LIVIVO - Search results -

Search results

Result 1 - 10 of total 12

Search options

Article ; Online: Structural and Biochemical Characterization of Endo-β-1,4-glucanase from Dictyoglomus thermophilum , a Hyperthermostable and Halotolerant Cellulase

Rita Berisio / Giovanni Barra / Maria Romano / Flavia Squeglia / Alessia Ruggiero

Catalysts, Vol 12, Iss 302, p

2022 Volume 302

Abstract: Enzymatic conversion of polysaccharides in the lignocellulosic biomass is currently the subject of intensive research and will be a key technology in future biorefineries. Using a bioinformatics approach, we previously identified a putative endo-β-1,4- ... ...

Abstract	Enzymatic conversion of polysaccharides in the lignocellulosic biomass is currently the subject of intensive research and will be a key technology in future biorefineries. Using a bioinformatics approach, we previously identified a putative endo-β-1,4-glucanase (DtCel5A) from Dictyoglomus thermophilum , a chemoorganotrophic and thermophilic bacterium. Here, we structurally and functionally characterize DtCel5A and show that it is endowed with remarkable thermal and chemical stability. The structural features of DtCel5A and of its complex with cellobiose have been investigated by combining X-ray crystallography and other biophysical studies. Importantly, biochemical assays show that DtCel5A retains its activity on cellulose at high temperatures and at elevated salt concentrations. These features make DtCel5A an enzyme with interesting biotechnological applications for biomass degradation.
Keywords	crystal structure ; thermostability ; endoglucanase ; enzyme ; cell wall ; Chemical technology ; TP1-1185 ; Chemistry ; QD1-999
Subject code	540
Language	English
Publishing date	2022-03-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

Full text online

Full text

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: The Cell Wall Hydrolytic NlpC/P60 Endopeptidases in Mycobacterial Cytokinesis

Flavia Squeglia / Miguel Moreira / Alessia Ruggiero / Rita Berisio

Cells, Vol 8, Iss 6, p

A Structural Perspective

2019 Volume 609

Abstract: In preparation for division, bacteria replicate their DNA and segregate the newly formed chromosomes. A division septum then assembles between the chromosomes, and the mother cell splits into two identical daughters due to septum degradation. A major ... ...

Abstract	In preparation for division, bacteria replicate their DNA and segregate the newly formed chromosomes. A division septum then assembles between the chromosomes, and the mother cell splits into two identical daughters due to septum degradation. A major constituent of bacterial septa and of the whole cell wall is peptidoglycan (PGN), an essential cell wall polymer, formed by glycan chains of β−(1-4)-linked- N -acetylglucosamine (GlcNAc) and N-acetylmuramic acid (MurNAc), cross-linked by short peptide stems. Depending on the amino acid located at the third position of the peptide stem, PGN is classified as either Lys-type or meso-diaminopimelic acid (DAP)-type. Hydrolytic enzymes play a crucial role in the degradation of bacterial septa to split the cell wall material shared by adjacent daughter cells to promote their separation. In mycobacteria, a key PGN hydrolase, belonging to the NlpC/P60 endopeptidase family and denoted as RipA, is responsible for the degradation of septa, as the deletion of the gene encoding for this enzyme generates abnormal bacteria with multiple septa. This review provides an update of structural and functional data highlighting the central role of RipA in mycobacterial cytokinesis and the fine regulation of its catalytic activity, which involves multiple molecular partners.
Keywords	cell division ; mycobacteria ; structure ; peptidoglycan ; NlpC/P60 endopeptidase ; RipA ; Biology (General) ; QH301-705.5
Subject code	571
Language	English
Publishing date	2019-06-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

Full text online

Full text

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: Host DDX Helicases as Possible SARS-CoV-2 Proviral Factors

Flavia Squeglia / Maria Romano / Alessia Ruggiero / Giovanni Maga / Rita Berisio

Frontiers in Chemistry, Vol

A Structural Overview of Their Hijacking Through Multiple Viral Proteins

2020 Volume 8

Abstract: As intracellular parasites, viruses hijack the host cell metabolic machinery for their replication. Among other cellular proteins, the DEAD-box (DDX) RNA helicases have been shown to be hijacked by coronaviruses and to participate in essential DDX- ... ...

Abstract	As intracellular parasites, viruses hijack the host cell metabolic machinery for their replication. Among other cellular proteins, the DEAD-box (DDX) RNA helicases have been shown to be hijacked by coronaviruses and to participate in essential DDX-mediated viral replication steps. Human DDX RNA helicases play essential roles in a broad array of biological processes and serve multiple roles at the virus-host interface. The viral proteins responsible for DDX interactions are highly conserved among coronaviruses, suggesting that they might also play conserved functions in the SARS-CoV-2 replication cycle. In this review, we provide an update of the structural and functional data of DDX as possible key factors involved in SARS-CoV-2 hijacking mechanisms. We also attempt to fill the existing gaps in the available structural information through homology modeling. Based on this information, we propose possible paths exploited by the virus to replicate more efficiently by taking advantage of host DDX proteins. As a general rule, sequestration of DDX helicases by SARS-CoV-2 is expected to play a pro-viral role in two ways: by enhancing key steps of the virus life cycle and, at the same time, by suppressing the host innate immune response.
Keywords	SARS-CoV-2 ; COVID19 ; protein structure ; viral infection ; DDX helicases ; Chemistry ; QD1-999
Subject code	570
Language	English
Publishing date	2020-12-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

Full text online

Full text

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Book ; Online: A Structural View of SARS-CoV-2 RNA Replication Machinery

Maria Romano / Alessia Ruggiero / Flavia Squeglia / Giovanni Maga / Rita Berisio

Cells ; Volume 9 ; Issue 5

RNA Synthesis, Proofreading and Final Capping

2020

Abstract: The current coronavirus disease-2019 (COVID-19) pandemic is due to the novel coronavirus SARS-CoV-2. The scientific community has mounted a strong response by accelerating research and innovation, and has quickly set the foundation for understanding the ... ...

Abstract	The current coronavirus disease-2019 (COVID-19) pandemic is due to the novel coronavirus SARS-CoV-2. The scientific community has mounted a strong response by accelerating research and innovation, and has quickly set the foundation for understanding the molecular determinants of the disease for the development of targeted therapeutic interventions. The replication of the viral genome within the infected cells is a key stage of the SARS-CoV-2 life cycle. It is a complex process involving the action of several viral and host proteins in order to perform RNA polymerization, proofreading and final capping. This review provides an update of the structural and functional data on the key actors of the replicatory machinery of SARS-CoV-2, to fill the gaps in the currently available structural data, which is mainly obtained through homology modeling. Moreover, learning from similar viruses, we collect data from the literature to reconstruct the pattern of interactions among the protein actors of the SARS-CoV-2 RNA polymerase machinery. Here, an important role is played by co-factors such as Nsp8 and Nsp10, not only as allosteric activators but also as molecular connectors that hold the entire machinery together to enhance the efficiency of RNA replication.
Keywords	SARS-CoV-2 ; COVID19 ; RNA replication ; protein structure ; infectious disease ; covid19
Language	English
Publishing date	2020-05-20
Publisher	Multidisciplinary Digital Publishing Institute
Publishing country	ch
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

Full text online

Full text

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: A Structural View of SARS-CoV-2 RNA Replication Machinery

Maria Romano / Alessia Ruggiero / Flavia Squeglia / Giovanni Maga / Rita Berisio

Cells, Vol 9, Iss 1267, p

RNA Synthesis, Proofreading and Final Capping

2020 Volume 1267

Abstract	The current coronavirus disease-2019 (COVID-19) pandemic is due to the novel coronavirus SARS-CoV-2. The scientific community has mounted a strong response by accelerating research and innovation, and has quickly set the foundation for understanding the molecular determinants of the disease for the development of targeted therapeutic interventions. The replication of the viral genome within the infected cells is a key stage of the SARS-CoV-2 life cycle. It is a complex process involving the action of several viral and host proteins in order to perform RNA polymerization, proofreading and final capping. This review provides an update of the structural and functional data on the key actors of the replicatory machinery of SARS-CoV-2, to fill the gaps in the currently available structural data, which is mainly obtained through homology modeling. Moreover, learning from similar viruses, we collect data from the literature to reconstruct the pattern of interactions among the protein actors of the SARS-CoV-2 RNA polymerase machinery. Here, an important role is played by co-factors such as Nsp8 and Nsp10, not only as allosteric activators but also as molecular connectors that hold the entire machinery together to enhance the efficiency of RNA replication.
Keywords	SARS-CoV-2 ; COVID19 ; RNA replication ; protein structure ; infectious disease ; Biology (General) ; QH301-705.5 ; covid19
Subject code	612
Language	English
Publishing date	2020-05-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

Full text online

Full text

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: PE_PGRS33, an Important Virulence Factor of Mycobacterium tuberculosis and Potential Target of Host Humoral Immune Response

Eliza Kramarska / Flavia Squeglia / Flavio De Maio / Giovanni Delogu / Rita Berisio

Cells, Vol 10, Iss 161, p

2021 Volume 161

Abstract: PE_PGRS proteins are surface antigens of Mycobacterium tuberculosis ( Mtb ) and a few other pathogenic mycobacteria. The PE_PGRS33 protein is among the most studied PE_PGRSs. It is known that the PE domain of PE_PGRS33 is required for the protein ... ...

Abstract	PE_PGRS proteins are surface antigens of Mycobacterium tuberculosis ( Mtb ) and a few other pathogenic mycobacteria. The PE_PGRS33 protein is among the most studied PE_PGRSs. It is known that the PE domain of PE_PGRS33 is required for the protein translocation through the mycobacterial cell wall, where the PGRS domain remains available for interaction with host receptors. Interaction with Toll like receptor 2 (TLR2) promotes secretion of inflammatory chemokines and cytokines, which are key in the immunopathogenesis of tuberculosis (TB). In this review, we briefly address some key challenges in the development of a TB vaccine and attempt to provide a rationale for the development of new vaccines aimed at fostering a humoral response against Mtb . Using PE_PGRS33 as a model for a surface-exposed antigen, we exploit the availability of current structural data using homology modeling to gather insights on the PGRS domain features. Our study suggests that the PGRS domain of PE_PGRS33 exposes four PGII sandwiches on the outer surface, which, we propose, are directly involved through their loops in the interactions with the host receptors and, as such, are promising targets for a vaccination strategy aimed at inducing a humoral response.
Keywords	vaccine ; protein structure ; tuberculosis ; infectious disease ; Biology (General) ; QH301-705.5
Subject code	570
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

Full text online

Full text

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: Structure-Based Development of SARS-CoV-2 Spike Interactors

Flavia Squeglia / Maria Romano / Luciana Esposito / Giovanni Barra / Pietro Campiglia / Marina Sala / Maria Carmina Scala / Alessia Ruggiero / Rita Berisio

International Journal of Molecular Sciences, Vol 23, Iss 5601, p

2022 Volume 5601

Abstract: Coronaviruses, including SARS-CoV-2 (the etiological agent of the current COVID-19 pandemic), rely on the surface spike glycoprotein to access the host cells, mainly through the interaction of their receptor-binding domain (RBD) with the human ... ...

Abstract	Coronaviruses, including SARS-CoV-2 (the etiological agent of the current COVID-19 pandemic), rely on the surface spike glycoprotein to access the host cells, mainly through the interaction of their receptor-binding domain (RBD) with the human angiotensin-converting enzyme 2 (ACE2). Therefore, molecular entities able to interfere with the binding of the SARS-CoV-2 spike protein to ACE2 have great potential to inhibit viral entry. Starting from the available structural data on the interaction between SARS-CoV-2 spike protein and the host ACE2 receptor, we engineered a set of soluble and stable spike interactors, here denoted as S-plugs. Starting from the prototype S-plug, we adopted a computational approach by combining stability prediction, associated to single-point mutations, with molecular dynamics to enhance both S-plug thermostability and binding affinity to the spike protein. The best developed molecule, S-plug3, possesses a highly stable α-helical con-formation (with melting temperature Tm of 54 °C) and can interact with the spike RBD and S1 domains with similar low nanomolar affinities. Importantly, S-plug3 exposes the spike RBD to almost the same interface as the human ACE2 receptor, aimed at the recognition of all ACE2-accessing coronaviruses. Consistently, S-plug3 preserves a low nanomolar dissociation constant with the delta B.1.617.2 variant of SARS-CoV-2 spike protein (K D = 29.2 ± 0.6 nM). Taken together, we provide valid starting data for the development of therapeutical and diagnostic tools against coronaviruses accessing through ACE2.
Keywords	SARS-CoV-2 ; COVID-19 ; viral entry ; spike protein ; protein structure ; infectious disease ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Subject code	612
Language	English
Publishing date	2022-05-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

Full text online

Full text

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: Structure based design of effective HtpG-derived vaccine antigens against M. tuberculosis

Alessia Ruggiero / Han-Gyu Choi / Giovanni Barra / Flavia Squeglia / Young Woo Back / Hwa-Jung Kim / Rita Berisio

Frontiers in Molecular Biosciences, Vol

2022 Volume 9

Abstract: Vaccine development against Tuberculosis is a strong need, given the low efficacy of the sole vaccine hitherto used, the Bacillus Calmette–Guérin (BCG) vaccine. The chaperone-like protein HtpGMtb of M. tuberculosis is a large dimeric and multi-domain ... ...

Abstract	Vaccine development against Tuberculosis is a strong need, given the low efficacy of the sole vaccine hitherto used, the Bacillus Calmette–Guérin (BCG) vaccine. The chaperone-like protein HtpGMtb of M. tuberculosis is a large dimeric and multi-domain protein with promising antigenic properties. We here used biophysical and biochemical studies to improve our understanding of the structural basis of HtpGMtb functional role and immunogenicity, a precious information to engineer improved antigens. We showed that HtpGMtb is a dimeric nucleotide-binding protein and identified the dimerisation interface on the C-terminal domain of the protein. We also showed that the most immunoreactive regions of the molecule are located on the C-terminal and middle domains of the protein, whereas no role is played by the catalytic N-terminal domain in the elicitation of the immune response. Based on these observations, we experimentally validated our predictions in mice, using a plethora of immunological assays. As an outcome, we designed vaccine antigens with enhanced biophysical properties and ease of production, albeit conserved or enhanced antigenic properties. Our results prove the efficacy of structural vaccinology approaches in improving our understanding of the structural basis of immunogenicity, a precious information to engineer more stable, homogeneous, efficiently produced, and effective vaccine antigens.
Keywords	protein structure ; vaccine ; infectious disease ; folding ; antigen ; chaperone ; Biology (General) ; QH301-705.5
Subject code	570
Language	English
Publishing date	2022-08-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

Full text online

Full text

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article: PASTA sequence composition is a predictive tool for protein class identification

Calvanese, Luisa / Flavia Squeglia / Gabriella D’Auria / Lucia Falcigno / Rita Berisio

Amino acids. 2018 Oct., v. 50, no. 10

2018

Abstract: PASTA domains are small modules expressed in bacteria and found in one or multiple copies at the C-terminal end of several penicillin binding proteins (PBPs) and Ser/Thr protein kinases (STPKs) and represent potential targets for a new class of ... ...

Abstract	PASTA domains are small modules expressed in bacteria and found in one or multiple copies at the C-terminal end of several penicillin binding proteins (PBPs) and Ser/Thr protein kinases (STPKs) and represent potential targets for a new class of antibiotics. PASTA domains are currently annotated as sensor domains, as they are thought to activate their cognate proteins in response to binding to opportune ligands. However, recent studies have shown that PASTA domains linked to proteins of different classes, STPKs or PBPs, do not share the same binding abilities. Despite this, there is currently no way to distinguish between PASTA domains from the two classes, since all of them share the same fold, independent of the class they belong to. To identify a predictive tool of class identification, we here analyse a pool of parameters, including amino acid compositions and total charges of PASTA domains either linked to PBPs or to STPKs. We screened sequences from Actinobacteria, Firmicutes and Bacteroidetes. The first two phyla include some of the most dangerous micro-organisms for human health such as Mycobacterium tuberculosis and Staphylococcus aureus. Based on this analysis, our study proposes a predictive method to assign PASTA domains with unknown origin to their corresponding enzyme class, based solely on sequence information.
Keywords	amino acid composition ; bacteria ; Bacteroidetes ; binding capacity ; binding proteins ; human health ; ligands ; Mycobacterium tuberculosis ; penicillins ; protein kinases ; Staphylococcus aureus
Language	English
Dates of publication	2018-10
Size	p. 1441-1450.
Publishing place	Springer Vienna
Document type	Article
ZDB-ID	1121341-3
ISSN	1438-2199 ; 0939-4451
ISSN (online)	1438-2199
ISSN	0939-4451
DOI	10.1007/s00726-018-2621-8
Database	NAL-Catalogue (AGRICOLA)

In stock of ZB MED Cologne/Königswinter

Zs.A 3490: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (2.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

Details ▾
- See ZB MED holdings
- Order with fees

Article: The structure of Resuscitation promoting factor B from M. tuberculosis reveals unexpected ubiquitin-like domains

Ruggiero, Alessia / Alfonso De Simone / Flavia Squeglia / Luigi Vitagliano / Maria Romano / Rita Berisio

Biochimica et biophysica acta. 2016 Feb., v. 1860, no. 2

2016

Abstract: RpfB is a key factor in resuscitation from dormancy of Mycobacterium tuberculosis. This protein is a cell-wall glycosidase, which cleaves cell-wall peptidoglycan. RpfB is structurally complex and is composed of three types of domains, including a ... ...

Abstract	RpfB is a key factor in resuscitation from dormancy of Mycobacterium tuberculosis. This protein is a cell-wall glycosidase, which cleaves cell-wall peptidoglycan. RpfB is structurally complex and is composed of three types of domains, including a catalytic, a G5 and three DUF348 domains. Structural information is currently limited to a portion of the protein including only the catalytic and G5 domains. To gain insights into the structure and function of all domains we have undertaken structural investigations on a large protein fragment containing all three types of domains that constitute RpfB (RpfB3D).The structural features of RpfB3D have been investigated combining x-ray crystallography and biophysical studies.The crystal structure of RpfB3D provides the first structural characterization of a DUF348 domain and revealed an unexpected structural relationship with ubiquitin. The crystal structure also provides specific structural features of these domains explaining their frequent association with G5 domains.Results provided novel insights into the mechanism of peptidoglycan degradation necessary to the resuscitation of M. tuberculosis. Features of the DUF348 domain add structural data to a large set of proteins embedding this domain. Based on its structural similarity to ubiquitin and frequent association to the G5 domain, we propose to name this domain as G5-linked-Ubiquitin-like domain, UBLG5.
Keywords	crystal structure ; dormancy ; Mycobacterium tuberculosis ; peptidoglycans ; ubiquitin ; X-ray diffraction
Language	English
Dates of publication	2016-02
Size	p. 445-451.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	840755-1
ISSN	0304-4165
ISSN	0304-4165
DOI	10.1016/j.bbagen.2015.11.001
Database	NAL-Catalogue (AGRICOLA)

In stock of ZB MED Cologne/Königswinter

Uc I Zs.247: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

To top

Full text online

More links

Kategorien

Inter-library loan at ZB MED

Full text online

More links

Kategorien

Inter-library loan at ZB MED

Full text online

More links

Kategorien

Inter-library loan at ZB MED

Full text online

More links

Kategorien

Inter-library loan at ZB MED

Full text online

More links

Kategorien

Inter-library loan at ZB MED

Full text online

More links

Kategorien

Inter-library loan at ZB MED

Full text online

More links

Kategorien

Inter-library loan at ZB MED

Full text online

More links

Kategorien

Inter-library loan at ZB MED

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito