LIVIVO - The Search Portal for Life Sciences

zur deutschen Oberfläche wechseln
Advanced search

Search results

Result 1 - 10 of total 106

Search options

  1. Article ; Online: Publisher Correction: Loop dynamics and the evolution of enzyme activity.

    Corbella, Marina / Pinto, Gaspar P / Kamerlin, Shina C L

    Nature reviews. Chemistry

    2023  Volume 7, Issue 8, Page(s) 591

    Language English
    Publishing date 2023-06-20
    Publishing country England
    Document type Published Erratum
    ISSN 2397-3358
    ISSN (online) 2397-3358
    DOI 10.1038/s41570-023-00515-9
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    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.

    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.

  2. Article ; Online: Correction to "Micelle Maker: An Online Tool for Generating Equilibrated Micelles as Direct Input for Molecular Dynamics Simulations".

    Krüger, Dennis M / Kamerlin, Shina C L

    ACS omega

    2023  Volume 8, Issue 49, Page(s) 47316

    Abstract: This corrects the article DOI: 10.1021/acsomega.7b00820.]. ...

    Abstract [This corrects the article DOI: 10.1021/acsomega.7b00820.].
    Language English
    Publishing date 2023-11-28
    Publishing country United States
    Document type Published Erratum
    ISSN 2470-1343
    ISSN (online) 2470-1343
    DOI 10.1021/acsomega.3c08868
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    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.

    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.

  3. Article ; Online: Key interaction networks: Identifying evolutionarily conserved non-covalent interaction networks across protein families.

    Yehorova, Dariia / Crean, Rory M / Kasson, Peter M / Kamerlin, Shina C L

    Protein science : a publication of the Protein Society

    2024  Volume 33, Issue 3, Page(s) e4911

    Abstract: Protein structure (and thus function) is dictated by non-covalent interaction networks. These can be highly evolutionarily conserved across protein families, the members of which can diverge in sequence and evolutionary history. Here we present KIN, a ... ...

    Abstract Protein structure (and thus function) is dictated by non-covalent interaction networks. These can be highly evolutionarily conserved across protein families, the members of which can diverge in sequence and evolutionary history. Here we present KIN, a tool to identify and analyze conserved non-covalent interaction networks across evolutionarily related groups of proteins. KIN is available for download under a GNU General Public License, version 2, from https://www.github.com/kamerlinlab/KIN. KIN can operate on experimentally determined structures, predicted structures, or molecular dynamics trajectories, providing insight into both conserved and missing interactions across evolutionarily related proteins. This provides useful insight both into protein evolution, as well as a tool that can be exploited for protein engineering efforts. As a showcase system, we demonstrate applications of this tool to understanding the evolutionary-relevant conserved interaction networks across the class A β-lactamases.
    MeSH term(s) Algorithms ; Proteins/chemistry
    Chemical Substances Proteins
    Language English
    Publishing date 2024-02-12
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1106283-6
    ISSN 1469-896X ; 0961-8368
    ISSN (online) 1469-896X
    ISSN 0961-8368
    DOI 10.1002/pro.4911
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 3407: 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)
    Zs.MO 1: Show issues

    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.

  4. Article ; Online: Correction to “Micelle Maker

    Dennis M. Krüger / Shina C. L. Kamerlin

    ACS Omega, Vol 8, Iss 49, Pp 47316-

    An Online Tool for Generating Equilibrated Micelles as Direct Input for Molecular Dynamics Simulations”

    2023  Volume 47316

    Keywords Chemistry ; QD1-999
    Language English
    Publishing date 2023-11-01T00:00:00Z
    Publisher American Chemical Society
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

    More links

    Kategorien

    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.

  5. Article ; Online: Loop dynamics and the evolution of enzyme activity.

    Corbella, Marina / Pinto, Gaspar P / Kamerlin, Shina C L

    Nature reviews. Chemistry

    2023  Volume 7, Issue 8, Page(s) 536–547

    Abstract: In the early 2000s, Tawfik presented his 'New View' on enzyme evolution, highlighting the role of conformational plasticity in expanding the functional diversity of limited repertoires of sequences. This view is gaining increasing traction with ... ...

    Abstract In the early 2000s, Tawfik presented his 'New View' on enzyme evolution, highlighting the role of conformational plasticity in expanding the functional diversity of limited repertoires of sequences. This view is gaining increasing traction with increasing evidence of the importance of conformational dynamics in both natural and laboratory evolution of enzymes. The past years have seen several elegant examples of harnessing conformational (particularly loop) dynamics to successfully manipulate protein function. This Review revisits flexible loops as critical participants in regulating enzyme activity. We showcase several systems of particular interest: triosephosphate isomerase barrel proteins, protein tyrosine phosphatases and β-lactamases, while briefly discussing other systems in which loop dynamics are important for selectivity and turnover. We then discuss the implications for engineering, presenting examples of successful loop manipulation in either improving catalytic efficiency, or changing selectivity completely. Overall, it is becoming clearer that mimicking nature by manipulating the conformational dynamics of key protein loops is a powerful method of tailoring enzyme activity, without needing to target active-site residues.
    MeSH term(s) Humans ; Triose-Phosphate Isomerase/genetics ; Catalysis
    Chemical Substances Triose-Phosphate Isomerase (EC 5.3.1.1)
    Language English
    Publishing date 2023-05-24
    Publishing country England
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ISSN 2397-3358
    ISSN (online) 2397-3358
    DOI 10.1038/s41570-023-00495-w
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    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.

    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.

  6. Article ; Online: Sequence - dynamics - function relationships in protein tyrosine phosphatases.

    Crean, Rory M / Corbella, Marina / Calixto, Ana R / Hengge, Alvan C / Kamerlin, Shina C L

    QRB discovery

    2024  Volume 5, Page(s) e4

    Abstract: Protein tyrosine phosphatases (PTPs) are crucial regulators of cellular signaling. Their activity is regulated by the motion of a conserved loop, the WPD-loop, from a catalytically inactive open to a catalytically active closed conformation. WPD-loop ... ...

    Abstract Protein tyrosine phosphatases (PTPs) are crucial regulators of cellular signaling. Their activity is regulated by the motion of a conserved loop, the WPD-loop, from a catalytically inactive open to a catalytically active closed conformation. WPD-loop motion optimally positions a catalytically critical residue into the active site, and is directly linked to the turnover number of these enzymes. Crystal structures of chimeric PTPs constructed by grafting parts of the WPD-loop sequence of PTP1B onto the scaffold of YopH showed WPD-loops in a wide-open conformation never previously observed in either parent enzyme. This wide-open conformation has, however, been observed upon binding of small molecule inhibitors to other PTPs, suggesting the potential of targeting it for drug discovery efforts. Here, we have performed simulations of both enzymes and show that there are negligible energetic differences in the chemical step of catalysis, but significant differences in the dynamical properties of the WPD-loop. Detailed interaction network analysis provides insight into the molecular basis for this population shift to a wide-open conformation. Taken together, our study provides insight into the links between loop dynamics and chemistry in these YopH variants specifically, and how WPD-loop dynamic can be engineered through modification of the internal protein interaction network.
    Language English
    Publishing date 2024-01-24
    Publishing country England
    Document type Journal Article
    ISSN 2633-2892
    ISSN (online) 2633-2892
    DOI 10.1017/qrd.2024.3
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    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.

    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.

  7. Article ; Online: Conformational Selection of a Tryptophan Side Chain Drives the Generalized Increase in Activity of PET Hydrolases through a Ser/Ile Double Mutation.

    Crnjar, Alessandro / Griñen, Aransa / Kamerlin, Shina C L / Ramírez-Sarmiento, César A

    ACS organic & inorganic Au

    2023  Volume 3, Issue 2, Page(s) 109–119

    Abstract: Poly(ethylene terephthalate) (PET) is the most common polyester plastic in the packaging industry and a major source of environmental pollution due to its single use. Several enzymes, termed PET hydrolases, have been found to hydrolyze this polymer at ... ...

    Abstract Poly(ethylene terephthalate) (PET) is the most common polyester plastic in the packaging industry and a major source of environmental pollution due to its single use. Several enzymes, termed PET hydrolases, have been found to hydrolyze this polymer at different temperatures, with the enzyme from
    Language English
    Publishing date 2023-01-09
    Publishing country United States
    Document type Journal Article
    ISSN 2694-247X
    ISSN (online) 2694-247X
    DOI 10.1021/acsorginorgau.2c00054
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    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.

    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.

  8. Article ; Online: Harnessing Conformational Plasticity to Generate Designer Enzymes.

    Crean, Rory M / Gardner, Jasmine M / Kamerlin, Shina C L

    Journal of the American Chemical Society

    2020  Volume 142, Issue 26, Page(s) 11324–11342

    Abstract: Recent years have witnessed an explosion of interest in understanding the role of conformational dynamics both in the evolution of new enzymatic activities from existing enzymes and in facilitating the emergence of enzymatic ... ...

    Abstract Recent years have witnessed an explosion of interest in understanding the role of conformational dynamics both in the evolution of new enzymatic activities from existing enzymes and in facilitating the emergence of enzymatic activity
    MeSH term(s) Biocatalysis ; Enzymes/chemistry ; Enzymes/metabolism ; Humans ; Molecular Dynamics Simulation ; Protein Conformation ; Protein Engineering
    Chemical Substances Enzymes
    Language English
    Publishing date 2020-06-17
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 3155-0
    ISSN 1520-5126 ; 0002-7863
    ISSN (online) 1520-5126
    ISSN 0002-7863
    DOI 10.1021/jacs.0c04924
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Bonn / Germany

    Z 4' 55/32: Show issues
    Z 7.3: Show issues

    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.

    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.

  9. Article ; Online: Correction to "Loop Dynamics and Enzyme Catalysis in Protein Tyrosine Phosphatases".

    Crean, Rory M / Biler, Michal / Corbella, Marina / Calixto, Ana R / van der Kamp, Marc W / Hengge, Alvan C / Kamerlin, Shina C L

    Journal of the American Chemical Society

    2022  Volume 144, Issue 22, Page(s) 10091–10093

    Language English
    Publishing date 2022-05-24
    Publishing country United States
    Document type Published Erratum
    ZDB-ID 3155-0
    ISSN 1520-5126 ; 0002-7863
    ISSN (online) 1520-5126
    ISSN 0002-7863
    DOI 10.1021/jacs.2c04624
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Bonn / Germany

    Z 4' 55/32: Show issues
    Z 7.3: Show issues

    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.

    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.

  10. Article ; Online: Managing Coronavirus Disease 2019 Spread With Voluntary Public Health Measures: Sweden as a Case Study for Pandemic Control.

    Kamerlin, Shina C L / Kasson, Peter M

    Clinical infectious diseases : an official publication of the Infectious Diseases Society of America

    2020  Volume 71, Issue 12, Page(s) 3174–3181

    Abstract: Background: The coronavirus disease 19 (COVID-19) pandemic has spread globally, causing extensive illness and mortality. In advance of effective antiviral therapies, countries have applied different public health strategies to control spread and manage ... ...

    Abstract Background: The coronavirus disease 19 (COVID-19) pandemic has spread globally, causing extensive illness and mortality. In advance of effective antiviral therapies, countries have applied different public health strategies to control spread and manage healthcare need. Sweden has taken a unique approach of not implementing strict closures, instead urging personal responsibility. We analyze the results of this and other potential strategies for pandemic control in Sweden.
    Methods: We implemented individual-based modeling of COVID-19 spread in Sweden using population, employment, and household data. Epidemiological parameters for COVID-19 were validated on a limited date range; where substantial uncertainties remained, multiple parameters were tested. The effects of different public health strategies were tested over a 160-day period, analyzed for their effects on intensive care unit (ICU) demand and death rate, and compared with Swedish data for April 2020.
    Results: Swedish mortality rates are intermediate between rates for European countries that quickly imposed stringent public health controls and those for countries that acted later. Models most closely reproducing reported mortality data suggest that large portions of the population voluntarily self-isolate. Swedish ICU use rates remained lower than predicted, but a large fraction of deaths occurred in non-ICU patients. This suggests that patient prognosis was considered in ICU admission, reducing healthcare load at a cost of decreased survival in patients not admitted.
    Conclusions: The Swedish COVID-19 strategy has thus far yielded a striking result: mild mandates overlaid with voluntary measures can achieve results highly similar to late-onset stringent mandates. However, this policy causes more healthcare demand and more deaths than early stringent control and depends on continued public will.
    MeSH term(s) Adult ; Aged ; COVID-19 ; Europe ; Humans ; Pandemics ; Public Health ; SARS-CoV-2 ; Sweden ; Young Adult
    Keywords covid19
    Language English
    Publishing date 2020-06-30
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1099781-7
    ISSN 1537-6591 ; 1058-4838
    ISSN (online) 1537-6591
    ISSN 1058-4838
    DOI 10.1093/cid/ciaa864
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 1505: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)
    Zs.MO 480: Show issues

    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.

To top