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Article
Chemistry, Physical
Gilberto Valdes-Garcia et al.
Summary: Biomolecular condensation, particularly liquid-liquid phase separation, is a significant physical process in various biological functions. A new computationally efficient and physically realistic model, COCOMO, is introduced to investigate the driving forces of biomolecular condensation based on molecular composition. The model effectively combines polymer behavior and phase separation propensity and demonstrates good agreement with experimental data. COCOMO enables simulation of biomolecular condensation at spatial and temporal scales using moderate computational resources.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Biochemistry & Molecular Biology
Damiano Piovesan et al.
Summary: The MobiDB database is a knowledge base of intrinsically disordered proteins, which collects annotations and predictions to provide new knowledge about the functional significance of disordered regions. The latest release of MobiDB focuses on improving user experience and database content, integrating AlphaFoldDB predictions and implementing the homology transfer pipeline.
NUCLEIC ACIDS RESEARCH
(2023)
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Chemistry, Medicinal
Eric Fagerberg et al.
Summary: Coarse-graining is commonly used to reduce computational cost in simulations, but it is known to have lower transferability and accuracy for systems beyond its parametrization scope. In this study, we compared the performance of a bead-necklace model and a modified Martini 2 model, both coarse-grained models, using a set of intrinsically disordered proteins with different degrees of coarse-graining. The results showed that the naive expectation of the least coarse-grained model performing the best was not true, indicating that a more advanced model is not necessarily better in model choice.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Biochemistry & Molecular Biology
Alessio Del Conte et al.
Summary: Intrinsic disorder (ID) in proteins is a well-established phenomenon in structural biology, but measuring its behavior on a large scale is challenging. To address this issue, CAID benchmarks ID predictors and creates a web server, the CAID Prediction Portal, which executes all CAID methods on user-defined sequences. The server generates standardized output, facilitates comparison between methods, and provides a valuable resource for researchers studying ID in proteins.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Giacomo Janson et al.
Summary: Computational methods for studying protein structural dynamics are costly. The authors propose a machine learning approach to efficiently generate protein conformational ensembles and validate the method using intrinsically disordered peptides. Dynamics and conformational sampling are crucial for understanding the relationship between protein structure and biological function.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
D. Sala et al.
Summary: Many proteins switch among different structures to exert their function, and understanding these conformational ensembles is crucial for unraveling key mechanistic aspects of protein function. Experimental determination of these structures is limited by cost, time, and technical challenges, but the machine-learning technology AlphaFold has shown promising accuracy in predicting the three-dimensional structure of monomeric proteins. However, AlphaFold typically represents a single conformational state with minimal structural heterogeneity, leading to the development of pipelines to expand the diversity or bias the prediction towards desired conformational states. In this study, we analyze the functionality, limitations, and future directions of these pipelines.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2023)
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Biochemistry & Molecular Biology
Javier González-Delgado et al.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
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Biochemistry & Molecular Biology
Alessio Del Conte et al.
Summary: Protein intrinsic disorder is a complex and challenging phenomenon for prediction methods due to its diverse nature and context-dependent transitions. The CAID2 challenge evaluated different prediction methods using benchmarks and the annotation provided by the DisProt database. The challenge demonstrated the need for versatile and efficient prediction software, and highlighted the varying performance of different methods.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2023)
Article
Biochemistry & Molecular Biology
Sergio Gomes Ramalli et al.
Summary: The Protein Circular Dichroism Data Bank (PCDDB) is a valuable resource for the scientific community, providing access to validated protein circular dichroism (CD) spectra and associated data. It includes primary and final spectral data, as well as sample and validation information. The PCDDB has recently expanded its metadata content and structural breadth, and it complements data from other databases. It has been used for the development of new analytical methodologies and for studying protein structures and functions.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Mihaly Varadi et al.
Summary: AlphaFold DB is an openly accessible database with high-accuracy protein-structure predictions, powered by DeepMind's AlphaFold v2.0. It provides programmatic access to a vast number of predicted structures and is expanding to cover more sequences.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Noemi del Toro et al.
Summary: IntAct is a curated database of molecular interactions derived from scientific literature, containing over one million binary interactions curated by twelve global partners. The IMEx curation policy emphasizes fine-grained data and curation model to capture essential experimental details for interpretation of the molecular interaction data. Recently, IntAct has introduced a completely redeveloped website to present data in a more user-friendly and detailed way.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Mihaly Varadi et al.
Summary: PDBe-KB is an open collaboration platform that aims to integrate functional and biophysical annotations from world-leading specialist data resources, serving the Protein Data Bank. By developing standardized data exchange formats and integrating functional annotations from partner resources, PDBe-KB aims to place macromolecular structure data in a biological context and provide valuable biological insights.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Andras Hatos et al.
Summary: Fuzzy interactions are specific and variable contacts between proteins and other biomolecules formed in accordance with the cellular context. Recent studies have shown their regulatory role in biomolecular condensates. The FuzDB v4.0 database compiles experimentally identified examples of fuzzy interactions and provides insights into complex cellular interaction behaviors.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Chemistry, Physical
F. Emil Thomasen et al.
Summary: Coarse-grained molecular dynamics simulations are useful for determining conformational ensembles of proteins. However, the currently used coarse-grained forcefield underestimates the sizes of intrinsically disordered proteins (IDPs) and multidomain proteins. Increasing the strength of protein-water interactions can improve this underestimation.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Biology
Diego del Alamo et al.
Summary: This article presents an approach to drive AlphaFold2 to sample multiple conformations of membrane proteins and demonstrates that this approach can generate accurate models. The results suggest the need for the next generation of deep learning algorithms to be designed to predict ensembles of biophysically relevant states.
Article
Chemistry, Multidisciplinary
Irina Ritsch et al.
Summary: The interaction between hnRNP A1 and specific RNA induces liquid-droplet formation, which depends on RNA concentration and sequence. Additionally, point mutations in RNA affect local protein dynamics.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Physical
Joao M. C. Teixeira et al.
Summary: The study presents IDPConformerGenerator, a software platform for generating ensembles of disordered protein states. It uses sequence constraints to build diverse conformations, offering insights into the structural characteristics and biological functions of intrinsically disordered proteins.
JOURNAL OF PHYSICAL CHEMISTRY A
(2022)
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Biochemistry & Molecular Biology
Damiano Piovesan et al.
Summary: AlphaFoldDB offers a fresh perspective on IDR prediction and demonstrates the plasticity of the disorder to structure continuum.
Article
Biochemistry & Molecular Biology
Juan Jose Galano-Frutos et al.
Summary: Molten globule (MG) is a compact, non-native conformation of proteins that plays important roles in protein folding and misfolding. This article presents an atomistic model of MG formed by the apoflavodoxin from the human pathogen Helicobacter pylori, and successfully explains its characteristic spectral and thermodynamic features.
Article
Multidisciplinary Sciences
Jiaqi Zhu et al.
Summary: This study elucidates the atomically detailed binding mechanisms of small molecule drugs to the intrinsically disordered region of the androgen receptor, providing insights for developing more potent inhibitors and strategies for disordered protein drug design.
NATURE COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Richard A. Stein et al.
Summary: This study presents a general approach to drive Alphafold2 to model alternate protein conformations through manipulation of the multiple sequence alignment. The applicability of this approach is demonstrated through the investigation of membrane proteins, expanding the potential uses of Alphafold2.
PLOS COMPUTATIONAL BIOLOGY
(2022)
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Biochemistry & Molecular Biology
Damiano Piovesan et al.
Summary: AlphaFoldDB provides a fresh perspective on predicting intrinsically disordered regions (IDRs) and conditionally folded binding regions, showing high competitiveness in these predictions and demonstrating the plasticity of the disorder to structure continuum.
Article
Biochemistry & Molecular Biology
Juan Jose Galano-Frutos et al.
Summary: Molten globule (MG) is a compact, non-native conformation of proteins that has been studied for over 40 years due to its implications in protein folding, cell functions, and misfolding diseases. Researchers have successfully developed an integrative atomistic model of an MG by analyzing stability of mutants and conducting biased molecular dynamics simulations, shedding light on the energetics and roles of these elusive conformations.
Article
Chemistry, Physical
Florencia Klein et al.
Summary: The CG SIRAH force field shows a good ability to describe the dynamical behavior of IDPs and unstructured peptides, and it can effectively capture the effect of point mutations in loosely structured peptides.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Biochemical Research Methods
Marco Necci et al.
Summary: Intrinsically disordered proteins present a challenge to traditional protein structure-function analysis, with computational methods, particularly deep learning techniques, showing superior performance in predicting disorder. However, predicting disordered binding regions remains difficult, and there is a significant variation in computational times among methods.
Article
Biochemistry & Molecular Biology
Jiaxing Chen et al.
Summary: Research using discrete molecular dynamics simulations and various experimental methods explored the conformational space of the alpha-synuclein monomer, revealing stable conformations. These results contribute to understanding the mechanisms by which alpha-synuclein functions in membrane interaction, oligomer, and fibril formation.
Review
Biochemistry & Molecular Biology
Kresten Lindorff-Larsen et al.
Summary: Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) play important roles in a wide range of biological functions and reveal novel mechanisms of interactions. Computational methods, including machine learning, are crucial for predicting the structures and functions of IDPs and IDRs. Experiments provide insights into complexes and may enable more accurate predictions.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Multidisciplinary Sciences
John Jumper et al.
Summary: Proteins are essential for life, and accurate prediction of their structures is a crucial research problem. Current experimental methods are time-consuming, highlighting the need for accurate computational approaches to address the gap in structural coverage. Despite recent progress, existing methods fall short of atomic accuracy in protein structure prediction.
Article
Multidisciplinary Sciences
Minkyung Baek et al.
Summary: Through the three-track network, we achieved accuracies approaching those of DeepMind in CASP14, enabling rapid solution of challenging x-ray crystallography and cryo-electron microscopy structure modeling problems, and providing insights into the functions of proteins with currently unknown structure.
Article
Biochemistry & Molecular Biology
Tamas Lazar et al.
Summary: The Protein Ensemble Database (PED) has been significantly updated to version 4.0, with cutting-edge technology and an increased amount of data. The database now includes a renewed graphical interface, interactive feature viewer, and high-quality data guaranteed by a new submission process. Additionally, a new search engine allows users to build advanced queries and search all entry fields.
NUCLEIC ACIDS RESEARCH
(2021)
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Satoshi Fukuchi et al.
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