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Zavrtanik U, Medved T, Purič S, Vranken W, Lah J, Hadži S. Leucine Motifs Stabilize Residual Helical Structure in Disordered Proteins. J Mol Biol 2024; 436:168444. [PMID: 38218366 DOI: 10.1016/j.jmb.2024.168444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 12/31/2023] [Accepted: 01/09/2024] [Indexed: 01/15/2024]
Abstract
Many examples are known of regions of intrinsically disordered proteins that fold into α-helices upon binding to their targets. These helical binding motifs (HBMs) can be partially helical also in the unbound state, and this so-called residual structure can affect binding affinity and kinetics. To investigate the underlying mechanisms governing the formation of residual helical structure, we assembled a dataset of experimental helix contents of 65 peptides containing HBM that fold-upon-binding. The average residual helicity is 17% and increases to 60% upon target binding. The helix contents of residual and target-bound structures do not correlate, however the relative location of helix elements in both states shows a strong overlap. Compared to the general disordered regions, HBMs are enriched in amino acids with high helix preference and these residues are typically involved in target binding, explaining the overlap in helix positions. In particular, we find that leucine residues and leucine motifs in HBMs are the major contributors to helix stabilization and target-binding. For the two model peptides, we show that substitution of leucine motifs to other hydrophobic residues (valine or isoleucine) leads to reduction of residual helicity, supporting the role of leucine as helix stabilizer. From the three hydrophobic residues only leucine can efficiently stabilize residual helical structure. We suggest that the high occurrence of leucine motifs and a general preference for leucine at binding interfaces in HBMs can be explained by its unique ability to stabilize helical elements.
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Affiliation(s)
- Uroš Zavrtanik
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Tadej Medved
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Samo Purič
- Graduate Study Program, Faculty of Chemistry and Chemical Technology, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Wim Vranken
- Artificial Intelligence Laboratory, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; Interuniversity Institute of Bioinformatics in Brussels, ULB/VUB, Triomflaan, 1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, Brussels 1050, Belgium; VIB Structural Biology Research Centre, Brussels 1050, Belgium
| | - Jurij Lah
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - San Hadži
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia.
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Dixit B, Vranken W, Ghysels A. Conformational dynamics of α-1 acid glycoprotein (AGP) in cancer: A comparative study of glycosylated and unglycosylated AGP. Proteins 2024; 92:246-264. [PMID: 37837263 DOI: 10.1002/prot.26607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 09/01/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023]
Abstract
α-1 acid glycoprotein (AGP) is one of the most abundant plasma proteins. It fulfills two important functions: immunomodulation, and binding to various drugs and receptors. These different functions are closely associated and modulated via changes in glycosylation and cancer missense mutations. From a structural point of view, glycans alter the local biophysical properties of the protein leading to a diverse ligand-binding spectrum. However, glycans can typically not be observed in the resolved X-ray crystallography structure of AGP due to their high flexibility and microheterogeneity, so limiting our understanding of AGP's conformational dynamics 70 years after its discovery. We here investigate how mutations and glycosylation interfere with AGP's conformational dynamics changing its biophysical behavior, by using molecular dynamics (MD) simulations and sequence-based dynamics predictions. The MD trajectories show that glycosylation decreases the local backbone flexibility of AGP and increases the flexibility of distant regions through allosteric effects. We observe that mutations near the glycosylation site affect glycan's conformational preferences. Thus, we conclude that mutations control glycan dynamics which modulates the protein's backbone flexibility directly affecting its accessibility. These findings may assist in the drug design targeting AGP's glycosylation and mutations in cancer.
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Affiliation(s)
- Bhawna Dixit
- IBiTech-BioMMeda Group, Ghent University, Ghent, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Wim Vranken
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - An Ghysels
- IBiTech-BioMMeda Group, Ghent University, Ghent, Belgium
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Hou Q, Waury K, Gogishvili D, Feenstra KA. Ten quick tips for sequence-based prediction of protein properties using machine learning. PLoS Comput Biol 2022; 18:e1010669. [PMID: 36454728 PMCID: PMC9714715 DOI: 10.1371/journal.pcbi.1010669] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
The ubiquitous availability of genome sequencing data explains the popularity of machine learning-based methods for the prediction of protein properties from their amino acid sequences. Over the years, while revising our own work, reading submitted manuscripts as well as published papers, we have noticed several recurring issues, which make some reported findings hard to understand and replicate. We suspect this may be due to biologists being unfamiliar with machine learning methodology, or conversely, machine learning experts may miss some of the knowledge needed to correctly apply their methods to proteins. Here, we aim to bridge this gap for developers of such methods. The most striking issues are linked to a lack of clarity: how were annotations of interest obtained; which benchmark metrics were used; how are positives and negatives defined. Others relate to a lack of rigor: If you sneak in structural information, your method is not sequence-based; if you compare your own model to "state-of-the-art," take the best methods; if you want to conclude that some method is better than another, obtain a significance estimate to support this claim. These, and other issues, we will cover in detail. These points may have seemed obvious to the authors during writing; however, they are not always clear-cut to the readers. We also expect many of these tips to hold for other machine learning-based applications in biology. Therefore, many computational biologists who develop methods in this particular subject will benefit from a concise overview of what to avoid and what to do instead.
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Affiliation(s)
- Qingzhen Hou
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Shandong, P. R. China
- National Institute of Health Data Science of China, Shandong University, Shandong, P. R. China
| | - Katharina Waury
- Department of Computer Science, Bioinformatics Group, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Dea Gogishvili
- Department of Computer Science, Bioinformatics Group, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - K. Anton Feenstra
- Department of Computer Science, Bioinformatics Group, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
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Roca-Martinez J, Lazar T, Gavalda-Garcia J, Bickel D, Pancsa R, Dixit B, Tzavella K, Ramasamy P, Sanchez-Fornaris M, Grau I, Vranken WF. Challenges in describing the conformation and dynamics of proteins with ambiguous behavior. Front Mol Biosci 2022; 9:959956. [PMID: 35992270 PMCID: PMC9382080 DOI: 10.3389/fmolb.2022.959956] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 06/27/2022] [Indexed: 11/13/2022] Open
Abstract
Traditionally, our understanding of how proteins operate and how evolution shapes them is based on two main data sources: the overall protein fold and the protein amino acid sequence. However, a significant part of the proteome shows highly dynamic and/or structurally ambiguous behavior, which cannot be correctly represented by the traditional fixed set of static coordinates. Representing such protein behaviors remains challenging and necessarily involves a complex interpretation of conformational states, including probabilistic descriptions. Relating protein dynamics and multiple conformations to their function as well as their physiological context (e.g., post-translational modifications and subcellular localization), therefore, remains elusive for much of the proteome, with studies to investigate the effect of protein dynamics relying heavily on computational models. We here investigate the possibility of delineating three classes of protein conformational behavior: order, disorder, and ambiguity. These definitions are explored based on three different datasets, using interpretable machine learning from a set of features, from AlphaFold2 to sequence-based predictions, to understand the overlap and differences between these datasets. This forms the basis for a discussion on the current limitations in describing the behavior of dynamic and ambiguous proteins.
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Affiliation(s)
- Joel Roca-Martinez
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, VUB/ULB, Brussels, Belgium
| | - Tamas Lazar
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
- VIB-VUB Center for Structural Biology, Brussels, Belgium
| | - Jose Gavalda-Garcia
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, VUB/ULB, Brussels, Belgium
| | - David Bickel
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, VUB/ULB, Brussels, Belgium
| | - Rita Pancsa
- Research Centre for Natural Sciences, Institute of Enzymology, Budapest, Hungary
| | - Bhawna Dixit
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, VUB/ULB, Brussels, Belgium
- IBiTech-Biommeda, Universiteit Gent, Gent, Belgium
| | - Konstantina Tzavella
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, VUB/ULB, Brussels, Belgium
| | - Pathmanaban Ramasamy
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, VUB/ULB, Brussels, Belgium
- VIB-UGent Center for Medical Biotechnology, Universiteit Gent, Gent, Belgium
| | - Maite Sanchez-Fornaris
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, VUB/ULB, Brussels, Belgium
- Department of Computer Sciences, University of Camagüey, Camagüey, Cuba
| | - Isel Grau
- Information Systems, Eindhoven University of Technology, Eindhoven, Netherlands
| | - Wim F. Vranken
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, VUB/ULB, Brussels, Belgium
- *Correspondence: Wim F. Vranken,
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Orlando G, Raimondi D, Codice F, Tabaro F, Vranken W. Prediction of disordered regions in proteins with recurrent Neural Networks and protein dynamics. J Mol Biol 2022; 434:167579. [DOI: 10.1016/j.jmb.2022.167579] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 03/21/2022] [Accepted: 03/31/2022] [Indexed: 10/18/2022]
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