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Article ; Online: Regulation of interactions with sliding clamps during DNA replication and repair.

López de Saro, Francisco J

2009 Volume 10, Issue 3, Page(s) 206–215

Abstract: The molecular machines that replicate the genome consist of many interacting components. Essential to the organization of the replication machinery are ring-shaped proteins, like PCNA (Proliferating Cell Nuclear Antigen) or the beta- clamp, collectively ... ...

Abstract	The molecular machines that replicate the genome consist of many interacting components. Essential to the organization of the replication machinery are ring-shaped proteins, like PCNA (Proliferating Cell Nuclear Antigen) or the beta- clamp, collectively named sliding clamps. They encircle the DNA molecule and slide on it freely and bidirectionally. Sliding clamps are typically associated to DNA polymerases and provide these enzymes with the processivity required to synthesize large chromosomes. Additionally, they interact with a large array of proteins that perform enzymatic reactions on DNA, targeting and orchestrating their functions. In recent years there have been a large number of studies that have analyzed the structural details of how sliding clamps interact with their ligands. However, much remains to be learned in relation to how these interactions are regulated to occur coordinately and sequentially. Since sliding clamps participate in reactions in which many different enzymes bind and then release from the clamp in an orchestrated way, it is critical to analyze how these changes in affinity take place. In this review I focus the attention on the mechanisms by which various types of enzymes interact with sliding clamps and what is known about the regulation of this binding. Especially I describe emerging paradigms on how enzymes switch places on sliding clamps during DNA replication and repair of prokaryotic and eukaryotic genomes.
Language	English
Publishing date	2009-11-02
Publishing country	United Arab Emirates
Document type	Journal Article
ZDB-ID	2033677-9
ISSN	1875-5488 ; 1389-2029
ISSN (online)	1875-5488
ISSN	1389-2029
DOI	10.2174/138920209788185234
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Article ; Online: Implementation of a program to improve influenza vaccination rates among medical students: a comparative study involving two university affiliated hospitals.

Saro-Buendía, Miguel / Marrero-Sánchez, Ángel / García-Ruiz de Morales, Daniel / Chiara-Graciani, Guillermo / Coderch-Carretero, Jaime / Pérez-Jacoiste Asín, María Asunción / Silva, José Tiago / Fernández-Ruiz, Mario / Arrazola, Pilar / Aguado, José María / López-Medrano, Francisco

Human vaccines & immunotherapeutics

2021 Volume 17, Issue 10, Page(s) 3662–3669

Abstract: Background and ... ...

Abstract	Background and objectives
MeSH term(s)	Attitude of Health Personnel ; Cross-Sectional Studies ; Health Personnel ; Hospitals, University ; Humans ; Influenza Vaccines ; Influenza, Human/prevention & control ; Students, Medical ; Vaccination
Chemical Substances	Influenza Vaccines
Language	English
Publishing date	2021-06-15
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2664176-8
ISSN	2164-554X ; 2164-5515
ISSN (online)	2164-554X
ISSN	2164-5515
DOI	10.1080/21645515.2021.1920269
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Article ; Online: Large-scale genomic analysis suggests a neutral punctuated dynamics of transposable elements in bacterial genomes.

Iranzo, Jaime / Gómez, Manuel J / López de Saro, Francisco J / Manrubia, Susanna

PLoS computational biology

2014 Volume 10, Issue 6, Page(s) e1003680

Abstract: Insertion sequences (IS) are the simplest and most abundant form of transposable DNA found in bacterial genomes. When present in multiple copies, it is thought that they can promote genomic plasticity and genetic exchange, thus being a major force of ... ...

Abstract	Insertion sequences (IS) are the simplest and most abundant form of transposable DNA found in bacterial genomes. When present in multiple copies, it is thought that they can promote genomic plasticity and genetic exchange, thus being a major force of evolutionary change. The main processes that determine IS content in genomes are, though, a matter of debate. In this work, we take advantage of the large amount of genomic data currently available and study the abundance distributions of 33 IS families in 1811 bacterial chromosomes. This allows us to test simple models of IS dynamics and estimate their key parameters by means of a maximum likelihood approach. We evaluate the roles played by duplication, lateral gene transfer, deletion and purifying selection. We find that the observed IS abundances are compatible with a neutral scenario where IS proliferation is controlled by deletions instead of purifying selection. Even if there may be some cases driven by selection, neutral behavior dominates over large evolutionary scales. According to this view, IS and hosts tend to coexist in a dynamic equilibrium state for most of the time. Our approach also allows for a detection of recent IS expansions, and supports the hypothesis that rapid expansions constitute transient events-punctuations-during which the state of coexistence of IS and host becomes perturbated.
MeSH term(s)	DNA Transposable Elements/genetics ; Evolution, Molecular ; Gene Duplication/genetics ; Gene Transfer, Horizontal/genetics ; Genome, Bacterial/genetics ; Genomics/methods ; Models, Genetic
Chemical Substances	DNA Transposable Elements
Language	English
Publishing date	2014-06-26
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2193340-6
ISSN	1553-7358 ; 1553-734X
ISSN (online)	1553-7358
ISSN	1553-734X
DOI	10.1371/journal.pcbi.1003680
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Article ; Online: Chromosomal replication dynamics and interaction with the β sliding clamp determine orientation of bacterial transposable elements.

Gómez, Manuel J / Díaz-Maldonado, Héctor / González-Tortuero, Enrique / López de Saro, Francisco J

Genome biology and evolution

2014 Volume 6, Issue 3, Page(s) 727–740

Abstract: Insertion sequences (ISs) are small transposable elements widespread in bacterial genomes, where they play an essential role in chromosome evolution by stimulating recombination and genetic flow. Despite their ubiquity, it is unclear how ISs interact ... ...

Abstract	Insertion sequences (ISs) are small transposable elements widespread in bacterial genomes, where they play an essential role in chromosome evolution by stimulating recombination and genetic flow. Despite their ubiquity, it is unclear how ISs interact with the host. Here, we report a survey of the orientation patterns of ISs in bacterial chromosomes with the objective of gaining insight into the interplay between ISs and host chromosomal functions. We find that a significant fraction of IS families present a consistent and family-specific orientation bias with respect to chromosomal DNA replication, especially in Firmicutes. Additionally, we find that the transposases of up to nine different IS families with different transposition pathways interact with the β sliding clamp, an essential replication factor, suggesting that this is a widespread mechanism of interaction with the host. Although we find evidence that the interaction with the β sliding clamp is common to all bacterial phyla, it also could explain the observed strong orientation bias found in Firmicutes, because in this group β is asymmetrically distributed during synthesis of the leading or lagging strands. Besides the interaction with the β sliding clamp, other asymmetries also play a role in the biased orientation of some IS families. The utilization of the highly conserved replication sliding clamps suggests a mechanism for host regulation of IS proliferation and also a universal platform for IS dispersal and transmission within bacterial populations and among phylogenetically distant species.
MeSH term(s)	Chromosomes, Bacterial/genetics ; DNA Replication ; DNA Transposable Elements ; DNA, Bacterial/genetics ; Escherichia coli/enzymology ; Escherichia coli/genetics ; Evolution, Molecular ; Genome, Bacterial ; Phylogeny ; Sequence Analysis, DNA ; Transposases/genetics
Chemical Substances	DNA Transposable Elements ; DNA, Bacterial ; Transposases (EC 2.7.7.-)
Language	English
Publishing date	2014-03-10
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2495328-3
ISSN	1759-6653 ; 1759-6653
ISSN (online)	1759-6653
ISSN	1759-6653
DOI	10.1093/gbe/evu052
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Article ; Online: Large-scale genomic analysis suggests a neutral punctuated dynamics of transposable elements in bacterial genomes.

Jaime Iranzo / Manuel J Gómez / Francisco J López de Saro / Susanna Manrubia

PLoS Computational Biology, Vol 10, Iss 6, p e

2014 Volume 1003680

Abstract	Insertion sequences (IS) are the simplest and most abundant form of transposable DNA found in bacterial genomes. When present in multiple copies, it is thought that they can promote genomic plasticity and genetic exchange, thus being a major force of evolutionary change. The main processes that determine IS content in genomes are, though, a matter of debate. In this work, we take advantage of the large amount of genomic data currently available and study the abundance distributions of 33 IS families in 1811 bacterial chromosomes. This allows us to test simple models of IS dynamics and estimate their key parameters by means of a maximum likelihood approach. We evaluate the roles played by duplication, lateral gene transfer, deletion and purifying selection. We find that the observed IS abundances are compatible with a neutral scenario where IS proliferation is controlled by deletions instead of purifying selection. Even if there may be some cases driven by selection, neutral behavior dominates over large evolutionary scales. According to this view, IS and hosts tend to coexist in a dynamic equilibrium state for most of the time. Our approach also allows for a detection of recent IS expansions, and supports the hypothesis that rapid expansions constitute transient events-punctuations-during which the state of coexistence of IS and host becomes perturbated.
Keywords	Biology (General) ; QH301-705.5
Subject code	612
Language	English
Publishing date	2014-06-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Combination therapy with tocilizumab and corticosteroids for aged patients with severe COVID-19 pneumonia: A single-center retrospective study.

López-Medrano, Francisco / Pérez-Jacoiste Asín, María Asunción / Fernández-Ruiz, Mario / Carretero, Octavio / Lalueza, Antonio / Maestro de la Calle, Guillermo / Caro, José Manuel / de la Calle, Cristina / Catalán, Mercedes / García-García, Rocío / Martínez-López, Joaquín / Origüen, Julia / Ripoll, Mar / San Juan, Rafael / Trujillo, Hernando / Sevillano, Ángel / Gutiérrez, Eduardo / de Miguel, Borja / Aguilar, Fernando /

Gómez, Carlos / Silva, José Tiago / García-Ruiz de Morales, Daniel / Saro-Buendía, Miguel / Marrero-Sánchez, Ángel / Chiara-Graciani, Guillermo / Bueno, Héctor / Paz-Artal, Estela / Lumbreras, Carlos / Pablos, José L / Aguado, José María

International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases

2021 Volume 105, Page(s) 487–494

Abstract: Background: The role of combination immunomodulatory therapy with systemic corticosteroids and tocilizumab (TCZ) for aged patients with COVID-19-associated cytokine release syndrome remains unclear.: Methods: A retrospective single-center study was ... ...

Abstract	Background: The role of combination immunomodulatory therapy with systemic corticosteroids and tocilizumab (TCZ) for aged patients with COVID-19-associated cytokine release syndrome remains unclear. Methods: A retrospective single-center study was conducted on consecutive patients aged ≥65 years who developed severe COVID-19 between 03 March and 01 May 2020 and were treated with corticosteroids at various doses (methylprednisolone 0.5mg/kg/12h to 250mg/24h), either alone (CS group) or associated with intravenous tocilizumab (400-600mg, one to three doses) (CS-TCZ group). The primary outcome was all-cause mortality by day +14, whereas secondary outcomes included mortality by day +28 and clinical improvement (discharge and/or a ≥2 point decrease on a 6-point ordinal scale) by day +14. Propensity score (PS)-based adjustment and inverse probability of treatment weights (IPTW) were applied. Results: Totals of 181 and 80 patients were included in the CS and CS-TCZ groups, respectively. All-cause 14-day mortality was lower in the CS-TCZ group, both in the PS-adjusted (hazard ratio [HR]: 0.34; 95% confidence interval [CI]: 0.17-0.68; P=0.002) and IPTW-weighted models (odds ratio [OR]: 0.38; 95% CI: 0.21-0.68; P=0.001). This protective effect was also observed for 28-day mortality (PS-adjusted HR: 0.38; 95% CI: 0.21-0.72; P=0.003). Clinical improvement by day +14 was higher in the CS-TCZ group with IPTW analysis only (OR: 2.26; 95% CI: 1.49-3.41; P<0.001). The occurrence of secondary infection was similar between both groups. Conclusions: The combination of corticosteroids and TCZ was associated with better outcomes among patients aged ≥65 years with severe COVID-19.
MeSH term(s)	Aged ; Aged, 80 and over ; Antibodies, Monoclonal, Humanized/administration & dosage ; COVID-19/drug therapy ; Drug Therapy, Combination ; Female ; Humans ; Male ; Methylprednisolone/administration & dosage ; Middle Aged ; Retrospective Studies ; SARS-CoV-2
Chemical Substances	Antibodies, Monoclonal, Humanized ; tocilizumab (I031V2H011) ; Methylprednisolone (X4W7ZR7023)
Language	English
Publishing date	2021-02-26
Publishing country	Canada
Document type	Journal Article
ZDB-ID	1331197-9
ISSN	1878-3511 ; 1201-9712
ISSN (online)	1878-3511
ISSN	1201-9712
DOI	10.1016/j.ijid.2021.02.099
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Zs.A 4516: Show issues

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Article ; Online: Transposase interaction with the β sliding clamp: effects on insertion sequence proliferation and transposition rate.

Díaz-Maldonado, Héctor / Gómez, Manuel J / Moreno-Paz, Mercedes / San Martín-Úriz, Patxi / Amils, Ricardo / Parro, Víctor / López de Saro, Francisco J

Scientific reports

2015 Volume 5, Page(s) 13329

Abstract: Insertion sequences (ISs) are ubiquitous and abundant mobile genetic elements in prokaryotic genomes. ISs often encode only one protein, the transposase, which catalyzes their transposition. Recent studies have shown that transposases of many different ... ...

Abstract	Insertion sequences (ISs) are ubiquitous and abundant mobile genetic elements in prokaryotic genomes. ISs often encode only one protein, the transposase, which catalyzes their transposition. Recent studies have shown that transposases of many different IS families interact with the β sliding clamp, a DNA replication factor of the host. However, it was unclear to what extent this interaction limits or favors the ability of ISs to colonize a chromosome from a phylogenetically-distant organism, or if the strength of this interaction affects the transposition rate. Here we describe the proliferation of a member of the IS1634 family in Acidiphilium over ~600 generations of cultured growth. We demonstrate that the purified transposase binds to the β sliding clamp of Acidiphilium, Leptospirillum and E. coli. Further, we also demonstrate that the Acidiphilium IS1634 transposase binds to the archaeal sliding clamp (PCNA) from Methanosarcina, and that the transposase encoded by Methanosarcina IS1634 binds to Acidiphilium β. Finally, we demonstrate that increasing the strength of the interaction between β and transposase results in a higher transposition rate in vivo. Our results suggest that the interaction could determine the potential of ISs to be mobilized in bacterial populations and also their ability to proliferate within chromosomes.
MeSH term(s)	Acidiphilium/genetics ; DNA Replication/genetics ; DNA Transposable Elements/genetics ; DNA, Bacterial/genetics ; Evolution, Molecular
Chemical Substances	DNA Transposable Elements ; DNA, Bacterial
Language	English
Publishing date	2015-08-26
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/srep13329
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Article: A peptide switch regulates DNA polymerase processivity.

López de Saro, Francisco J / Georgescu, Roxana E / O'Donnell, Mike

Proceedings of the National Academy of Sciences of the United States of America

2003 Volume 100, Issue 25, Page(s) 14689–14694

Abstract: Chromosomal DNA polymerases are tethered to DNA by a circular sliding clamp for high processivity. However, lagging strand synthesis requires the polymerase to rapidly dissociate on finishing each Okazaki fragment. The Escherichia coli replicase contains ...

Abstract	Chromosomal DNA polymerases are tethered to DNA by a circular sliding clamp for high processivity. However, lagging strand synthesis requires the polymerase to rapidly dissociate on finishing each Okazaki fragment. The Escherichia coli replicase contains a subunit (tau) that promotes separation of polymerase from its clamp on finishing DNA segments. This report reveals the mechanism of this process. We find that tau binds the C-terminal residues of the DNA polymerase. Surprisingly, this same C-terminal "tail" of the polymerase interacts with the beta clamp, and tau competes with beta for this sequence. Moreover, tau acts as a DNA sensor. On binding primed DNA, tau releases the polymerase tail, allowing polymerase to bind beta for processive synthesis. But on sensing the DNA is complete (duplex), tau sequesters the polymerase tail from beta, disengaging polymerase from DNA. Therefore, DNA sensing by tau switches the polymerase peptide tail on and off the clamp and coordinates the dynamic turnover of polymerase during lagging strand synthesis.
MeSH term(s)	Animals ; Cattle ; Chromatography, Gel ; Cysteine/chemistry ; DNA/chemistry ; DNA/metabolism ; DNA Polymerase III/chemistry ; DNA-Directed DNA Polymerase/chemistry ; DNA-Directed DNA Polymerase/metabolism ; Dose-Response Relationship, Drug ; Electrophoresis, Polyacrylamide Gel ; Escherichia coli/enzymology ; Escherichia coli/metabolism ; Kinetics ; Models, Biological ; Peptides/chemistry ; Protein Binding ; Protein Structure, Tertiary ; Recombinant Proteins/chemistry ; Spectrometry, Fluorescence ; Thymus Gland/metabolism ; Time Factors
Chemical Substances	Okazaki fragments ; Peptides ; Recombinant Proteins ; DNA (9007-49-2) ; DNA Polymerase III (EC 2.7.7.-) ; DNA replicase (EC 2.7.7.-) ; DNA-Directed DNA Polymerase (EC 2.7.7.7) ; Cysteine (K848JZ4886)
Language	English
Publishing date	2003-12-09
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, P.H.S.
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2435454100
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Zs.A 1148: Show issues

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Article: The beta sliding clamp binds to multiple sites within MutL and MutS.

López de Saro, Francisco J / Marinus, Martin G / Modrich, Paul / O'Donnell, Mike

The Journal of biological chemistry

2006 Volume 281, Issue 20, Page(s) 14340–14349

Abstract: The MutL and MutS proteins are the central components of the DNA repair machinery that corrects mismatches generated by DNA polymerases during synthesis. We find that MutL interacts directly with the beta sliding clamp, a ring-shaped dimeric protein that ...

Abstract	The MutL and MutS proteins are the central components of the DNA repair machinery that corrects mismatches generated by DNA polymerases during synthesis. We find that MutL interacts directly with the beta sliding clamp, a ring-shaped dimeric protein that confers processivity to DNA polymerases by tethering them to their substrates. Interestingly, the interaction of MutL with beta only occurs in the presence of single-stranded DNA. We find that the interaction occurs via a loop in MutL near the ATP-binding site. The binding site of MutL on beta locates to the hydrophobic pocket between domains two and three of the clamp. Site-specific replacement of two residues in MutL diminished interaction with beta without disrupting MutL function with helicase II. In vivo studies reveal that this mutant MutL is no longer functional in mismatch repair. In addition, the human MLH1 has a close match to the proliferating cell nuclear antigen clamp binding motif in the region that corresponds to the beta interaction site in Escherichia coli MutL, and a peptide corresponding to this site binds proliferating cell nuclear antigen. The current report also examines in detail the interaction of beta with MutS. We find that two distinct regions of MutS interact with beta. One is located near the C terminus and the other is close to the N terminus, within the mismatch binding domain. Complementation studies using genes encoding different MutS mutants reveal that the N-terminal beta interaction motif on MutS is essential for activity in vivo, but the C-terminal interaction site for beta is not. In light of these results, we propose roles for the beta clamp in orchestrating the sequence of events that lead to mismatch repair in the cell.
MeSH term(s)	Adaptor Proteins, Signal Transducing ; Adenosine Triphosphatases/chemistry ; Adenosine Triphosphatases/metabolism ; Amino Acid Sequence ; Carrier Proteins/chemistry ; DNA Repair ; DNA, Single-Stranded/chemistry ; Dose-Response Relationship, Drug ; Escherichia coli/metabolism ; Escherichia coli Proteins/chemistry ; Escherichia coli Proteins/metabolism ; Genetic Complementation Test ; Humans ; Models, Molecular ; Molecular Sequence Data ; MutL Protein Homolog 1 ; MutL Proteins ; MutS DNA Mismatch-Binding Protein/chemistry ; MutS DNA Mismatch-Binding Protein/metabolism ; Nuclear Proteins/chemistry ; Protein Binding ; Sequence Homology, Amino Acid
Chemical Substances	Adaptor Proteins, Signal Transducing ; Carrier Proteins ; DNA, Single-Stranded ; Escherichia coli Proteins ; MLH1 protein, human ; MutL protein, E coli ; Nuclear Proteins ; Adenosine Triphosphatases (EC 3.6.1.-) ; MutL Protein Homolog 1 (EC 3.6.1.3) ; MutL Proteins (EC 3.6.1.3) ; MutS DNA Mismatch-Binding Protein (EC 3.6.1.3) ; MutS protein, E coli (EC 3.6.1.3)
Language	English
Publishing date	2006-03-16
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1074/jbc.M601264200
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Article ; Online: Short-Peptide Supramolecular Hydrogels for In Situ Growth of Metal-Organic Framework-Peptide Biocomposites.

Illescas-Lopez, Sara / Martin-Romera, Javier D / Mañas-Torres, Mari C / Lopez-Lopez, Modesto T / Cuerva, Juan M / Gavira, José A / Carmona, Francisco J / Álvarez de Cienfuegos, Luis

ACS applied materials & interfaces

2023 Volume 15, Issue 27, Page(s) 32597–32609

Abstract: The development of bio-MOFs or MOF biocomposites through the combination of MOFs with biopolymers offers the possibility of expanding the potential applications of MOFs, making use of more environmentally benign processes and reagents and giving rise to ... ...

Abstract	The development of bio-MOFs or MOF biocomposites through the combination of MOFs with biopolymers offers the possibility of expanding the potential applications of MOFs, making use of more environmentally benign processes and reagents and giving rise to a new generation of greener and more bio-oriented composite materials. Now, with the increasing use of MOFs for biotechnological applications, the development of new protocols and materials to obtain novel bio-MOFs compatible with biomedical or biotechnological uses is needed. Herein, and as a proof of concept, we have explored the possibility of using short-peptide supramolecular hydrogels as media to promote the growth of MOF particles, giving rise to a new family of bio-MOFs. Short-peptide supramolecular hydrogels are very versatile materials that have shown excellent in vitro and in vivo biomedical applications such as tissue engineering and drug delivery vehicles, among others. These peptides self-assemble by noncovalent interactions, and, as such, these hydrogels are easily reversible, being more biocompatible and biodegradable. These peptides can self-assemble by a multitude of stimuli, such as changes in pH, temperature, solvent, adding salts, enzymatic activity, and so forth. In this work, we have taken advantage of this ability to promote peptide self-assembly with some of the components required to form MOF particles, giving rise to more homogeneous and well-integrated composite materials. Hydrogel formation has been triggered using Zn
MeSH term(s)	Metal-Organic Frameworks/chemistry ; Hydrogels/chemistry ; Salts ; Peptides ; Drug Delivery Systems
Chemical Substances	Metal-Organic Frameworks ; Hydrogels ; Salts ; Peptides
Language	English
Publishing date	2023-06-30
Publishing country	United States
Document type	Journal Article
ISSN	1944-8252
ISSN (online)	1944-8252
DOI	10.1021/acsami.3c06943
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