif Abou-Elela, Guy Lemay and Martin Bisaillon

Int. J. Mol. Sci. 2023, 24(1), 727; https://doi.org/10.3390/ijms24010727 - 31 Dec 2022

Cited by 1 | Viewed by 2050

Abstract

Mammalian orthoreovirus (MRV) is a double-stranded RNA virus from the Reoviridae family that infects a large range of mammals, including humans. Recently, studies have shown that MRV alters cellular alternative splicing (AS) during viral infection. The structural protein μ2 appears to be the main determinant of these AS modifications by decreasing the levels of U5 core components EFTUD2, PRPF8, and SNRNP200 during infection. In the present study, we investigated the mechanism by which μ2 exerts this effect on the U5 components. Our results revealed that μ2 has no impact on steady-state mRNA levels, RNA export, and protein stability of these U5 snRNP proteins. However, polysome profiling and metabolic labeling of newly synthesized proteins revealed that μ2 exerts an inhibitory effect on global translation. Moreover, we showed that μ2 mutants unable to accumulate in the nucleus retain most of the ability to reduce PRPF8 protein levels, indicating that the effect of μ2 on U5 snRNP components mainly occurs in the cytoplasm. Finally, co-expression experiments demonstrated that μ2 suppresses the expression of U5 snRNP proteins in a dose-dependent manner, and that the expression of specific U5 snRNP core components have different sensitivities to μ2’s presence. Altogether, these results suggest a novel mechanism by which the μ2 protein reduces the levels of U5 core components through translation inhibition, allowing this viral protein to alter cellular AS during infection. Full article

(This article belongs to the Special Issue Protein Structure and Function in Microorganisms)

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14 pages, 7257 KiB

Open AccessArticle

Effects of Salinity and Temperature on the Flexibility and Function of a Polyextremophilic Enzyme

by Victoria J. Laye, Shahlo Solieva, Vincent A. Voelz and Shiladitya DasSarma

Int. J. Mol. Sci. 2022, 23(24), 15620; https://doi.org/10.3390/ijms232415620 - 9 Dec 2022

Cited by 4 | Viewed by 1805

Abstract

The polyextremophilic β-galactosidase enzyme of the haloarchaeon Halorubrum lacusprofundi functions in extremely cold and hypersaline conditions. To better understand the basis of polyextremophilic activity, the enzyme was studied using steady-state kinetics and molecular dynamics at temperatures ranging from 10 °C to 50 °C and salt concentrations from 1 M to 4 M KCl. Kinetic analysis showed that while catalytic efficiency (k_cat/K_m) improves with increasing temperature and salinity, K_m is reduced with decreasing temperatures and increasing salinity, consistent with improved substrate binding at low temperatures. In contrast, k_cat was similar from 2–4 M KCl across the temperature range, with the calculated enthalpic and entropic components indicating a threshold of 2 M KCl to lower the activation barrier for catalysis. With molecular dynamics simulations, the increase in per-residue root-mean-square fluctuation (RMSF) was observed with higher temperature and salinity, with trends like those seen with the catalytic efficiency, consistent with the enzyme’s function being related to its flexibility. Domain A had the smallest change in flexibility across the conditions tested, suggesting the adaptation to extreme conditions occurs via regions distant to the active site and surface accessible residues. Increased flexibility was most apparent in the distal active sites, indicating their importance in conferring salinity and temperature-dependent effects. Full article

(This article belongs to the Special Issue Protein Structure and Function in Microorganisms)

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17 pages, 2824 KiB

Open AccessArticle

Insights into the Structure of the Highly Glycosylated Ffase from Rhodotorula dairenensis Enhance Its Biotechnological Potential

by Elena Jiménez-Ortega, Egle Narmontaite, Beatriz González-Pérez, Francisco J. Plou, María Fernández-Lobato and Julia Sanz-Aparicio

Int. J. Mol. Sci. 2022, 23(23), 14981; https://doi.org/10.3390/ijms232314981 - 29 Nov 2022

Cited by 4 | Viewed by 2100

Abstract

Rhodotorula dairenensis β-fructofuranosidase is a highly glycosylated enzyme with broad substrate specificity that catalyzes the synthesis of 6-kestose and a mixture of the three series of fructooligosaccharides (FOS), fructosylating a variety of carbohydrates and other molecules as alditols. We report here its three-dimensional structure, showing the expected bimodular arrangement and also a unique long elongation at its N-terminus containing extensive O-glycosylation sites that form a peculiar arrangement with a protruding loop within the dimer. This region is not required for activity but could provide a molecular tool to target the dimeric protein to its receptor cellular compartment in the yeast. A truncated inactivated form was used to obtain complexes with fructose, sucrose and raffinose, and a Bis-Tris molecule was trapped, mimicking a putative acceptor substrate. The crystal structure of the complexes reveals the major traits of the active site, with Asn387 controlling the substrate binding mode. Relevant residues were selected for mutagenesis, the variants being biochemically characterized through their hydrolytic and transfructosylating activity. All changes decrease the hydrolytic efficiency against sucrose, proving their key role in the activity. Moreover, some of the generated variants exhibit redesigned transfructosylating specificity, which may be used for biotechnological purposes to produce novel fructosyl-derivatives. Full article

(This article belongs to the Special Issue Protein Structure and Function in Microorganisms)

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16 pages, 4123 KiB

Open AccessArticle

Identification of the Key Functional Domains of Bombyx mori Nucleopolyhedrovirus IE1 Protein

by Zhi-Gang Hu, Zhan-Qi Dong, Jiang-Hao Miao, Ke-Jie Li, Jie Wang, Peng Chen, Cheng Lu and Min-Hui Pan

Int. J. Mol. Sci. 2022, 23(18), 10276; https://doi.org/10.3390/ijms231810276 - 7 Sep 2022

Viewed by 1665

Abstract

The immediate early protein 1 (IE1) acts as a transcriptional activator and is essential for viral gene transcription and viral DNA replication. However, the key regulatory domains of IE1 remain poorly understood. Here, we analyzed the sequence characteristics of Bombyx mori nucleopolyhedrovirus (BmNPV) IE1 and identified the key functional domains of BmNPV IE1 by stepwise truncation. Our results showed that BmNPV IE1 was highly similar to Autographa californica nucleopolyhedrovirus (AcMNPV) IE1, but was less conserved with IE1 of other baculoviruses, the C-terminus of IE1 was more conserved than the N-terminus, and BmNPV IE1 was also necessary for BmNPV proliferation. Moreover, we found that IE1_158–208 was a major nuclear localization element, and IE1_1–157 and IE1_539–559 were minor nuclear localization elements, but the combination of these two minor elements was equally sufficient to fully mediate the nuclear entry of IE1. Meanwhile, IE1_1–258, IE1_560–584, and the association of amino acids 258 and 259 were indispensable for the transactivation activity of BmNPV IE1. These results systematically resolve the functional domains of BmNPV IE1, which contribute to the understanding of the mechanism of baculovirus infection and provide a possibility to synthesize a small molecule IE1-truncated mutant as an agonist or antagonist. Full article

(This article belongs to the Special Issue Protein Structure and Function in Microorganisms)

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10 pages, 1878 KiB

Open AccessArticle

Conformational Changes of α-Crystallin Proteins Induced by Heat Stress

by Yu-Yung Chang, Meng-Hsuan Hsieh, Yen-Chieh Huang, Chun-Jung Chen and Ming-Tao Lee

Int. J. Mol. Sci. 2022, 23(16), 9347; https://doi.org/10.3390/ijms23169347 - 19 Aug 2022

Cited by 1 | Viewed by 1719

Abstract

α-crystallin is a major structural protein in the eye lenses of vertebrates that is composed of two relative subunits, αA and αB crystallin, which function in maintaining lens transparency. As a member of the small heat-shock protein family (sHsp), α-crystallin exhibits chaperone-like activity to prevent the misfolding or aggregation of critical proteins in the lens, which is associated with cataract disease. In this study, high-purity αA and αB crystallin proteins were expressed from E. coli and purified by affinity and size-exclusion chromatography. The size-exclusion chromatography experiment showed that both αA and αB crystallins exhibited oligomeric complexes in solution. Here, we present the structural characteristics of α-crystallin proteins from low to high temperature by combining circular dichroism (CD) and small-angle X-ray scattering (SAXS). Not only the CD data, but also SAXS data show that α-crystallin proteins exhibit transition behavior on conformation with temperature increasing. Although their protein sequences are highly conserved, the analysis of their thermal stability showed different properties in αA and αB crystallin. In this study, taken together, the data discussed were provided to demonstrate more insights into the chaperone-like activity of α-crystallin proteins. Full article

(This article belongs to the Special Issue Protein Structure and Function in Microorganisms)

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