☆ 4.7 Review

Recent Advances in NMR Protein Structure Prediction with ROSETTA

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2023)

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Review Biochemistry & Molecular Biology

Solid-state NMR studies of amyloids

Jing Liu et al.

Summary: Amyloids have unique structural properties and play a role in various biological functions. They are associated with a group of incurable neurodegenerative diseases. Solid-state NMR has been widely used to study amyloid structures and dynamics, leading to significant progress in understanding amyloids and related diseases.

STRUCTURE (2023)

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Article Biotechnology & Applied Microbiology

Protein structure prediction with in-cell photo-crosslinking mass spectrometry and deep learning

Kolja Stahl et al.

Summary: Limitations of Alphafold2 structure prediction are overcome by incorporating experimentally determined distance constraints using AlphaLink. This modified version improves prediction for challenging targets by utilizing sparse experimental contacts and can predict distinct protein conformations. Experimental data on residue-residue contacts obtained through crosslinking mass spectrometry validates the improved performance. The noise-tolerant framework for integrating data allows accurate characterization of protein structures from in-cell data.

NATURE BIOTECHNOLOGY (2023)

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Review Chemistry, Multidisciplinary

Pseudocontact Shifts in Biomolecular NMR Spectroscopy

Thomas Muntener et al.

Summary: Paramagnetic centers, such as metal ions bound to proteins, can affect the nuclei in their surroundings through the pseudocontact shift (PCS). PCS provides spatial information and can be used to characterize the structure, function, and dynamics of biomolecules. It has various applications, including structure refinement, magnifying dynamics, resonance assignments, intermolecular positioning, and structural information under sensitivity-limited situations. This review discusses the applications of PCS in biomolecular solution NMR spectroscopy and emphasizes its potential in structural biology.

CHEMICAL REVIEWS (2022)

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Review Chemistry, Multidisciplinary

Paramagnetic Chemical Probes for Studying Biological Macromolecules

Qing Miao et al.

Summary: Paramagnetic chemical probes have been widely used in EPR and NMR spectroscopy, especially in the study of biological macromolecules. Recent developments include an increase in the variety of paramagnetic probes, the development of lanthanoid probes for protein studies, and the development of isotropic paramagnetic probes for NMR and EPR measurements.

CHEMICAL REVIEWS (2022)

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Article Biochemistry & Molecular Biology

AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models

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)

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Article Biochemistry & Molecular Biology

Protein structure prediction using residue-resolved protection factors from-deuterium NMR

Tung T. Nguyen et al.

Summary: Hydrogen-deuterium exchange (HDX) measured by nuclear magnetic resonance (NMR) provides structural information for proteins. However, it cannot be exclusively used for structure elucidation. In this study, researchers developed an algorithm using qualitative HDX-NMR data and quantitative protection factors (PFs) to predict protein structures. A scoring function was presented to quantify the agreement with HDX data based on observed correlations between PFs and solvent accessibility/flexibility measures. The algorithm showed an average improvement of 5.13 angstrom in root-mean-square deviation (RMSD) compared to inaccurate predictions by Rosetta. Seven out of 10 predictions were accurate without HDX data, and nine out of 10 were accurate when using the PF-based HDX score.

STRUCTURE (2022)

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Article Biochemistry & Molecular Biology

AlphaFold2: A Role for Disordered Protein/Region Prediction?

Carter J. Wilson et al.

Summary: The development of AlphaFold2 has brought a paradigm shift in structural biology and has shown excellent performance in predicting disordered regions. The accuracy of the constructed disorder predictor from AlphaFold2 structures varies, with the naive assumption of assigning residues to ordered or disordered based on helices, strands, and H-bond stabilized turns leading to a significant overestimation of disorder. The predicted local distance difference test (pLDDT) provides a reliable measure of residue-wise disorder and shows an interesting relationship with secondary structure.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2022)

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Article Biochemistry & Molecular Biology

Multi-state modeling of G-protein coupled receptors at experimental accuracy

Lim Heo et al.

Summary: The paper introduces a protocol that uses AlphaFold2 and GPCR databases to predict the active or inactive states of GPCRs with high accuracy. The predicted models capture the structural changes upon activation of GPCRs and are more suitable for protein-ligand docking.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2022)

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Article Biology

Sampling alternative conformational states of transporters and receptors with AlphaFold2

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.

ELIFE (2022)

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Review Immunology

Computational Structure Prediction for Antibody-Antigen Complexes From Hydrogen-Deuterium Exchange Mass Spectrometry: Challenges and Outlook

Minh H. Tran et al.

Summary: Although computational structure prediction has made great strides in recent years, it still struggles with accurately predicting protein-protein interactions. Incorporating experimental data, such as hydrogen-deuterium exchange mass spectrometry (HDX-MS), can greatly improve the performance of computational docking. This paper reviews the current state of HDX-MS in studying protein interactions, specifically antibody-antigen interactions, and its use in informing computational structure prediction calculations.

FRONTIERS IN IMMUNOLOGY (2022)

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Review Biochemistry & Molecular Biology

AlphaFold 2 and NMR Spectroscopy: Partners to Understand Protein Structure, Dynamics and Function

Douglas V. Laurents

Summary: The artificial intelligence program AlphaFold 2 accurately predicts the 3D structure of two thirds of the human proteome, but it cannot provide insights into protein folding, stability, dynamics, and the impact of post translational modifications, mutations, or ligand binding. This is complemented by NMR spectroscopy which provides information on protein folding, dynamics, biomolecular condensates, amyloids, and their modulation.

FRONTIERS IN MOLECULAR BIOSCIENCES (2022)

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Article Multidisciplinary Sciences

Protein complex prediction using Rosetta, AlphaFold, and mass spectrometry covalent labeling

Zachary C. Drake et al.

Summary: Covalent labeling (CL) in combination with mass spectrometry is a useful tool for studying and determining structural properties of protein-protein complexes. However, the data from these experiments is limited and does not provide a clear understanding of protein structure. This study presents a hybrid method that combines models of protein complex subunits generated with AlphaFold and differential CL data through a CL-guided protein-protein docking in Rosetta. The results show that this integrated approach can effectively utilize CL data to distinguish between nativelike and non-nativelike models.

NATURE COMMUNICATIONS (2022)

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Article Biochemistry & Molecular Biology

AlphaFold Models of Small Proteins Rival the Accuracy of Solution NMR Structures

Roberto Tejero et al.

Summary: Recent advances in molecular modeling, particularly AlphaFold, have the potential to revolutionize structural biology, as it provides protein structure models with accuracies similar to or even better than experimental data. This holds promise for guiding the analysis of experimental data and has broader applications in the field.

FRONTIERS IN MOLECULAR BIOSCIENCES (2022)

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Review Chemistry, Physical

Solvent paramagnetic relaxation enhancement as a versatile method for studying structure and dynamics of biomolecular systems

Aneta J. Lenard et al.

Summary: Solvent paramagnetic relaxation enhancement (sPRE) is a versatile NMR-based method that characterizes the structure and dynamics of biomolecular systems by providing quantitative experimental information on the solvent accessibility of NMR-active nuclei. This review discusses recent progress in sPRE-based characterization of biomolecules and their complexes, highlighting the diverse applications of the method. By combining sPRE with complementary biophysical techniques, it is possible to advance biomolecular structure determination, identify interaction surfaces within protein complexes, probe conformational changes and low-population transient states, and gain insights into weak, nonspecific, and transient interactions between proteins and co-solutes. Additionally, the incorporation of solvent paramagnetic probes can improve the sensitivity of NMR experiments and hold promise for applications in metabolomics, drug discovery, and the study of intrinsically disordered proteins.

PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY (2022)

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Article Biochemical Research Methods

SPEACH_AF: Sampling protein ensembles and conformational heterogeneity with Alphafold2

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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Article Chemistry, Physical

The evolution of paramagnetic NMR as a tool in structural biology

Enrico Ravera et al.

Summary: Paramagnetic NMR data provide highly accurate long-range information on metalloprotein structures. They are a powerful tool for refining protein models, monitoring complex formation, and highlighting conformational heterogeneity.

PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2022)

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Review Chemistry, Multidisciplinary

Paramagnetic Chemical Probes for Studying Biological Macromolecules

Qing Miao et al.

Summary: This review provides a comprehensive overview of the existing paramagnetic chemical probes, including chemical synthetic approaches, functional properties, and selected applications in the study of biological macromolecules. Recent developments have seen a rapid expansion of lanthanoid probes with anisotropic magnetic susceptibilities and isotropic paramagnetic probes for protein studies and investigations of biological macromolecules.

CHEMICAL REVIEWS (2022)

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Review Chemistry, Multidisciplinary

Pseudocontact Shifts in Biomolecular NMR Spectroscopy

Thomas Muntener et al.

Summary: Paramagnetic centers in biomolecules, such as specific metal ions bound to proteins, can induce pseudocontact shift effects on surrounding nuclei, providing spatial information that can be utilized for structural, functional, and dynamic studies.

CHEMICAL REVIEWS (2022)

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Article Biophysics

Modeling of Hidden Structures Using Sparse Chemical Shift Data from NMR Relaxation Dispersion

R. Bryn Fenwick et al.

Summary: NMR relaxation dispersion measurements were used to study conformational changes in DHFR on the millisecond-microsecond timescale, generating structural models of alternative conformations using unsigned chemical shift changes. The combination of fragment modeling with sparse chemical shift data successfully characterized a minor conformational state of DHFR sampled on the microsecond-millisecond timescale, showing potential for in silico drug screening and contributing to understanding the role of minor states in biology and molecular evolution.

BIOPHYSICAL JOURNAL (2021)

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Article Multidisciplinary Sciences

An N-terminal conserved region in human Atg3 couples membrane curvature sensitivity to conjugase activity during autophagy

Yansheng Ye et al.

Summary: The enzyme Atg3 is crucial for autophagosome formation, facilitating the connection of LC3 to PE lipids. The N-terminal conserved region of human Atg3 communicates information from the curvature-sensing domain to the active site, promoting spatial regulation of LC3-PE conjugation on target membranes.

NATURE COMMUNICATIONS (2021)

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Review Biochemistry & Molecular Biology

AlphaFold and the amyloid landscape

Francisca Pinheiro et al.

Summary: Protein aggregation is a widespread phenomenon with functional amyloids playing important roles in physiology, while structural details of most amyloidogenic species remain elusive.

JOURNAL OF MOLECULAR BIOLOGY (2021)

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Article Multidisciplinary Sciences

Structure-based classification of tauopathies

Yang Shi et al.

Summary: The structures of tau filaments from different tauopathies vary, allowing for a hierarchical classification of these diseases. Some tauopathies share similar filament folds, while others have distinct folding patterns.

NATURE (2021)

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Article Biochemical Research Methods

The trRosetta server for fast and accurate protein structure prediction

Zongyang Du et al.

Summary: The trRosetta server is a web-based platform for fast and accurate protein structure prediction using deep learning and Rosetta, which distinguishes itself from other similar servers in terms of rapid and accurate prediction of novel structures.

NATURE PROTOCOLS (2021)

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Article Chemistry, Physical

Hydrophobic Gate of Mechanosensitive Channel of Large Conductance in Lipid Bilayers Revealed by Solid-State NMR Spectroscopy

Xuning Zhang et al.

Summary: In this study, the hydrophobic gate of MscL was investigated using solid-state nuclear magnetic resonance (ssNMR) techniques and functional assays. It was found that residues I21-T30 in transmembrane helix 1 constitute the hydrophobic gate, and the packing of aromatic rings of F23 in each subunit is critical to gate function. Hydrophilic substitutions of residues A22 and G26 modulate channel gating by affecting the hydrophobicity of F23 constriction.

JOURNAL OF PHYSICAL CHEMISTRY B (2021)

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Article Multidisciplinary Sciences

Computed structures of core eukaryotic protein complexes

Ian R. Humphreys et al.

Summary: By utilizing proteome-wide amino acid coevolution analysis and deep-learning-based structure modeling, we systematically identified and built accurate models of core eukaryotic protein complexes within the Saccharomyces cerevisiae proteome. These models cover nearly 800 previously uncharacterized assemblies, providing comprehensive insights into key processes in eukaryotic cells.

SCIENCE (2021)

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Article Biology

Structure of membrane diacylglycerol kinase in lipid bilayers

Jianping Li et al.

Summary: The study presents a well-defined homo-trimeric structure of DgkA in phospholipid bilayers determined by solid-state NMR spectroscopy, providing insights into the influence of membrane mimetic environments on membrane proteins. Comparisons with structures solved by solution NMR and X-ray crystallography highlight differences in symmetry and dynamics, demonstrating the significance of membrane mimetic environments in shaping the structure and dynamics of membrane proteins.

COMMUNICATIONS BIOLOGY (2021)

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Article Chemistry, Physical

Protein Structure Prediction from NMR Hydrogen-Deuterium Exchange Data

Daniel R. Marzolf et al.

Summary: Incorporating HDX-NMR data into protein structure prediction using the Rosetta software framework significantly improves the accuracy and selection of models. Analysis of experimental data from 38 proteins demonstrates the importance of HDX-NMR in protein structure prediction, showing significant improvements in model accuracy and selection.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2021)

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Article Multidisciplinary Sciences

Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences

Alexander Rives et al.

Summary: The deep contextual language model trained through unsupervised learning on protein sequences contains information about biological properties, has a multiscale structural organization, and can be used to improve predictions for protein mutational effects, secondary structure, and long-range contacts.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2021)

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Review Biochemistry & Molecular Biology

AlphaFold and Implications for Intrinsically Disordered Proteins

Kiersten M. Ruff et al.

Summary: Accurate predictions of protein structures using AlphaFold have made significant progress. Most protein sequences in the human proteome have been structurally annotated, with over 30% of regions being disordered.

JOURNAL OF MOLECULAR BIOLOGY (2021)

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Article Multidisciplinary Sciences

Highly accurate protein structure prediction with AlphaFold

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.

NATURE (2021)

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Article Multidisciplinary Sciences

Highly accurate protein structure prediction for the human proteome

Kathryn Tunyasuvunakool et al.

Summary: Using the AlphaFold method, the structural coverage of the proteome has been significantly expanded, covering 98.5% of human proteins with 58% of residues having confident predictions and 36% having very high confidence. Introducing new metrics to interpret the dataset and identify disordered regions, this study aims to provide high-quality predictions for generating biological hypotheses.

NATURE (2021)

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Article Biochemistry & Molecular Biology

NMR hawk-eyed view of AlphaFold2 structures

Markus Zweckstetter

Summary: The AlphaFold2 method has shown the ability to accurately predict protein structures in solution, matching well with experimental data, and holds promise as a powerful tool for studying structural changes in proteins.

PROTEIN SCIENCE (2021)

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Article Multidisciplinary Sciences

Accurate prediction of protein structures and interactions using a three-track neural network

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.

SCIENCE (2021)

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Review Multidisciplinary Sciences

Solid-state NMR spectroscopy

Bernd Reif et al.

Summary: Solid-state nuclear magnetic resonance (NMR) spectroscopy is an atomic-level method to determine the chemical structure, 3D structure, and dynamics of solids and semi-solids, with most high-resolution solid-state NMR spectra measured under magic-angle spinning (MAS). Common experiments and data analysis approaches in solid-state NMR are summarized, highlighting applications in biology, chemistry, and materials sciences.

NATURE REVIEWS METHODS PRIMERS (2021)

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DALI and the persistence of protein shape

Liisa Holm

PROTEIN SCIENCE (2020)

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Review Biochemistry & Molecular Biology

The (un)structural biology of biomolecular liquid-liquid phase separation using NMR spectroscopy

Anastasia C. Murthy et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2020)

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Article Multidisciplinary Sciences

Improved protein structure prediction using predicted interresidue orientations

Jianyi Yang et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

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Article Biophysics

Protein Structure Prediction and Design in a Biologically Realistic Implicit Membrane

Rebecca F. Alford et al.

BIOPHYSICAL JOURNAL (2020)

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Macromolecular modeling and design in Rosetta: recent methods and frameworks

Julia Koehler Leman et al.

NATURE METHODS (2020)

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Article Biochemistry & Molecular Biology

ARIAweb: a server for automated NMR structure calculation

Fabrice Allain et al.

NUCLEIC ACIDS RESEARCH (2020)

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Article Biochemistry & Molecular Biology

Paramagnetic NMR in drug discovery

Charlotte A. Softley et al.

JOURNAL OF BIOMOLECULAR NMR (2020)

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A Unified De Novo Approach for Predicting the Structures of Ordered and Disordered Proteins

John J. Ferrie et al.

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Solution NMR spectroscopy of membrane proteins

Gaddafi I. Danmaliki et al.

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Residual Structure of Unfolded Ubiquitin as Revealed by Hydrogen/Deuterium-Exchange 2D NMR

Maho Yagi-Utsumi et al.

BIOPHYSICAL JOURNAL (2020)

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A Structural Model of the Endogenous Human BAF Complex Informs Disease Mechanisms

Nazar Mashtalir et al.

CELL (2020)

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Review Biochemistry & Molecular Biology

Cryo-EM structures of tau filaments

Sjors H. W. Scheres et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2020)

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Book Biochemical Research Methods

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PROTEIN STRUCTURE PREDICTION, 4 EDITION (2020)

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Article Biochemistry & Molecular Biology

Structural Model of Ghrelin Bound to its G Protein-Coupled Receptor

Brian Joseph Bender et al.

STRUCTURE (2019)

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Double Nitroxide Labeling by Copper-Catalyzed Azide-Alkyne Cycloadditions with Noncanonical Amino Acids for Electron Paramagnetic Resonance Spectroscopy

Pia Widder et al.

ACS CHEMICAL BIOLOGY (2019)

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NMR characterization of solvent accessibility and transient structure in intrinsically disordered proteins

Christoph Hartlmueller et al.

JOURNAL OF BIOMOLECULAR NMR (2019)

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Protein structure prediction using sparse NOE and RDC restraints with Rosetta in CASP13

Georg Kuenze et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2019)

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The Molecular Architecture of Native BBSome Obtained by an Integrated Structural Approach

Hui-Ting Chou et al.

STRUCTURE (2019)

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Measuring Intrinsic Disorder and Tracking Conformational Transitions Using Rosetta ResidueDisorder

Justin T. Seffernick et al.

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Design and applications of lanthanide chelating tags for pseudocontact shift NMR spectroscopy with biomacromolecules

Daniel Joss et al.

PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY (2019)

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Integrative Protein Modeling in RosettaNMR from Sparse Paramagnetic Restraints

Georg Kuenze et al.

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Integrating hydrogen deuterium exchange mass spectrometry with molecular dynamics simulations to probe lipid-modulated conformational changes in membrane proteins

Chloe Martens et al.

NATURE PROTOCOLS (2019)

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Web-accessible molecular modeling with Rosetta: The Rosetta Online Server that Includes Everyone (ROSIE)

Rocco Moretti et al.

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Rosetta Protein Structure Prediction from Hydroxyl Radical Protein Footprinting Mass Spectrometry Data

Melanie L. Aprahamian et al.

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Accurately Predicting Disordered Regions of Proteins Using Rosetta ResidueDisorder Application

Stephanie S. Kim et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2018)

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Gating Mechanism of Aquaporin Z in Synthetic Bilayers and Native Membranes Revealed by Solid-State NMR Spectroscopy

Yongxiang Zhao et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2018)

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Santrupti Nerli et al.

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Venkata S. Mandala et al.

ANNUAL REVIEW OF BIOPHYSICS, VOL 47 (2018)

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Interpreting Hydrogen-Deuterium Exchange Events in Proteins Using Atomistic Simulations: Case Studies on Regulators of G-Protein Signaling Proteins

Hossein Mohammadiarani et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2018)

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Residue-Centric Modeling and Design of Saccharide and Glycoconjugate Structures

Jason W. Labonte et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2017)

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Small-Angle X-ray Scattering Data in Combination with RosettaDock Improves the Docking Energy Landscape

Pernille Sonderby et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2017)

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The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design

Rebecca F. Alford et al.

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Yajun Jiang et al.

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RosettaES: a sampling strategy enabling automated interpretation of difficult cryo-EM maps

Brandon Frenz et al.

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Pseudocontact shifts in biomolecular NMR using paramagnetic metal tags

Christoph Nitsche et al.

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Christoph Hartlmueller et al.

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Combining H/D Exchange Mass Spectrometry and Computational Docking To Derive the Structure of Protein-Protein Complexes

Victoria A. Roberts et al.

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Application of NMR to studies of intrinsically disordered proteins

Eric B. Gibbs et al.

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Structure prediction using sparse simulated NOE restraints with Rosetta in CASP11

Sergey Ovchinnikov et al.

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Solid-state NMR structure of a pathogenic fibril of full-length human α-synuclein

Marcus D. Tuttle et al.

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Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta

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