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  1. Article ; Online: Editorial overview: Carbohydrates - structural glycobiology catches the wave of rapid progress.

    Malhotra, Sony / Ramsland, Paul A

    Current opinion in structural biology

    2020  Volume 62, Page(s) iii–v

    MeSH term(s) Carbohydrates/chemistry ; Glycomics/trends ; Humans ; Molecular Structure
    Chemical Substances Carbohydrates
    Language English
    Publishing date 2020-05-13
    Publishing country England
    Document type Editorial
    ZDB-ID 1068353-7
    ISSN 1879-033X ; 0959-440X
    ISSN (online) 1879-033X
    ISSN 0959-440X
    DOI 10.1016/j.sbi.2020.04.004
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  2. Article ; Online: The current structural glycome landscape and emerging technologies.

    Copoiu, Liviu / Malhotra, Sony

    Current opinion in structural biology

    2020  Volume 62, Page(s) 132–139

    Abstract: Carbohydrates represent one of the building blocks of life, along with nucleic acids, proteins and lipids. Although glycans are involved in a wide range of processes from embryogenesis to protein trafficking and pathogen infection, we are still a long ... ...

    Abstract Carbohydrates represent one of the building blocks of life, along with nucleic acids, proteins and lipids. Although glycans are involved in a wide range of processes from embryogenesis to protein trafficking and pathogen infection, we are still a long way from deciphering the glycocode. In this review, we aim to present a few of the challenges that researchers working in the area of glycobiology can encounter and what strategies can be utilised to overcome them. Our goal is to paint a comprehensive picture of the current saccharide landscape available in the Protein Data Bank (PDB). We also review recently updated repositories relevant to the topic proposed, the impact of software development on strategies to structurally solve carbohydrate moieties, and state-of-the-art molecular and cellular biology methods that can shed some light on the function and structure of glycans.
    MeSH term(s) Animals ; Databases, Protein ; Glycomics ; Humans ; Polysaccharides/chemistry ; Protein Binding ; Proteins/metabolism ; Software
    Chemical Substances Polysaccharides ; Proteins
    Language English
    Publishing date 2020-01-30
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 1068353-7
    ISSN 1879-033X ; 0959-440X
    ISSN (online) 1879-033X
    ISSN 0959-440X
    DOI 10.1016/j.sbi.2019.12.020
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Overview and applications of map and model validation tools in the CCP-EM software suite.

    Joseph, Agnel Praveen / Malhotra, Sony / Burnley, Tom / Winn, Martyn D

    Faraday discussions

    2022  Volume 240, Page(s) 196–209

    Abstract: Cryogenic electron microscopy (cryo-EM) has recently been established as a powerful technique for solving macromolecular structures. Although the best resolutions achievable are improving, a significant majority of data are still resolved at resolutions ... ...

    Abstract Cryogenic electron microscopy (cryo-EM) has recently been established as a powerful technique for solving macromolecular structures. Although the best resolutions achievable are improving, a significant majority of data are still resolved at resolutions worse than 3 Å, where it is non-trivial to build or fit atomic models. The map reconstructions and atomic models derived from the maps are also prone to errors accumulated through the different stages of data processing. Here, we highlight the need to evaluate both model geometry and fit to data at different resolutions. Assessment of cryo-EM structures from SARS-CoV-2 highlights a bias towards optimising the model geometry to agree with the most common conformations, compared to the agreement with data. We present the CoVal web service which provides multiple validation metrics to reflect the quality of atomic models derived from cryo-EM data of structures from SARS-CoV-2. We demonstrate that further refinement can lead to improvement of the agreement with data without the loss of geometric quality. We also discuss the recent CCP-EM developments aimed at addressing some of the current shortcomings.
    MeSH term(s) Humans ; COVID-19 ; Cryoelectron Microscopy/methods ; Models, Molecular ; Protein Conformation ; SARS-CoV-2 ; Software
    Language English
    Publishing date 2022-11-08
    Publishing country England
    Document type Journal Article ; Review
    ISSN 1364-5498
    ISSN (online) 1364-5498
    DOI 10.1039/d2fd00103a
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  4. Article ; Online: Assessment of protein–protein interfaces in cryo-EM derived assemblies

    Sony Malhotra / Agnel Praveen Joseph / Jeyan Thiyagalingam / Maya Topf

    Nature Communications, Vol 12, Iss 1, Pp 1-

    2021  Volume 12

    Abstract: Here, the authors present Protein Interface-score (PI-score), a machine learning-based metric that has been trained on protein–protein interfaces’ features from high-resolution crystal structures. They use the PI-score to evaluate the protein–protein ... ...

    Abstract Here, the authors present Protein Interface-score (PI-score), a machine learning-based metric that has been trained on protein–protein interfaces’ features from high-resolution crystal structures. They use the PI-score to evaluate the protein–protein interfaces in more than 1000 PDB-deposited cryo-EM structures and show that it can be used as a complementary assessment tool for cryo-EM model validation.
    Keywords Science ; Q
    Language English
    Publishing date 2021-06-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Assessment of protein-protein interfaces in cryo-EM derived assemblies.

    Malhotra, Sony / Joseph, Agnel Praveen / Thiyagalingam, Jeyan / Topf, Maya

    Nature communications

    2021  Volume 12, Issue 1, Page(s) 3399

    Abstract: Structures of macromolecular assemblies derived from cryo-EM maps often contain errors that become more abundant with decreasing resolution. Despite efforts in the cryo-EM community to develop metrics for map and atomistic model validation, thus far, no ... ...

    Abstract Structures of macromolecular assemblies derived from cryo-EM maps often contain errors that become more abundant with decreasing resolution. Despite efforts in the cryo-EM community to develop metrics for map and atomistic model validation, thus far, no specific scoring metrics have been applied systematically to assess the interface between the assembly subunits. Here, we comprehensively assessed protein-protein interfaces in macromolecular assemblies derived by cryo-EM. To this end, we developed Protein Interface-score (PI-score), a density-independent machine learning-based metric, trained using the features of protein-protein interfaces in crystal structures. We evaluated 5873 interfaces in 1053 PDB-deposited cryo-EM models (including SARS-CoV-2 complexes), as well as the models submitted to CASP13 cryo-EM targets and the EM model challenge. We further inspected the interfaces associated with low-scores and found that some of those, especially in intermediate-to-low resolution (worse than 4 Å) structures, were not captured by density-based assessment scores. A combined score incorporating PI-score and fit-to-density score showed discriminatory power, allowing our method to provide a powerful complementary assessment tool for the ever-increasing number of complexes solved by cryo-EM.
    MeSH term(s) Cryoelectron Microscopy/methods ; Humans ; Machine Learning ; Macromolecular Substances/chemistry ; Macromolecular Substances/metabolism ; Macromolecular Substances/ultrastructure ; Models, Molecular ; Neural Networks, Computer ; Protein Conformation ; Protein Interaction Domains and Motifs ; Protein Interaction Mapping/methods ; Protein Interaction Maps ; Protein Multimerization ; Proteins/chemistry ; Proteins/metabolism ; Proteins/ultrastructure ; Support Vector Machine ; Viral Nonstructural Proteins/chemistry ; Viral Nonstructural Proteins/metabolism ; Viral Nonstructural Proteins/ultrastructure
    Chemical Substances Macromolecular Substances ; NSP1 protein, SARS-CoV-2 ; Proteins ; Viral Nonstructural Proteins
    Language English
    Publishing date 2021-06-07
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-021-23692-x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: RIBFIND2: Identifying rigid bodies in protein and nucleic acid structures.

    Malhotra, Sony / Mulvaney, Thomas / Cragnolini, Tristan / Sidhu, Haneesh / Joseph, Agnel P / Beton, Joseph G / Topf, Maya

    Nucleic acids research

    2023  Volume 51, Issue 18, Page(s) 9567–9575

    Abstract: Molecular structures are often fitted into cryo-EM maps by flexible fitting. When this requires large conformational changes, identifying rigid bodies can help optimize the model-map fit. Tools for identifying rigid bodies in protein structures exist, ... ...

    Abstract Molecular structures are often fitted into cryo-EM maps by flexible fitting. When this requires large conformational changes, identifying rigid bodies can help optimize the model-map fit. Tools for identifying rigid bodies in protein structures exist, however an equivalent for nucleic acid structures is lacking. With the increase in cryo-EM maps containing RNA and progress in RNA structure prediction, there is a need for such tools. We previously developed RIBFIND, a program for clustering protein secondary structures into rigid bodies. In RIBFIND2, this approach is extended to nucleic acid structures. RIBFIND2 can identify biologically relevant rigid bodies in important groups of complex RNA structures, capturing a wide range of dynamics, including large rigid-body movements. The usefulness of RIBFIND2-assigned rigid bodies in cryo-EM model refinement was demonstrated on three examples, with two conformations each: Group II Intron complexed IEP, Internal Ribosome Entry Site and the Processome, using cryo-EM maps at 2.7-5 Å resolution. A hierarchical refinement approach, performed on progressively smaller sets of RIBFIND2 rigid bodies, was clearly shown to have an advantage over classical all-atom refinement. RIBFIND2 is available via a web server with structure visualization and as a standalone tool.
    MeSH term(s) Models, Molecular ; Protein Conformation ; Proteins/chemistry ; RNA/chemistry ; Software ; Nucleic Acid Conformation
    Chemical Substances Proteins ; RNA (63231-63-0)
    Language English
    Publishing date 2023-09-05
    Publishing country England
    Document type Journal Article
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkad721
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    Zs.A 1067: Show issues Location:
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  7. Article: Structure-Guided Computational Approaches to Unravel Druggable Proteomic Landscape of

    Vedithi, Sundeep Chaitanya / Malhotra, Sony / Acebrón-García-de-Eulate, Marta / Matusevicius, Modestas / Torres, Pedro Henrique Monteiro / Blundell, Tom L

    Frontiers in molecular biosciences

    2021  Volume 8, Page(s) 663301

    Abstract: Leprosy, caused ... ...

    Abstract Leprosy, caused by
    Language English
    Publishing date 2021-05-07
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2814330-9
    ISSN 2296-889X
    ISSN 2296-889X
    DOI 10.3389/fmolb.2021.663301
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  8. Article ; Online: The pore conformation of lymphocyte perforin.

    Ivanova, Marina E / Lukoyanova, Natalya / Malhotra, Sony / Topf, Maya / Trapani, Joseph A / Voskoboinik, Ilia / Saibil, Helen R

    Science advances

    2022  Volume 8, Issue 6, Page(s) eabk3147

    Abstract: Perforin is a pore-forming protein that facilitates rapid killing of pathogen-infected or cancerous cells by the immune system. Perforin is released from cytotoxic lymphocytes, together with proapoptotic granzymes, to bind to a target cell membrane where ...

    Abstract Perforin is a pore-forming protein that facilitates rapid killing of pathogen-infected or cancerous cells by the immune system. Perforin is released from cytotoxic lymphocytes, together with proapoptotic granzymes, to bind to a target cell membrane where it oligomerizes and forms pores. The pores allow granzyme entry, which rapidly triggers the apoptotic death of the target cell. Here, we present a 4-Å resolution cryo-electron microscopy structure of the perforin pore, revealing previously unidentified inter- and intramolecular interactions stabilizing the assembly. During pore formation, the helix-turn-helix motif moves away from the bend in the central β sheet to form an intermolecular contact. Cryo-electron tomography shows that prepores form on the membrane surface with minimal conformational changes. Our findings suggest the sequence of conformational changes underlying oligomerization and membrane insertion, and explain how several pathogenic mutations affect function.
    Language English
    Publishing date 2022-02-11
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2810933-8
    ISSN 2375-2548 ; 2375-2548
    ISSN (online) 2375-2548
    ISSN 2375-2548
    DOI 10.1126/sciadv.abk3147
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  9. Article ; Online: Atomic model validation using the CCP-EM software suite.

    Joseph, Agnel Praveen / Olek, Mateusz / Malhotra, Sony / Zhang, Peijun / Cowtan, Kevin / Burnley, Tom / Winn, Martyn D

    Acta crystallographica. Section D, Structural biology

    2022  Volume 78, Issue Pt 2, Page(s) 152–161

    Abstract: Recently, there has been a dramatic improvement in the quality and quantity of data derived using cryogenic electron microscopy (cryo-EM). This is also associated with a large increase in the number of atomic models built. Although the best resolutions ... ...

    Abstract Recently, there has been a dramatic improvement in the quality and quantity of data derived using cryogenic electron microscopy (cryo-EM). This is also associated with a large increase in the number of atomic models built. Although the best resolutions that are achievable are improving, often the local resolution is variable, and a significant majority of data are still resolved at resolutions worse than 3 Å. Model building and refinement is often challenging at these resolutions, and hence atomic model validation becomes even more crucial to identify less reliable regions of the model. Here, a graphical user interface for atomic model validation, implemented in the CCP-EM software suite, is presented. It is aimed to develop this into a platform where users can access multiple complementary validation metrics that work across a range of resolutions and obtain a summary of evaluations. Based on the validation estimates from atomic models associated with cryo-EM structures from SARS-CoV-2, it was observed that models typically favor adopting the most common conformations over fitting the observations when compared with the model agreement with data. At low resolutions, the stereochemical quality may be favored over data fit, but care should be taken to ensure that the model agrees with the data in terms of resolvable features. It is demonstrated that further re-refinement can lead to improvement of the agreement with data without the loss of geometric quality. This also highlights the need for improved resolution-dependent weight optimization in model refinement and an effective test for overfitting that would help to guide the refinement process.
    MeSH term(s) COVID-19 ; Cryoelectron Microscopy/methods ; Image Processing, Computer-Assisted ; Models, Molecular ; Reproducibility of Results ; Software ; Software Validation ; User-Computer Interface
    Language English
    Publishing date 2022-01-24
    Publishing country United States
    Document type Journal Article ; Validation Study
    ZDB-ID 2968623-4
    ISSN 2059-7983 ; 0907-4449
    ISSN (online) 2059-7983
    ISSN 0907-4449
    DOI 10.1107/S205979832101278X
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Modelling structures in cryo-EM maps.

    Malhotra, Sony / Träger, Sylvain / Dal Peraro, Matteo / Topf, Maya

    Current opinion in structural biology

    2019  Volume 58, Page(s) 105–114

    Abstract: Recent advances in structure determination of sub-cellular structures using cryo-electron microscopy and tomography have enabled us to understand their architecture in a more detailed manner and gain insight into their function. The choice of approach to ...

    Abstract Recent advances in structure determination of sub-cellular structures using cryo-electron microscopy and tomography have enabled us to understand their architecture in a more detailed manner and gain insight into their function. The choice of approach to use for atomic model building, fitting, refinement and validation in the 3D map resulting from these experiments depends primarily on the resolution of the map and the prior information on the corresponding model. Here, we survey some of such methods and approaches and highlight their uses in specific recent examples.
    MeSH term(s) Cryoelectron Microscopy/methods ; Models, Molecular ; Proteins/chemistry
    Chemical Substances Proteins
    Language English
    Publishing date 2019-08-05
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 1068353-7
    ISSN 1879-033X ; 0959-440X
    ISSN (online) 1879-033X
    ISSN 0959-440X
    DOI 10.1016/j.sbi.2019.05.024
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