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Zhao K, Zhao P, Wang S, Xia Y, Zhang G. FoldPAthreader: predicting protein folding pathway using a novel folding force field model derived from known protein universe. Genome Biol 2024; 25:152. [PMID: 38862984 PMCID: PMC11167914 DOI: 10.1186/s13059-024-03291-x] [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: 01/10/2024] [Accepted: 05/29/2024] [Indexed: 06/13/2024] Open
Abstract
Protein folding has become a tractable problem with the significant advances in deep learning-driven protein structure prediction. Here we propose FoldPAthreader, a protein folding pathway prediction method that uses a novel folding force field model by exploring the intrinsic relationship between protein evolution and folding from the known protein universe. Further, the folding force field is used to guide Monte Carlo conformational sampling, driving the protein chain fold into its native state by exploring potential intermediates. On 30 example targets, FoldPAthreader successfully predicts 70% of the proteins whose folding pathway is consistent with biological experimental data.
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Affiliation(s)
- Kailong Zhao
- College of Information Engineering, Zhejiang University of Technology, HangZhou, 310023, China
| | - Pengxin Zhao
- College of Information Engineering, Zhejiang University of Technology, HangZhou, 310023, China
| | - Suhui Wang
- College of Information Engineering, Zhejiang University of Technology, HangZhou, 310023, China
| | - Yuhao Xia
- College of Information Engineering, Zhejiang University of Technology, HangZhou, 310023, China
| | - Guijun Zhang
- College of Information Engineering, Zhejiang University of Technology, HangZhou, 310023, China.
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2
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Cleary SR, Seflova J, Cho EE, Bisht K, Khandelia H, Espinoza-Fonseca LM, Robia SL. Phospholamban inhibits the cardiac calcium pump by interrupting an allosteric activation pathway. J Biol Chem 2024; 300:107267. [PMID: 38583863 PMCID: PMC11098958 DOI: 10.1016/j.jbc.2024.107267] [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: 09/07/2023] [Revised: 03/20/2024] [Accepted: 04/02/2024] [Indexed: 04/09/2024] Open
Abstract
Phospholamban (PLB) is a transmembrane micropeptide that regulates the sarcoplasmic reticulum Ca2+-ATPase (SERCA) in cardiac muscle, but the physical mechanism of this regulation remains poorly understood. PLB reduces the Ca2+ sensitivity of active SERCA, increasing the Ca2+ concentration required for pump cycling. However, PLB does not decrease Ca2+ binding to SERCA when ATP is absent, suggesting PLB does not inhibit SERCA Ca2+ affinity. The prevailing explanation for these seemingly conflicting results is that PLB slows transitions in the SERCA enzymatic cycle associated with Ca2+ binding, altering transport Ca2+ dependence without actually affecting the equilibrium binding affinity of the Ca2+-coordinating sites. Here, we consider another hypothesis, that measurements of Ca2+ binding in the absence of ATP overlook important allosteric effects of nucleotide binding that increase SERCA Ca2+ binding affinity. We speculated that PLB inhibits SERCA by reversing this allostery. To test this, we used a fluorescent SERCA biosensor to quantify the Ca2+ affinity of non-cycling SERCA in the presence and absence of a non-hydrolyzable ATP-analog, AMPPCP. Nucleotide activation increased SERCA Ca2+ affinity, and this effect was reversed by co-expression of PLB. Interestingly, PLB had no effect on Ca2+ affinity in the absence of nucleotide. These results reconcile the previous conflicting observations from ATPase assays versus Ca2+ binding assays. Moreover, structural analysis of SERCA revealed a novel allosteric pathway connecting the ATP- and Ca2+-binding sites. We propose this pathway is disrupted by PLB binding. Thus, PLB reduces the equilibrium Ca2+ affinity of SERCA by interrupting allosteric activation of the pump by ATP.
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Affiliation(s)
- Sean R Cleary
- Department of Cell and Molecular Physiology, Loyola University Chicago, Maywood, Illinois, USA
| | - Jaroslava Seflova
- Department of Cell and Molecular Physiology, Loyola University Chicago, Maywood, Illinois, USA
| | - Ellen E Cho
- Department of Cell and Molecular Physiology, Loyola University Chicago, Maywood, Illinois, USA
| | - Konark Bisht
- Department of Physics, Chemistry, and Pharmacy, PHYLIFE: Physical Life Science, University of Southern Denmark, Odense, Denmark
| | - Himanshu Khandelia
- Department of Physics, Chemistry, and Pharmacy, PHYLIFE: Physical Life Science, University of Southern Denmark, Odense, Denmark
| | - L Michel Espinoza-Fonseca
- Division of Cardiovascular Medicine, Department of Internal Medicine, Center for Arrhythmia Research, University of Michigan, Ann Arbor, Michigan, USA
| | - Seth L Robia
- Department of Cell and Molecular Physiology, Loyola University Chicago, Maywood, Illinois, USA.
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3
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Yang S, Liu D, Song Y, Liang Y, Yu H, Zuo Y. Designing a structure-function alphabet of helix based on reduced amino acid clusters. Arch Biochem Biophys 2024; 754:109942. [PMID: 38387828 DOI: 10.1016/j.abb.2024.109942] [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: 01/12/2024] [Revised: 02/16/2024] [Accepted: 02/19/2024] [Indexed: 02/24/2024]
Abstract
Several simple secondary structures could form complex and diverse functional proteins, meaning that secondary structures may contain a lot of hidden information and are arranged according to certain principles, to carry enough information of functional specificity and diversity. However, these inner information and principles have not been understood systematically. In our study, we designed a structure-function alphabet of helix based on reduced amino acid clusters to describe the typical features of helices and delve into the information. Firstly, we selected 480 typical helices from membrane proteins, zymoproteins, transcription factors, and other proteins to define and calculate the interval range, and the helices are classified in terms of hydrophilicity, charge and length: (1) hydrophobic helix (≤43%), amphiphilic helix (43%∼71%), and hydrophilic helix (≥71%). (2) positive helix, negative helix, electrically neutral helix and uncharged helix. (3) short helix (≤8 aa), medium-length helix (9-28 aa), and long helix (≥29 aa). Then, we designed an alphabet containing 36 triplet codes according to the above classification, so that the main features of each helix can be represented by only three letters. This alphabet not only preliminarily defined the helix characteristics, but also greatly reduced the informational dimension of protein structure. Finally, we present an application example to demonstrate the value of the structure-function alphabet in protein functional determination and differentiation.
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Affiliation(s)
- Siqi Yang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010021, China
| | - Dongyang Liu
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China; University of Chinese Academy of Sciences, Beijing, China
| | - Yancheng Song
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010021, China
| | - Yuchao Liang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010021, China
| | - Haoyu Yu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010021, China
| | - Yongchun Zuo
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010021, China.
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Abbass J, Parisi C. Machine learning-based prediction of proteins' architecture using sequences of amino acids and structural alphabets. J Biomol Struct Dyn 2024:1-16. [PMID: 38505995 DOI: 10.1080/07391102.2024.2328736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 03/05/2024] [Indexed: 03/21/2024]
Abstract
In addition to the growth of protein structures generated through wet laboratory experiments and deposited in the PDB repository, AlphaFold predictions have significantly contributed to the creation of a much larger database of protein structures. Annotating such a vast number of structures has become an increasingly challenging task. CATH is widely recognized as one the most common platforms for addressing this challenge, as it classifies proteins based on their structural and evolutionary relationships, offering the scientific community an invaluable resource for uncovering various properties, including functional annotations. While CATH annotation involves - to some extent - human intervention, keeping up with the classification of the rapidly expanding repositories of protein structures has become exceedingly difficult. Therefore, there is a pressing need for a fully automated approach. On the other hand, the abundance of protein sequences stemming from next generation sequencing technologies, lacking structural annotations, presents an additional challenge to the scientific community. Consequently, 'pre-annotating' protein sequences with structural features, ensuring a high level of precision, could prove highly advantageous. In this paper, after a thorough investigation, we introduce a novel machine-learning model capable of classifying any protein domain, whether it has a known structure or not, into one of the 40 main CATH Architectures. We achieve an F1 Score of 0.92 using only the amino acid sequence and a score of 0.94 using both the sequence of amino acids and the sequence of structural alphabets.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jad Abbass
- School of Computer Science and Mathematics, Kingston University, London, UK
| | - Charles Parisi
- School of Computer Science and Mathematics, Kingston University, London, UK
- Telecom Physique Strasbourg, Strasbourg University, Strasbourg, France
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Alrouji M, Benjamin LS, Alhumaydhi FA, Al Abdulmonem W, Baeesa SS, Rehan M, Shahwan M, Shamsi A, Akhtar A. Unlocking potential inhibitors for Bruton's tyrosine kinase through in-silico drug repurposing strategies. Sci Rep 2023; 13:17684. [PMID: 37848584 PMCID: PMC10582150 DOI: 10.1038/s41598-023-44956-0] [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: 02/20/2023] [Accepted: 10/13/2023] [Indexed: 10/19/2023] Open
Abstract
Bruton's tyrosine kinase (BTK) is a non-receptor protein kinase that plays a crucial role in various biological processes, including immune system function and cancer development. Therefore, inhibition of BTK has been proposed as a therapeutic strategy for various complex diseases. In this study, we aimed to identify potential inhibitors of BTK by using a drug repurposing approach. To identify potential inhibitors, we performed a molecular docking-based virtual screening using a library of repurposed drugs from DrugBank. We then used various filtrations followed by molecular dynamics (MD) simulations, principal component analysis (PCA), and Molecular Mechanics Poisson Boltzmann Surface Area (MM-PBSA) analysis to further evaluate the binding interactions and stability of the top-ranking compounds. Molecular docking-based virtual screening approach identified several repurposed drugs as potential BTK inhibitors, including Eltrombopag and Alectinib, which have already been approved for human use. All-atom MD simulations provided insights into the binding interactions and stability of the identified compounds, which will be helpful for further experimental validation and optimization. Overall, our study demonstrates that drug repurposing is a promising approach to identify potential inhibitors of BTK and highlights the importance of computational methods in drug discovery.
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Affiliation(s)
- Mohammed Alrouji
- Department of Medical Laboratories, College of Applied Medical Sciences, Shaqra University, 11961, Shaqra, Saudi Arabia
| | - Lizy Sonia Benjamin
- College of Nursing, King Khalid University (KKU), Abha, Kingdom of Saudi Arabia
| | - Fahad A Alhumaydhi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, 52571, Buraydah, Saudi Arabia
| | - Waleed Al Abdulmonem
- Department of Pathology, College of Medicine, Qassim University, Buraydah, Saudi Arabia
| | - Saleh Salem Baeesa
- Division of Neurosurgery, College of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohd Rehan
- King Fahd Medical Research Center, King Abdulaziz University, 21589, Jeddah, Saudi Arabia
| | - Moyad Shahwan
- College of Pharmacy and Health Sciences, Ajman University, Ajman, UAE
- Center for Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman, UAE
| | - Anas Shamsi
- Center for Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman, UAE.
| | - Atiya Akhtar
- Department of Pharmacognosy, College of Pharmacy, King Khalid University (KKU), Guraiger St., 62529, Abha, Saudi Arabia.
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Alrouji M, Majrashi TA, Alhumaydhi FA, Zari A, Zari TA, Al Abdulmonem W, Sharaf SE, Shahwan M, Anwar S, Shamsi A, Atiya A. Unveiling Phytoconstituents with Inhibitory Potential Against Tyrosine-Protein Kinase Fyn: A Comprehensive Virtual Screening Approach Targeting Alzheimer's Disease. J Alzheimers Dis 2023; 96:827-844. [PMID: 37899058 DOI: 10.3233/jad-230828] [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] [Indexed: 10/31/2023]
Abstract
BACKGROUND Tyrosine-protein kinase Fyn (Fyn) is a critical signaling molecule involved in various cellular processes, including neuronal development, synaptic plasticity, and disease pathogenesis. Dysregulation of Fyn kinase has been implicated in various complex diseases, including neurodegenerative disorders such as Alzheimer's and Parkinson's diseases, as well as different cancer types. Therefore, identifying small molecule inhibitors that can inhibit Fyn activity holds substantial significance in drug discovery. OBJECTIVE The aim of this study was to identify potential small-molecule inhibitors among bioactive phytoconstituents against tyrosine-protein kinase Fyn. METHODS Through a comprehensive approach involving molecular docking, drug likeliness filters, and molecular dynamics (MD) simulations, we performed a virtual screening of a natural compounds library. This methodology aimed to pinpoint compounds potentially interacting with Fyn kinase and inhibiting its activity. RESULTS This study finds two potential natural compounds: Dehydromillettone and Tanshinone B. These compoundsdemonstrated substantial affinity and specific interactions towards the Fyn binding pocket. Their conformations exhibitedcompatibility and stability, indicating the formation of robust protein-ligand complexes. A significant array of non-covalentinteractions supported the structural integrity of these complexes. CONCLUSION Dehydromillettone and Tanshinone B emerge as promising candidates, poised for further optimization as Fynkinase inhibitors with therapeutic applications. In a broader context, this study demonstrates the potential of computationaldrug discovery, underscoring its utility in identifying compounds with clinical significance. The identified inhibitors holdpromise in addressing a spectrum of cancer and neurodegenerative disorders. However, their efficacy and safety necessitatevalidation through subsequent experimental studies.
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Affiliation(s)
- Mohammed Alrouji
- Department of Medical Laboratories, College of Applied Medical Sciences, Shaqra University, Shaqra, Saudi Arabia
| | - Taghreed A Majrashi
- Department of Pharmacognosy, College of Pharmacy, King Khalid University (KKU), Guraiger, Abha, Saudi Arabia
| | - Fahad A Alhumaydhi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Ali Zari
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Princess Dr. Najla Bint Saud Al-Saud Center for Excellence Research in Biotechnology, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Talal A Zari
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Waleed Al Abdulmonem
- Department of Pathology, College of Medicine, Qassim University, Buraydah, Saudi Arabia
| | - Sharaf E Sharaf
- Pharmaceutical Chemistry Department, College of Pharmacy Umm Al-Qura University Makkah, Saudi Arabia
| | - Moyad Shahwan
- Center for Medical and Bio-Allied Health Sciences, Ajman University, Ajman, UAE
| | - Saleha Anwar
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, India
| | - Anas Shamsi
- Center for Medical and Bio-Allied Health Sciences, Ajman University, Ajman, UAE
| | - Akhtar Atiya
- Department of Pharmacognosy, College of Pharmacy, King Khalid University (KKU), Guraiger, Abha, Saudi Arabia
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Lytridis C, Kaburlasos VG, Bazinas C, Papakostas GA, Sidiropoulos G, Nikopoulou VA, Holeva V, Papadopoulou M, Evangeliou A. Behavioral Data Analysis of Robot-Assisted Autism Spectrum Disorder (ASD) Interventions Based on Lattice Computing Techniques. SENSORS 2022; 22:s22020621. [PMID: 35062582 PMCID: PMC8778181 DOI: 10.3390/s22020621] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/12/2022] [Accepted: 01/13/2022] [Indexed: 11/25/2022]
Abstract
Recent years have witnessed the proliferation of social robots in various domains including special education. However, specialized tools to assess their effect on human behavior, as well as to holistically design social robot applications, are often missing. In response, this work presents novel tools for analysis of human behavior data regarding robot-assisted special education. The objectives include, first, an understanding of human behavior in response to an array of robot actions and, second, an improved intervention design based on suitable mathematical instruments. To achieve these objectives, Lattice Computing (LC) models in conjunction with machine learning techniques have been employed to construct a representation of a child’s behavioral state. Using data collected during real-world robot-assisted interventions with children diagnosed with Autism Spectrum Disorder (ASD) and the aforementioned behavioral state representation, time series of behavioral states were constructed. The paper then investigates the causal relationship between specific robot actions and the observed child behavioral states in order to determine how the different interaction modalities of the social robot affected the child’s behavior.
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Affiliation(s)
- Chris Lytridis
- HUMAIN-Lab, International Hellenic University (IHU), 65404 Kavala, Greece; (C.L.); (C.B.); (G.S.)
| | - Vassilis G. Kaburlasos
- HUMAIN-Lab, International Hellenic University (IHU), 65404 Kavala, Greece; (C.L.); (C.B.); (G.S.)
- Correspondence: ; Tel.: +30-2510-462-320
| | - Christos Bazinas
- HUMAIN-Lab, International Hellenic University (IHU), 65404 Kavala, Greece; (C.L.); (C.B.); (G.S.)
| | - George A. Papakostas
- MLV Research Group, Department of Computer Science, International Hellenic University (IHU), 65404 Kavala, Greece;
| | - George Sidiropoulos
- HUMAIN-Lab, International Hellenic University (IHU), 65404 Kavala, Greece; (C.L.); (C.B.); (G.S.)
| | - Vasiliki-Aliki Nikopoulou
- 1st Psychiatric Clinic, Papageorgiou General Hospital, Aristotle University of Thessaloniki, 56403 Thessaloniki, Greece; (V.-A.N.); (V.H.)
| | - Vasiliki Holeva
- 1st Psychiatric Clinic, Papageorgiou General Hospital, Aristotle University of Thessaloniki, 56403 Thessaloniki, Greece; (V.-A.N.); (V.H.)
| | - Maria Papadopoulou
- 4th Department of Pediatrics, Papageorgiou General Hospital, Aristotle University of Thessaloniki, 56403 Thessaloniki, Greece; (M.P.); (A.E.)
| | - Athanasios Evangeliou
- 4th Department of Pediatrics, Papageorgiou General Hospital, Aristotle University of Thessaloniki, 56403 Thessaloniki, Greece; (M.P.); (A.E.)
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Fas BA, Maiani E, Sora V, Kumar M, Mashkoor M, Lambrughi M, Tiberti M, Papaleo E. The conformational and mutational landscape of the ubiquitin-like marker for autophagosome formation in cancer. Autophagy 2021; 17:2818-2841. [PMID: 33302793 PMCID: PMC8525936 DOI: 10.1080/15548627.2020.1847443] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 10/28/2020] [Accepted: 11/03/2020] [Indexed: 02/06/2023] Open
Abstract
Macroautophagy/autophagy is a cellular process to recycle damaged cellular components, and its modulation can be exploited for disease treatments. A key autophagy player is the ubiquitin-like protein MAP1LC3B/LC3B. Mutations and changes in MAP1LC3B expression occur in cancer samples. However, the investigation of the effects of these mutations on MAP1LC3B protein structure is still missing. Despite many LC3B structures that have been solved, a comprehensive study, including dynamics, has not yet been undertaken. To address this knowledge gap, we assessed nine physical models for biomolecular simulations for their capabilities to describe the structural ensemble of MAP1LC3B. With the resulting MAP1LC3B structural ensembles, we characterized the impact of 26 missense mutations from pan-cancer studies with different approaches, and we experimentally validated our prediction for six variants using cellular assays. Our findings shed light on damaging or neutral mutations in MAP1LC3B, providing an atlas of its modifications in cancer. In particular, P32Q mutation was found detrimental for protein stability with a propensity to aggregation. In a broader context, our framework can be applied to assess the pathogenicity of protein mutations or to prioritize variants for experimental studies, allowing to comprehensively account for different aspects that mutational events alter in terms of protein structure and function.Abbreviations: ATG: autophagy-related; Cα: alpha carbon; CG: coarse-grained; CHARMM: Chemistry at Harvard macromolecular mechanics; CONAN: contact analysis; FUNDC1: FUN14 domain containing 1; FYCO1: FYVE and coiled-coil domain containing 1; GABARAP: GABA type A receptor-associated protein; GROMACS: Groningen machine for chemical simulations; HP: hydrophobic pocket; LIR: LC3 interacting region; MAP1LC3B/LC3B microtubule associated protein 1 light chain 3 B; MD: molecular dynamics; OPTN: optineurin; OSF: open software foundation; PE: phosphatidylethanolamine, PLEKHM1: pleckstrin homology domain-containing family M 1; PSN: protein structure network; PTM: post-translational modification; SA: structural alphabet; SLiM: short linear motif; SQSTM1/p62: sequestosome 1; WT: wild-type.
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Affiliation(s)
- Burcu Aykac Fas
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Emiliano Maiani
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Valentina Sora
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Mukesh Kumar
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Maliha Mashkoor
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Matteo Lambrughi
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Matteo Tiberti
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Elena Papaleo
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
- Translational Disease Systems Biology, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research University of Copenhagen, Copenhagen, Denmark
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Wang Y, Veglia G, Zhong D, Gao J. Activation mechanism of Drosophila cryptochrome through an allosteric switch. SCIENCE ADVANCES 2021; 7:7/25/eabg3815. [PMID: 34144991 PMCID: PMC8213227 DOI: 10.1126/sciadv.abg3815] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 05/05/2021] [Indexed: 06/12/2023]
Abstract
Cryptochromes are signaling proteins activated by photoexcitation of the flavin adenine dinucleotide (FAD) cofactor. Although extensive research has been performed, the mechanism for this allosteric process is still unknown. We constructed three computational models, corresponding to different redox states of the FAD cofactor in Drosophila cryptochrome (dCRY). Analyses of the dynamics trajectories reveal that the activation process occurs in the semiquinone state FAD-●, resulting from excited-state electron transfer. The Arg381-Asp410 salt bridge acts as an allosteric switch, regulated by the change in the redox state of FAD. In turn, Asp410 forms new hydrogen bonds, connecting allosteric networks of the amino-terminal and carboxyl-terminal domains initially separated in the resting state. The expansion to a global dynamic network leads to enhanced protein fluctuations, an increase in the radius of gyration, and the expulsion of the carboxyl-terminal tail. These structural features are in accord with mutations and spectroscopic experiments.
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Affiliation(s)
- Yingjie Wang
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Gianluigi Veglia
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA.
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Dongping Zhong
- Departments of Physics and Chemistry, The Ohio State University, Columbus, OH 43210, USA.
| | - Jiali Gao
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA.
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518132, China
- Beijing University Shenzhen Graduate School, Shenzhen 518055, China
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10
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Konagurthu AS, Subramanian R, Allison L, Abramson D, Stuckey PJ, Garcia de la Banda M, Lesk AM. Universal Architectural Concepts Underlying Protein Folding Patterns. Front Mol Biosci 2021; 7:612920. [PMID: 33996891 PMCID: PMC8120156 DOI: 10.3389/fmolb.2020.612920] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 12/16/2020] [Indexed: 11/17/2022] Open
Abstract
What is the architectural “basis set” of the observed universe of protein structures? Using information-theoretic inference, we answer this question with a dictionary of 1,493 substructures—called concepts—typically at a subdomain level, based on an unbiased subset of known protein structures. Each concept represents a topologically conserved assembly of helices and strands that make contact. Any protein structure can be dissected into instances of concepts from this dictionary. We dissected the Protein Data Bank and completely inventoried all the concept instances. This yields many insights, including correlations between concepts and catalytic activities or binding sites, useful for rational drug design; local amino-acid sequence–structure correlations, useful for ab initio structure prediction methods; and information supporting the recognition and exploration of evolutionary relationships, useful for structural studies. An interactive site, Proçodic, at http://lcb.infotech.monash.edu.au/prosodic (click), provides access to and navigation of the entire dictionary of concepts and their usages, and all associated information. This report is part of a continuing programme with the goal of elucidating fundamental principles of protein architecture, in the spirit of the work of Cyrus Chothia.
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Affiliation(s)
- Arun S Konagurthu
- Department of Data Science and Artificial Intelligence, Faculty of Information Technology, Monash University, Clayton, VIC, Australia
| | - Ramanan Subramanian
- Department of Data Science and Artificial Intelligence, Faculty of Information Technology, Monash University, Clayton, VIC, Australia
| | - Lloyd Allison
- Department of Data Science and Artificial Intelligence, Faculty of Information Technology, Monash University, Clayton, VIC, Australia
| | - David Abramson
- Research Computing Center, University of Queensland, Brisbane, QLD, Australia
| | - Peter J Stuckey
- Department of Data Science and Artificial Intelligence, Faculty of Information Technology, Monash University, Clayton, VIC, Australia.,School of Computing and Information Systems, University of Melbourne, Melbourne, VIC, Australia
| | - Maria Garcia de la Banda
- Department of Data Science and Artificial Intelligence, Faculty of Information Technology, Monash University, Clayton, VIC, Australia
| | - Arthur M Lesk
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, United States.,MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
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Kondra S, Sarkar T, Raghavan V, Xu W. Development of a TSR-Based Method for Protein 3-D Structural Comparison With Its Applications to Protein Classification and Motif Discovery. Front Chem 2021; 8:602291. [PMID: 33520934 PMCID: PMC7838567 DOI: 10.3389/fchem.2020.602291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 12/14/2020] [Indexed: 11/24/2022] Open
Abstract
Development of protein 3-D structural comparison methods is important in understanding protein functions. At the same time, developing such a method is very challenging. In the last 40 years, ever since the development of the first automated structural method, ~200 papers were published using different representations of structures. The existing methods can be divided into five categories: sequence-, distance-, secondary structure-, geometry-based, and network-based structural comparisons. Each has its uniqueness, but also limitations. We have developed a novel method where the 3-D structure of a protein is modeled using the concept of Triangular Spatial Relationship (TSR), where triangles are constructed with the Cα atoms of a protein as vertices. Every triangle is represented using an integer, which we denote as “key,” A key is computed using the length, angle, and vertex labels based on a rule-based formula, which ensures assignment of the same key to identical TSRs across proteins. A structure is thereby represented by a vector of integers. Our method is able to accurately quantify similarity of structure or substructure by matching numbers of identical keys between two proteins. The uniqueness of our method includes: (i) a unique way to represent structures to avoid performing structural superimposition; (ii) use of triangles to represent substructures as it is the simplest primitive to capture shape; (iii) complex structure comparison is achieved by matching integers corresponding to multiple TSRs. Every substructure of one protein is compared to every other substructure in a different protein. The method is used in the studies of proteases and kinases because they play essential roles in cell signaling, and a majority of these constitute drug targets. The new motifs or substructures we identified specifically for proteases and kinases provide a deeper insight into their structural relations. Furthermore, the method provides a unique way to study protein conformational changes. In addition, the results from CATH and SCOP data sets clearly demonstrate that our method can distinguish alpha helices from beta pleated sheets and vice versa. Our method has the potential to be developed into a powerful tool for efficient structure-BLAST search and comparison, just as BLAST is for sequence search and alignment.
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Affiliation(s)
- Sarika Kondra
- The Center for Advanced Computer Studies, University of Louisiana at Lafayette, Lafayette, LA, United States
| | - Titli Sarkar
- The Center for Advanced Computer Studies, University of Louisiana at Lafayette, Lafayette, LA, United States
| | - Vijay Raghavan
- The Center for Advanced Computer Studies, University of Louisiana at Lafayette, Lafayette, LA, United States
| | - Wu Xu
- Department of Chemistry, University of Louisiana at Lafayette, Lafayette, LA, United States
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12
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Dubey V, Bozorg B, Wüstner D, Khandelia H. Cholesterol binding to the sterol-sensing region of Niemann Pick C1 protein confines dynamics of its N-terminal domain. PLoS Comput Biol 2020; 16:e1007554. [PMID: 33021976 PMCID: PMC7537887 DOI: 10.1371/journal.pcbi.1007554] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 07/02/2020] [Indexed: 12/12/2022] Open
Abstract
Lysosomal accumulation of cholesterol is a hallmark of Niemann Pick type C (NPC) disease caused by mutations primarily in the lysosomal membrane protein NPC1. NPC1 contains a transmembrane sterol-sensing domain (SSD), which is supposed to regulate protein activity upon cholesterol binding, but the mechanisms underlying this process are poorly understood. Using atomistic simulations, we show that in the absence of cholesterol in the SSD, the luminal domains of NPC1 are highly dynamic, resulting in the disengagement of the NTD from the rest of the protein. The disengaged NPC1 adopts a flexed conformation that approaches the lipid bilayer, and could represent a conformational state primed to receive a sterol molecule from the soluble lysosomal cholesterol carrier NPC2. The binding of cholesterol to the SSD of NPC1 allosterically suppresses the conformational dynamics of the luminal domains resulting in an upright NTD conformation. The presence of an additional 20% cholesterol in the membrane has negligible impact on this process. The additional presence of an NTD-bound cholesterol suppresses the flexing of the NTD. We propose that cholesterol acts as an allosteric effector, and the modulation of NTD dynamics by the SSD-bound cholesterol constitutes an allosteric feedback mechanism in NPC1 that controls cholesterol abundance in the lysosomal membrane. Cholesterol is absorbed from LDL particles in esterified form, and is broken down to free cholesterol in the lysosomes of cells, from where cholesterol must be transported to other cellular compartments such as the plasma membrane. The Niemann Pick type C (NPC) diseases arise from deficient cholesterol transport and result from mutations in the cholesterol transport protein NPC1. Using computer simulations, we show that cholesterol, when bound to one part of NPC1, can control the structural transitions of an 8-nm distant, different part of NPC1 protein called the N-terminal domain (NTD). Such long-range control of protein conformations (allostery), controls a wide range of cellular functions mediated by proteins. Fundamental molecular insights into the function of the NPC1 protein can potentially lead to better pharmaceutical interventions for the NPC diseases.
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Affiliation(s)
- Vikas Dubey
- PhyLife Physical Life Sciences, Department of Physics Chemistry, and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
- Department of Physics Chemistry, and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Behruz Bozorg
- PhyLife Physical Life Sciences, Department of Physics Chemistry, and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
- Department of Physics Chemistry, and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Daniel Wüstner
- PhyLife Physical Life Sciences, Department of Physics Chemistry, and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Himanshu Khandelia
- PhyLife Physical Life Sciences, Department of Physics Chemistry, and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
- Department of Physics Chemistry, and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
- MEMPHYS: Center for Biomembrane Physics, Odense M, Denmark
- * E-mail:
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13
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Wheatley P, Gupta S, Pandini A, Chen Y, Petzold CJ, Ralston CY, Blair DF, Khan S. Allosteric Priming of E. coli CheY by the Flagellar Motor Protein FliM. Biophys J 2020; 119:1108-1122. [PMID: 32891187 DOI: 10.1016/j.bpj.2020.08.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 07/22/2020] [Accepted: 08/10/2020] [Indexed: 02/07/2023] Open
Abstract
Phosphorylation of Escherichia coli CheY protein transduces chemoreceptor stimulation to a highly cooperative flagellar motor response. CheY binds to the N-terminal peptide of the FliM motor protein (FliMN). Constitutively active D13K-Y106W CheY has been an important tool for motor physiology. The crystal structures of CheY and CheY ⋅ FliMN with and without D13K-Y106W have shown FliMN-bound CheY contains features of both active and inactive states. We used molecular dynamics (MD) simulations to characterize the CheY conformational landscape accessed by FliMN and D13K-Y106W. Mutual information measures identified the central features of the long-range CheY allosteric network between D57 phosphorylation site and the FliMN interface, namely the closure of the α4-β4 hinge and inward rotation of Y- or W106 with W58. We used hydroxy-radical foot printing with mass spectroscopy (XFMS) to track the solvent accessibility of these and other side chains. The solution XFMS oxidation rate correlated with the solvent-accessible area of the crystal structures. The protection of allosteric relay side chains reported by XFMS confirmed the intermediate conformation of the native CheY ⋅ FliMN complex, the inactive state of free D13K-Y106W CheY, and the MD-based network architecture. We extended the MD analysis to determine temporal coupling and energetics during activation. Coupled aromatic residue rotation was a graded rather than a binary switch, with Y- or W106 side-chain burial correlated with increased FliMN affinity. Activation entrained CheY fold stabilization to FliMN affinity. The CheY network could be partitioned into four dynamically coordinated sectors. Residue substitutions mapped to sectors around D57 or the FliMN interface according to phenotype. FliMN increased sector size and interactions. These sectors fused between the substituted K13-W106 residues to organize a tightly packed core and novel surfaces that may bind additional sites to explain the cooperative motor response. The community maps provide a more complete description of CheY priming than proposed thus far.
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Affiliation(s)
- Paige Wheatley
- Department of Biology, University of Utah, Salt Lake City, Utah
| | - Sayan Gupta
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Alessandro Pandini
- Department of Computer Science-Synthetic Biology Theme, Brunel University London, Uxbridge, United Kingdom; Computational Cell and Molecular Biology, the Francis Crick Institute, London, United Kingdom
| | - Yan Chen
- Biological Systems and Engineering, Lawrence, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Christopher J Petzold
- Biological Systems and Engineering, Lawrence, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Corie Y Ralston
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California
| | - David F Blair
- Department of Biology, University of Utah, Salt Lake City, Utah
| | - Shahid Khan
- Computational Cell and Molecular Biology, the Francis Crick Institute, London, United Kingdom; Molecular Biology Consortium, Lawrence Berkeley National Laboratory, Berkeley, California.
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14
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Badaczewska-Dawid AE, Kolinski A, Kmiecik S. Computational reconstruction of atomistic protein structures from coarse-grained models. Comput Struct Biotechnol J 2019; 18:162-176. [PMID: 31969975 PMCID: PMC6961067 DOI: 10.1016/j.csbj.2019.12.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 12/10/2019] [Indexed: 01/02/2023] Open
Abstract
Three-dimensional protein structures, whether determined experimentally or theoretically, are often too low resolution. In this mini-review, we outline the computational methods for protein structure reconstruction from incomplete coarse-grained to all atomistic models. Typical reconstruction schemes can be divided into four major steps. Usually, the first step is reconstruction of the protein backbone chain starting from the C-alpha trace. This is followed by side-chains rebuilding based on protein backbone geometry. Subsequently, hydrogen atoms can be reconstructed. Finally, the resulting all-atom models may require structure optimization. Many methods are available to perform each of these tasks. We discuss the available tools and their potential applications in integrative modeling pipelines that can transfer coarse-grained information from computational predictions, or experiment, to all atomistic structures.
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Affiliation(s)
| | | | - Sebastian Kmiecik
- Faculty of Chemistry, Biological and Chemical Research Center, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
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15
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Macpherson JA, Theisen A, Masino L, Fets L, Driscoll PC, Encheva V, Snijders AP, Martin SR, Kleinjung J, Barran PE, Fraternali F, Anastasiou D. Functional cross-talk between allosteric effects of activating and inhibiting ligands underlies PKM2 regulation. eLife 2019; 8:e45068. [PMID: 31264961 PMCID: PMC6636998 DOI: 10.7554/elife.45068] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Accepted: 07/01/2019] [Indexed: 12/18/2022] Open
Abstract
Several enzymes can simultaneously interact with multiple intracellular metabolites, however, how the allosteric effects of distinct ligands are integrated to coordinately control enzymatic activity remains poorly understood. We addressed this question using, as a model system, the glycolytic enzyme pyruvate kinase M2 (PKM2). We show that the PKM2 activator fructose 1,6-bisphosphate (FBP) alone promotes tetramerisation and increases PKM2 activity, but addition of the inhibitor L-phenylalanine (Phe) prevents maximal activation of FBP-bound PKM2 tetramers. We developed a method, AlloHubMat, that uses eigenvalue decomposition of mutual information derived from molecular dynamics trajectories to identify residues that mediate FBP-induced allostery. Experimental mutagenesis of these residues identified PKM2 variants in which activation by FBP remains intact but cannot be attenuated by Phe. Our findings reveal residues involved in FBP-induced allostery that enable the integration of allosteric input from Phe and provide a paradigm for the coordinate regulation of enzymatic activity by simultaneous allosteric inputs.
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Affiliation(s)
- Jamie A Macpherson
- Cancer Metabolism LaboratoryThe Francis Crick InstituteLondonUnited Kingdom
- Randall Centre for Cell and Molecular BiophysicsKing’s College LondonLondonUnited Kingdom
| | - Alina Theisen
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, School of ChemistryUniversity of ManchesterManchesterUnited Kingdom
| | - Laura Masino
- Structural Biology Science Technology PlatformThe Francis Crick InstituteLondonUnited Kingdom
| | - Louise Fets
- Cancer Metabolism LaboratoryThe Francis Crick InstituteLondonUnited Kingdom
| | - Paul C Driscoll
- Metabolomics Science Technology PlatformThe Francis Crick InstituteLondonUnited Kingdom
| | - Vesela Encheva
- Proteomics Science Technology PlatformThe Francis Crick InstituteLondonUnited Kingdom
| | - Ambrosius P Snijders
- Proteomics Science Technology PlatformThe Francis Crick InstituteLondonUnited Kingdom
| | - Stephen R Martin
- Structural Biology Science Technology PlatformThe Francis Crick InstituteLondonUnited Kingdom
| | - Jens Kleinjung
- Computational Biology Science Technology PlatformThe Francis Crick InstituteLondonUnited Kingdom
| | - Perdita E Barran
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, School of ChemistryUniversity of ManchesterManchesterUnited Kingdom
| | - Franca Fraternali
- Randall Centre for Cell and Molecular BiophysicsKing’s College LondonLondonUnited Kingdom
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16
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Conformational coupling by trans-phosphorylation in calcium calmodulin dependent kinase II. PLoS Comput Biol 2019; 15:e1006796. [PMID: 31150387 PMCID: PMC6576796 DOI: 10.1371/journal.pcbi.1006796] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 06/17/2019] [Accepted: 03/28/2019] [Indexed: 12/16/2022] Open
Abstract
The calcium calmodulin-dependent protein kinase II (CaMKII) is a dodecameric holoenzyme important for encoding memory. Its activation, triggered by binding of calcium-calmodulin, persists autonomously after calmodulin dissociation. One (receiver) kinase captures and subsequently phosphorylates the regulatory domain peptide of a donor kinase forming a chained dimer as the first stage of autonomous activation. Protein dynamics simulations examined the conformational changes triggered by dimer formation and phosphorylation, aimed to provide a molecular rationale for human mutations that result in learning disabilities. Ensembles generated from X-ray crystal structures were characterized by network centrality and community analysis. Mutual information related collective motions to local fragment dynamics encoded with a structural alphabet. Implicit solvent tCONCOORD conformational ensembles revealed the dynamic architecture of inactive kinase domains was co-opted in the activated dimer but the network hub shifted from the nucleotide binding cleft to the captured peptide. Explicit solvent molecular dynamics (MD) showed nucleotide and substrate binding determinants formed coupled nodes in long-range signal relays between regulatory peptides in the dimer. Strain in the extended captured peptide was balanced by reduced flexibility of the receiver kinase C-lobe core. The relays were organized around a hydrophobic patch between the captured peptide and a key binding helix. The human mutations aligned along the relays. Thus, these mutations could disrupt the allosteric network alternatively, or in addition, to altered binding affinities. Non-binding protein sectors distant from the binding sites mediated the allosteric signalling; providing possible targets for inhibitor design. Phosphorylation of the peptide modulated the dielectric of its binding pocket to strengthen the patch, non-binding sectors, domain interface and temporal correlations between parallel relays. These results provide the molecular details underlying the reported positive kinase cooperativity to enrich the discussion on how autonomous activation by phosphorylation leads to long-term behavioural effects. Protein kinases play central roles in intracellular signalling. Auto-phosphorylation by bound nucleotide typically precedes phosphate transfer to multiple substrates. Protein conformational changes are central to kinase function, altering binding affinities to change cellular location and shunt from one signal pathway to another. In the brain, the multi-subunit kinase, CaMKII is activated by calcium-calmodulin upon calcium jumps produced by synaptic stimulation. Auto-transphosphorylation of a regulatory peptide enables the kinase to remain activated and mediate long-term behavioural effects after return to basal calcium levels. A database of mutated residues responsible for these effects is difficult to reconcile solely with impaired nucleotide or substrate binding. Therefore, we have computationally generated interaction networks to map the conformational plasticity of the kinase domains where most mutations localize. The network generated from the atomic structure of a phosphorylated dimer resolves protein sectors based on their collective motions. The sectors link nucleotide and substrate binding sites in self-reinforcing relays between regulatory peptides. The self-reinforcement is strengthened by phosphorylation consistent with the reported positive cooperativity of kinase activity with calcium-calmodulin concentration. The network gives a better match with the mutations and, in addition, reveals target sites for drug development.
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17
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Tubiana L, Jurásek M, Coluzza I. Implementing efficient concerted rotations using Mathematica and C code ⋆. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2018; 41:87. [PMID: 30022359 DOI: 10.1140/epje/i2018-11694-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 06/28/2018] [Indexed: 06/08/2023]
Abstract
In this article we demonstrate a general and efficient metaprogramming implementation of concerted rotations using Mathematica. Concerted rotations allow the movement of a fixed portion of a polymer backbone with fixed bending angles, like a protein, while maintaining the correct geometry of the backbone and the initial and final points of the portion fixed. Our implementation uses Mathematica to generate a C code which is then wrapped in a library by a Python script. The user can modify the Mathematica notebook to generate a set of concerted rotations suited for a particular backbone geometry, without having to write the C code himself. The resulting code is highly optimized, performing on the order of thousands of operations per second.
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Affiliation(s)
- Luca Tubiana
- Computational Physics Department, University of Vienna, Sensengasse 8/10, 1090, Vienna, Austria.
| | - Miroslav Jurásek
- Faculty of Science, Masaryk University, Kotlářská 2, 602 00, Brno, Czech Republic
- CEITEC - Central European Institute of Technology, Kamenice 5, 625 00, Brno, Czech Republic
| | - Ivan Coluzza
- CIC biomaGUNE Parque Cientfico y Tecnolgico de Gipuzkoa, Paseo Miramn 182, 20014, Donostia / San Sebastin, Gipuzkoa, Spain
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18
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SAFlex: A structural alphabet extension to integrate protein structural flexibility and missing data information. PLoS One 2018; 13:e0198854. [PMID: 29975698 PMCID: PMC6033379 DOI: 10.1371/journal.pone.0198854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 05/25/2018] [Indexed: 11/19/2022] Open
Abstract
In this paper, we describe SAFlex (Structural Alphabet Flexibility), an extension of an existing structural alphabet (HMM-SA), to better explore increasing protein three dimensional structure information by encoding conformations of proteins in case of missing residues or uncertainties. An SA aims to reduce three dimensional conformations of proteins as well as their analysis and comparison complexity by simplifying any conformation in a series of structural letters. Our methodology presents several novelties. Firstly, it can account for the encoding uncertainty by providing a wide range of encoding options: the maximum a posteriori, the marginal posterior distribution, and the effective number of letters at each given position. Secondly, our new algorithm deals with the missing data in the protein structure files (concerning more than 75% of the proteins from the Protein Data Bank) in a rigorous probabilistic framework. Thirdly, SAFlex is able to encode and to build a consensus encoding from different replicates of a single protein such as several homomer chains. This allows localizing structural differences between different chains and detecting structural variability, which is essential for protein flexibility identification. These improvements are illustrated on different proteins, such as the crystal structure of an eukaryotic small heat shock protein. They are promising to explore increasing protein redundancy data and obtain useful quantification of their flexibility.
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19
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Fealey ME, Horn B, Coffman C, Miller R, Lin AY, Thompson AR, Schramel J, Groth E, Hinderliter A, Cembran A, Thomas DD. Dynamics of Dystrophin's Actin-Binding Domain. Biophys J 2018; 115:445-454. [PMID: 30007583 DOI: 10.1016/j.bpj.2018.05.039] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 05/25/2018] [Accepted: 05/31/2018] [Indexed: 01/30/2023] Open
Abstract
We have used pulsed electron paramagnetic resonance, calorimetry, and molecular dynamics simulations to examine the structural mechanism of binding for dystrophin's N-terminal actin-binding domain (ABD1) and compare it to utrophin's ABD1. Like other members of the spectrin superfamily, dystrophin's ABD1 consists of two calponin-homology (CH) domains, CH1 and CH2. Several mutations within dystrophin's ABD1 are associated with the development of severe degenerative muscle disorders Duchenne and Becker muscular dystrophies, highlighting the importance of understanding its structural biology. To investigate structural changes within dystrophin ABD1 upon binding to actin, we labeled the protein with spin probes and measured changes in inter-CH domain distance using double-electron electron resonance. Previous studies on the homologous protein utrophin showed that actin binding induces a complete structural opening of the CH domains, resulting in a highly ordered ABD1-actin complex. In this study, double-electron electron resonance shows that dystrophin ABD1 also undergoes a conformational opening upon binding F-actin, but this change is less complete and significantly more structurally disordered than observed for utrophin. Using molecular dynamics simulations, we identified a hinge in the linker region between the two CH domains that grants conformational flexibility to ABD1. The conformational dynamics of both dystrophin's and utrophin's ABD1 showed that compact conformations driven by hydrophobic interactions are preferred and that extended conformations are energetically accessible through a flat free-energy surface. Considering that the binding free energy of ABD1 to actin is on the order of 6-7 kcal/mole, our data are compatible with a mechanism in which binding to actin is largely dictated by specific interactions with CH1, but fine tuning of the binding affinity is achieved by the overlap between conformational ensembles of ABD1 free and bound to actin.
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Affiliation(s)
- Michael E Fealey
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, Minnesota
| | - Benjamin Horn
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, Minnesota
| | - Christian Coffman
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, Minnesota
| | - Robert Miller
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, Minnesota
| | - Ava Y Lin
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, Minnesota
| | - Andrew R Thompson
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, Minnesota
| | - Justine Schramel
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, Minnesota
| | - Erin Groth
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, Minnesota
| | - Anne Hinderliter
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, Minnesota
| | - Alessandro Cembran
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, Minnesota
| | - David D Thomas
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, Minnesota.
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20
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Hashem S, Tiberti M, Fornili A. Allosteric modulation of cardiac myosin dynamics by omecamtiv mecarbil. PLoS Comput Biol 2017; 13:e1005826. [PMID: 29108014 PMCID: PMC5690683 DOI: 10.1371/journal.pcbi.1005826] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 11/16/2017] [Accepted: 10/16/2017] [Indexed: 01/10/2023] Open
Abstract
New promising avenues for the pharmacological treatment of skeletal and heart muscle diseases rely on direct sarcomeric modulators, which are molecules that can directly bind to sarcomeric proteins and either inhibit or enhance their activity. A recent breakthrough has been the discovery of the myosin activator omecamtiv mecarbil (OM), which has been shown to increase the power output of the cardiac muscle and is currently in clinical trials for the treatment of heart failure. While the overall effect of OM on the mechano-chemical cycle of myosin is to increase the fraction of myosin molecules in the sarcomere that are strongly bound to actin, the molecular basis of its action is still not completely clear. We present here a Molecular Dynamics study of the motor domain of human cardiac myosin bound to OM, where the effects of the drug on the dynamical properties of the protein are investigated for the first time with atomistic resolution. We found that OM has a double effect on myosin dynamics, inducing a) an increased coupling of the motions of the converter and lever arm subdomains to the rest of the protein and b) a rewiring of the network of dynamic correlations, which produces preferential communication pathways between the OM binding site and distant functional regions. The location of the residues responsible for these effects suggests possible strategies for the future development of improved drugs and the targeting of specific cardiomyopathy-related mutations.
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Affiliation(s)
- Shaima Hashem
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Matteo Tiberti
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Arianna Fornili
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
- The Thomas Young Centre for Theory and Simulation of Materials, London, United Kingdom
- * E-mail:
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21
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Allosteric regulation of metabolism in cancer: endogenous mechanisms and considerations for drug design. Curr Opin Biotechnol 2017; 48:102-110. [PMID: 28431259 DOI: 10.1016/j.copbio.2017.03.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 03/24/2017] [Indexed: 01/21/2023]
Abstract
Alterations in metabolic processes have been linked to various diseases, including cancer. Although gene expression can dictate long-term metabolic adaptation, many metabolic changes found in cancer are associated with altered allosteric properties of the underlying enzymes. Small molecule-protein interactions and intracellular signalling converge to orchestrate these allosteric mechanisms, which, emerging evidence suggests, constitute a promising therapeutic avenue. In this review we focus on glucose and energy metabolism to illustrate the role of allostery in cancer physiology and we discuss approaches to streamline the process of targeting aberrant allosteric pathways with small molecules.
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22
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Pandini A, Morcos F, Khan S. The Gearbox of the Bacterial Flagellar Motor Switch. Structure 2016; 24:1209-20. [PMID: 27345932 PMCID: PMC4938800 DOI: 10.1016/j.str.2016.05.012] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 04/26/2016] [Accepted: 05/23/2016] [Indexed: 12/11/2022]
Abstract
Switching of flagellar motor rotation sense dictates bacterial chemotaxis. Multi-subunit FliM-FliG rotor rings couple signal protein binding in FliM with reversal of a distant FliG C-terminal (FliGC) helix involved in stator contacts. Subunit dynamics were examined in conformer ensembles generated by molecular simulations from the X-ray structures. Principal component analysis extracted collective motions. Interfacial loop immobilization by complex formation coupled elastic fluctuations of the FliM middle (FliMM) and FliG middle (FliGM) domains. Coevolved mutations captured interfacial dynamics as well as contacts. FliGM rotation was amplified via two central hinges to the FliGC helix. Intrinsic flexibility, reported by the FliGMC ensembles, reconciled conformers with opposite FliGC helix orientations. FliG domain stacking deformed the inter-domain linker and reduced flexibility; but conformational changes were not triggered by engineered linker deletions that cause a rotation-locked phenotype. These facts suggest that binary rotation states arise from conformational selection by stacking interactions. Switch complex exploits differential subunit stiffness for mechanical amplification Distinct rotor protein X-ray structures generate overlapping conformer ensembles Stacking constraints on a flexible helix linker could select diverse rotation states Non-contact elastic couplings at the subunit interface in the complex have coevolved
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Affiliation(s)
- Alessandro Pandini
- Department of Computer Science and Synthetic Biology Theme, Brunel University London, Uxbridge UB8 3PH, UK; Computational Cell and Molecular Biology, The Francis Crick Institute, London NW1 1AT, UK
| | - Faruck Morcos
- Department of Biological Sciences, University of Texas at Dallas, Richardson, TX 75080, USA
| | - Shahid Khan
- Molecular Biology Consortium, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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23
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Pandini A, Kleinjung J, Taylor WR, Junge W, Khan S. The Phylogenetic Signature Underlying ATP Synthase c-Ring Compliance. Biophys J 2016; 109:975-87. [PMID: 26331255 PMCID: PMC4564677 DOI: 10.1016/j.bpj.2015.07.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 06/20/2015] [Accepted: 07/09/2015] [Indexed: 12/28/2022] Open
Abstract
The proton-driven ATP synthase (FOF1) is comprised of two rotary, stepping motors (FO and F1) coupled by an elastic power transmission. The elastic compliance resides in the rotor module that includes the membrane-embedded FO c-ring. Proton transport by FO is firmly coupled to the rotation of the c-ring relative to other FO subunits (ab2). It drives ATP synthesis. We used a computational method to investigate the contribution of the c-ring to the total elastic compliance. We performed principal component analysis of conformational ensembles built using distance constraints from the bovine mitochondrial c-ring x-ray structure. Angular rotary twist, the dominant ring motion, was estimated to show that the c-ring accounted in part for the measured compliance. Ring rotation was entrained to rotation of the external helix within each hairpin-shaped c-subunit in the ring. Ensembles of monomer and dimers extracted from complete c-rings showed that the coupling between collective ring and the individual subunit motions was independent of the size of the c-ring, which varies between organisms. Molecular determinants were identified by covariance analysis of residue coevolution and structural-alphabet-based local dynamics correlations. The residue coevolution gave a readout of subunit architecture. The dynamic couplings revealed that the hinge for both ring and subunit helix rotations was constructed from the proton-binding site and the adjacent glycine motif (IB-GGGG) in the midmembrane plane. IB-GGGG motifs were linked by long-range couplings across the ring, while intrasubunit couplings connected the motif to the conserved cytoplasmic loop and adjacent segments. The correlation with principal collective motions shows that the couplings underlie both ring rotary and bending motions. Noncontact couplings between IB-GGGG motifs matched the coevolution signal as well as contact couplings. The residue coevolution reflects the physiological importance of the dynamics that may link proton transfer to ring compliance.
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Affiliation(s)
- Alessandro Pandini
- Department of Computer Science and Synthetic Biology Theme, Brunel University London, Uxbridge, United Kingdom
| | - Jens Kleinjung
- Mathematical Biology, The Francis Crick Institute (formerly the National Institute for Medical Research), London, United Kingdom
| | - Willie R Taylor
- Mathematical Biology, The Francis Crick Institute (formerly the National Institute for Medical Research), London, United Kingdom
| | - Wolfgang Junge
- Department of Biophysics, University of Osnabrück, Osnabrück, Germany
| | - Shahid Khan
- Molecular Biology Consortium, Lawrence Berkeley National Laboratory, Berkeley, California.
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24
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Pandini A, Fornili A. Using Local States To Drive the Sampling of Global Conformations in Proteins. J Chem Theory Comput 2016; 12:1368-79. [PMID: 26808351 PMCID: PMC5356493 DOI: 10.1021/acs.jctc.5b00992] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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Conformational
changes associated with protein function often occur
beyond the time scale currently accessible to unbiased molecular dynamics
(MD) simulations, so that different approaches have been developed
to accelerate their sampling. Here we investigate how the knowledge
of backbone conformations preferentially adopted by protein fragments,
as contained in precalculated libraries known as structural alphabets
(SA), can be used to explore the landscape of protein conformations
in MD simulations. We find that (a) enhancing the sampling of native
local states in both metadynamics and steered MD simulations allows
the recovery of global folded states in small proteins; (b) folded
states can still be recovered when the amount of information on the
native local states is reduced by using a low-resolution version of
the SA, where states are clustered into macrostates; and (c) sequences
of SA states derived from collections of structural motifs can be
used to sample alternative conformations of preselected protein regions.
The present findings have potential impact on several applications,
ranging from protein model refinement to protein folding and design.
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Affiliation(s)
- Alessandro Pandini
- Department of Computer Science, College of Engineering, Design and Physical Sciences and Synthetic Biology Theme, Institute of Environment, Health and Societies, Brunel University London , Uxbridge UB8 3PH, United Kingdom
| | - Arianna Fornili
- School of Biological and Chemical Sciences, Queen Mary University of London , Mile End Road, London E1 4NS, United Kingdom
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25
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Craveur P, Joseph AP, Esque J, Narwani TJ, Noël F, Shinada N, Goguet M, Leonard S, Poulain P, Bertrand O, Faure G, Rebehmed J, Ghozlane A, Swapna LS, Bhaskara RM, Barnoud J, Téletchéa S, Jallu V, Cerny J, Schneider B, Etchebest C, Srinivasan N, Gelly JC, de Brevern AG. Protein flexibility in the light of structural alphabets. Front Mol Biosci 2015; 2:20. [PMID: 26075209 PMCID: PMC4445325 DOI: 10.3389/fmolb.2015.00020] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Accepted: 04/30/2015] [Indexed: 01/01/2023] Open
Abstract
Protein structures are valuable tools to understand protein function. Nonetheless, proteins are often considered as rigid macromolecules while their structures exhibit specific flexibility, which is essential to complete their functions. Analyses of protein structures and dynamics are often performed with a simplified three-state description, i.e., the classical secondary structures. More precise and complete description of protein backbone conformation can be obtained using libraries of small protein fragments that are able to approximate every part of protein structures. These libraries, called structural alphabets (SAs), have been widely used in structure analysis field, from definition of ligand binding sites to superimposition of protein structures. SAs are also well suited to analyze the dynamics of protein structures. Here, we review innovative approaches that investigate protein flexibility based on SAs description. Coupled to various sources of experimental data (e.g., B-factor) and computational methodology (e.g., Molecular Dynamic simulation), SAs turn out to be powerful tools to analyze protein dynamics, e.g., to examine allosteric mechanisms in large set of structures in complexes, to identify order/disorder transition. SAs were also shown to be quite efficient to predict protein flexibility from amino-acid sequence. Finally, in this review, we exemplify the interest of SAs for studying flexibility with different cases of proteins implicated in pathologies and diseases.
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Affiliation(s)
- Pierrick Craveur
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France
| | - Agnel P Joseph
- Rutherford Appleton Laboratory, Science and Technology Facilities Council Didcot, UK
| | - Jeremy Esque
- Institut National de la Santé et de la Recherche Médicale U964,7 UMR Centre National de la Recherche Scientifique 7104, IGBMC, Université de Strasbourg Illkirch, France
| | - Tarun J Narwani
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France
| | - Floriane Noël
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France
| | - Nicolas Shinada
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France
| | - Matthieu Goguet
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France
| | - Sylvain Leonard
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France
| | - Pierre Poulain
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France ; Ets Poulain Pointe-Noire, Congo
| | - Olivier Bertrand
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France
| | - Guilhem Faure
- National Library of Medicine, National Center for Biotechnology Information, National Institutes of Health Bethesda, MD, USA
| | - Joseph Rebehmed
- Centre National de la Recherche Scientifique UMR7590, Sorbonne Universités, Université Pierre et Marie Curie - MNHN - IRD - IUC Paris, France
| | | | - Lakshmipuram S Swapna
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore Bangalore, India ; Hospital for Sick Children, and Departments of Biochemistry and Molecular Genetics, University of Toronto Toronto, ON, Canada
| | - Ramachandra M Bhaskara
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore Bangalore, India ; Department of Theoretical Biophysics, Max Planck Institute of Biophysics Frankfurt, Germany
| | - Jonathan Barnoud
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France ; Laboratoire de Physique, École Normale Supérieure de Lyon, Université de Lyon, Centre National de la Recherche Scientifique UMR 5672 Lyon, France
| | - Stéphane Téletchéa
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France ; Faculté des Sciences et Techniques, Université de Nantes, Unité Fonctionnalité et Ingénierie des Protéines, Centre National de la Recherche Scientifique UMR 6286, Université Nantes Nantes, France
| | - Vincent Jallu
- Platelet Unit, Institut National de la Transfusion Sanguine Paris, France
| | - Jiri Cerny
- Institute of Biotechnology, The Czech Academy of Sciences Prague, Czech Republic
| | - Bohdan Schneider
- Institute of Biotechnology, The Czech Academy of Sciences Prague, Czech Republic
| | - Catherine Etchebest
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France
| | | | - Jean-Christophe Gelly
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France
| | - Alexandre G de Brevern
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France
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26
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Ma J, Wang S. Algorithms, Applications, and Challenges of Protein Structure Alignment. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2014; 94:121-75. [DOI: 10.1016/b978-0-12-800168-4.00005-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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27
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Fornili A, Pandini A, Lu HC, Fraternali F. Specialized Dynamical Properties of Promiscuous Residues Revealed by Simulated Conformational Ensembles. J Chem Theory Comput 2013; 9:5127-5147. [PMID: 24250278 PMCID: PMC3827836 DOI: 10.1021/ct400486p] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2013] [Indexed: 12/13/2022]
Abstract
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The
ability to interact with different partners is one of the most
important features in proteins. Proteins that bind a large number
of partners (hubs) have been often associated with intrinsic disorder.
However, many examples exist of hubs with an ordered structure, and
evidence of a general mechanism promoting promiscuity in ordered proteins
is still elusive. An intriguing hypothesis is that promiscuous binding
sites have specific dynamical properties, distinct from the rest of
the interface and pre-existing in the protein isolated state. Here,
we present the first comprehensive study of the intrinsic dynamics
of promiscuous residues in a large protein data set. Different computational
methods, from coarse-grained elastic models to geometry-based sampling
methods and to full-atom Molecular Dynamics simulations, were used
to generate conformational ensembles for the isolated proteins. The
flexibility and dynamic correlations of interface residues with a
different degree of binding promiscuity were calculated and compared
considering side chain and backbone motions, the latter both on a
local and on a global scale. The study revealed that (a) promiscuous
residues tend to be more flexible than nonpromiscuous ones, (b) this
additional flexibility has a higher degree of organization, and (c)
evolutionary conservation and binding promiscuity have opposite effects
on intrinsic dynamics. Findings on simulated ensembles were also validated
on ensembles of experimental structures extracted from the Protein
Data Bank (PDB). Additionally, the low occurrence of single nucleotide
polymorphisms observed for promiscuous residues indicated a tendency
to preserve binding diversity at these positions. A case study on
two ubiquitin-like proteins exemplifies how binding promiscuity in
evolutionary related proteins can be modulated by the fine-tuning
of the interface dynamics. The interplay between promiscuity and flexibility
highlighted here can inspire new directions in protein–protein
interaction prediction and design methods.
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Affiliation(s)
- Arianna Fornili
- Randall Division of Cell and Molecular Biophysics, King's College London , New Hunt's House, London SE1 1UL, United Kingdom
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28
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MacDonald JT, Kelley LA, Freemont PS. Validating a Coarse-Grained Potential Energy Function through Protein Loop Modelling. PLoS One 2013; 8:e65770. [PMID: 23824634 PMCID: PMC3688807 DOI: 10.1371/journal.pone.0065770] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Accepted: 04/26/2013] [Indexed: 12/02/2022] Open
Abstract
Coarse-grained (CG) methods for sampling protein conformational space have the potential to increase computational efficiency by reducing the degrees of freedom. The gain in computational efficiency of CG methods often comes at the expense of non-protein like local conformational features. This could cause problems when transitioning to full atom models in a hierarchical framework. Here, a CG potential energy function was validated by applying it to the problem of loop prediction. A novel method to sample the conformational space of backbone atoms was benchmarked using a standard test set consisting of 351 distinct loops. This method used a sequence-independent CG potential energy function representing the protein using -carbon positions only and sampling conformations with a Monte Carlo simulated annealing based protocol. Backbone atoms were added using a method previously described and then gradient minimised in the Rosetta force field. Despite the CG potential energy function being sequence-independent, the method performed similarly to methods that explicitly use either fragments of known protein backbones with similar sequences or residue-specific /-maps to restrict the search space. The method was also able to predict with sub-Angstrom accuracy two out of seven loops from recently solved crystal structures of proteins with low sequence and structure similarity to previously deposited structures in the PDB. The ability to sample realistic loop conformations directly from a potential energy function enables the incorporation of additional geometric restraints and the use of more advanced sampling methods in a way that is not possible to do easily with fragment replacement methods and also enable multi-scale simulations for protein design and protein structure prediction. These restraints could be derived from experimental data or could be design restraints in the case of computational protein design. C++ source code is available for download from http://www.sbg.bio.ic.ac.uk/phyre2/PD2/.
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Affiliation(s)
- James T. MacDonald
- Division of Molecular Biosciences, Imperial College London, London, United Kingdom
- * E-mail:
| | - Lawrence A. Kelley
- Division of Molecular Biosciences, Imperial College London, London, United Kingdom
| | - Paul S. Freemont
- Division of Molecular Biosciences, Imperial College London, London, United Kingdom
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29
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Pandini A, Fornili A, Fraternali F, Kleinjung J. GSATools: analysis of allosteric communication and functional local motions using a structural alphabet. ACTA ACUST UNITED AC 2013; 29:2053-5. [PMID: 23740748 PMCID: PMC3722520 DOI: 10.1093/bioinformatics/btt326] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Motivation: GSATools is a free software package to analyze conformational ensembles and to detect functional motions in proteins by means of a structural alphabet. The software integrates with the widely used GROMACS simulation package and can generate a range of graphical outputs. Three applications can be supported: (i) investigation of the conformational variability of local structures; (ii) detection of allosteric communication; and (iii) identification of local regions that are critical for global functional motions. These analyses provide insights into the dynamics of proteins and allow for targeted design of functional mutants in theoretical and experimental studies. Availability: The C source code of the GSATools, along with a set of pre-compiled binaries, is freely available under GNU General Public License from http://mathbio.nimr.mrc.ac.uk/wiki/GSATools. Contact:alessandro.pandini@kcl.ac.uk or jkleinj@nimr.mrc.ac.uk Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Alessandro Pandini
- Randall Division of Cell and Molecular Biophysics, King's College London, London, UK.
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30
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Moore BL, Kelley LA, Barber J, Murray JW, MacDonald JT. High-quality protein backbone reconstruction from alpha carbons using Gaussian mixture models. J Comput Chem 2013; 34:1881-9. [PMID: 23703289 DOI: 10.1002/jcc.23330] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2013] [Revised: 04/01/2013] [Accepted: 04/21/2013] [Indexed: 11/08/2022]
Abstract
Coarse-grained protein structure models offer increased efficiency in structural modeling, but these must be coupled with fast and accurate methods to revert to a full-atom structure. Here, we present a novel algorithm to reconstruct mainchain models from C traces. This has been parameterized by fitting Gaussian mixture models (GMMs) to short backbone fragments centered on idealized peptide bonds. The method we have developed is statistically significantly more accurate than several competing methods, both in terms of RMSD values and dihedral angle differences. The method produced Ramachandran dihedral angle distributions that are closer to that observed in real proteins and better Phaser molecular replacement log-likelihood gains. Amino acid residue sidechain reconstruction accuracy using SCWRL4 was found to be statistically significantly correlated to backbone reconstruction accuracy. Finally, the PD2 method was found to produce significantly lower energy full-atom models using Rosetta which has implications for multiscale protein modeling using coarse-grained models. A webserver and C++ source code is freely available for noncommercial use from: http://www.sbg.bio.ic.ac.uk/phyre2/PD2_ca2main/.
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Affiliation(s)
- Benjamin L Moore
- Division of Molecular Biosciences, Imperial College, South Kensington Campus, London, United Kingdom
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31
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Hischenhuber B, Havlicek H, Todoric J, Höllrigl-Binder S, Schreiner W, Knapp B. Differential geometric analysis of alterations in MH α-helices. J Comput Chem 2013; 34:1862-79. [PMID: 23703160 PMCID: PMC3739936 DOI: 10.1002/jcc.23328] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Revised: 04/12/2013] [Accepted: 04/13/2013] [Indexed: 01/03/2023]
Abstract
Antigen presenting cells present processed peptides via their major histocompatibility (MH) complex to the T cell receptors (TRs) of T cells. If a peptide is immunogenic, a signaling cascade can be triggered within the T cell. However, the binding of different peptides and/or different TRs to MH is also known to influence the spatial arrangement of the MH α-helices which could itself be an additional level of T cell regulation. In this study, we introduce a new methodology based on differential geometric parameters to describe MH deformations in a detailed and comparable way. For this purpose, we represent MH α-helices by curves. On the basis of these curves, we calculate in a first step the curvature and torsion to describe each α-helix independently. In a second step, we calculate the distribution parameter and the conical curvature of the ruled surface to describe the relative orientation of the two α-helices. On the basis of four different test sets, we show how these differential geometric parameters can be used to describe changes in the spatial arrangement of the MH α-helices for different biological challenges. In the first test set, we illustrate on the basis of all available crystal structures for (TR)/pMH complexes how the binding of TRs influences the MH helices. In the second test set, we show a cross evaluation of different MH alleles with the same peptide and the same MH allele with different peptides. In the third test set, we present the spatial effects of different TRs on the same peptide/MH complex. In the fourth test set, we illustrate how a severe conformational change in an α-helix can be described quantitatively. Taken together, we provide a novel structural methodology to numerically describe subtle and severe alterations in MH α-helices for a broad range of applications.
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Affiliation(s)
- Birgit Hischenhuber
- Center for Medical Statistics, Informatics, and Intelligent Systems, Section for Biosimulation and Bioinformatics, Medical University of Vienna, Vienna, Austria
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32
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Baussand J, Kleinjung J. Specific Conformational States of Ras GTPase upon Effector Binding. J Chem Theory Comput 2012; 9:738-749. [PMID: 23316125 PMCID: PMC3541755 DOI: 10.1021/ct3007265] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Indexed: 12/31/2022]
Abstract
![]()
To uncover the structural and dynamical determinants
involved in
the highly specific binding of Ras GTPase to its effectors, the conformational
states of Ras in uncomplexed form and complexed to the downstream
effectors Byr2, PI3Kγ, PLCε, and RalGDS were investigated
using molecular dynamics and cross-comparison of the trajectories.
The subtle changes in the dynamics and conformations of Ras upon effector
binding require an analysis that targets local changes independent
of global motions. Using a structural alphabet, a computational procedure
is proposed to quantify local conformational changes. Positions detected
by this approach were characterized as either specific for a particular
effector, specific for an effector domain type, or as effector unspecific.
A set of nine structurally connected residues (Ras residues 5–8,
32–35, 39–42, 55–59, 73–78, and 161–165),
which link the effector binding site to the distant C-terminus, changed
dynamics upon effector binding, indicating a potential effector-unspecific
signaling route within the Ras structure. Additional conformational
changes were detected along the N-terminus of the central β-sheet.
Besides the Ras residues at the effector interface (e.g., D33, E37,
D38, and Y40), which adopt effector-specific local conformations,
the binding signal propagates from the interface to distant hot-spot
residues, in particular to Y5 and D57. The results of this study reveal
possible conformational mechanisms for the stabilization of the active
state of Ras upon downstream effector binding and for the structural
determinants responsible for effector specificity.
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Affiliation(s)
- Julie Baussand
- Division of Mathematical Biology, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, United Kingdom
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33
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Kleinjung J, Scott WRP, Allison JR, van Gunsteren WF, Fraternali F. Implicit Solvation Parameters Derived from Explicit Water Forces in Large-Scale Molecular Dynamics Simulations. J Chem Theory Comput 2012. [PMID: 23180979 PMCID: PMC3503459 DOI: 10.1021/ct200390j] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Implicit solvation is a mean force approach to model
solvent forces
acting on a solute molecule. It is frequently used in molecular simulations
to reduce the computational cost of solvent treatment. In the first
instance, the free energy of solvation and the associated solvent–solute
forces can be approximated by a function of the solvent-accessible
surface area (SASA) of the solute and differentiated by an atom–specific
solvation parameter σiSASA. A procedure
for the determination of values for the σiSASA parameters through matching of explicit and implicit solvation
forces is proposed. Using the results of Molecular Dynamics simulations
of 188 topologically diverse protein structures in water and in implicit
solvent, values for the σiSASA parameters
for atom types i of the standard amino acids in the
GROMOS force field have been determined. A simplified representation
based on groups of atom types σgSASA was
obtained via partitioning of the atom–type
σiSASA distributions by dynamic programming.
Three groups of atom types with well separated parameter ranges were
obtained, and their performance in implicit versus explicit simulations
was assessed. The solvent forces are available at http://mathbio.nimr.mrc.ac.uk/wiki/Solvent_Forces.
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Affiliation(s)
- Jens Kleinjung
- Division of Mathematical Biology, MRC National Institute for Medical Research , The Ridgeway, Mill Hill, London NW7 1AA, United Kingdom
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34
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Ceselli A, Fornili SL, Righini G. Algorithms for the design of maximum hydropathic complementarity molecules. J Comput Biol 2012; 19:261-70. [PMID: 22401590 DOI: 10.1089/cmb.2011.0084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In this article, we address the problem of designing a string with optimal complementarity properties with respect to another given string according to a given criterion. The motivation comes from a drug design application, in which the complementarity between two sequences (proteins) is measured according to the values of the hydropathic coefficients associated with the sequence elements (amino acids). We present heuristic and exact optimization algorithms, and we report on some computational experiments on amino peptides taken from Semaphorin and human Interleukin-1β, which have already been investigated in the literature using heuristic algorithms. With our techniques, we proved the optimality of a known solution for Semaphorin-3A, and we discovered several other optimal and near-optimal solutions in a short computing time; we also found in fractions of a second an optimal solution for human interleukin-1β, whose complementary value is one order of magnitude better than previously known ones. The source code of a prototype C++ implementation of our algorithms is freely available for noncommercial use on the web. As a main result, we showed that in this context mathematical programming methods are more successful than heuristics, such as simulated annealing. Our algorithm unfolds its potential, especially when different measures could be used for scoring peptides, and is able to provide not only a single optimal solution, but a ranking of provable good ones; this ranking can then be used by biologists as a starting basis for further refinements, simulations, or in vitro experiments.
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Affiliation(s)
- Alberto Ceselli
- Dipartimento di Tecnologie dell'Informazione, Università degli Studi di Milano, Crema, Italy.
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Pandini A, Fornili A, Fraternali F, Kleinjung J. Detection of allosteric signal transmission by information-theoretic analysis of protein dynamics. FASEB J 2012; 26:868-81. [PMID: 22071506 PMCID: PMC3290435 DOI: 10.1096/fj.11-190868] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Allostery offers a highly specific way to modulate protein function. Therefore, understanding this mechanism is of increasing interest for protein science and drug discovery. However, allosteric signal transmission is difficult to detect experimentally and to model because it is often mediated by local structural changes propagating along multiple pathways. To address this, we developed a method to identify communication pathways by an information-theoretical analysis of molecular dynamics simulations. Signal propagation was described as information exchange through a network of correlated local motions, modeled as transitions between canonical states of protein fragments. The method was used to describe allostery in two-component regulatory systems. In particular, the transmission from the allosteric site to the signaling surface of the receiver domain NtrC was shown to be mediated by a layer of hub residues. The location of hubs preferentially connected to the allosteric site was found in close agreement with key residues experimentally identified as involved in the signal transmission. The comparison with the networks of the homologues CheY and FixJ highlighted similarities in their dynamics. In particular, we showed that a preorganized network of fragment connections between the allosteric and functional sites exists already in the inactive state of all three proteins.
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Affiliation(s)
- Alessandro Pandini
- Division of Mathematical Biology, Medical Research Council National Institute for Medical Research, London, UK; ,Randall Division of Cell and Molecular Biophysics, King's College London, London, UK; and , Correspondence: Division of Mathematical Biology, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, NW7 1AA London, UK. E-mail: A.P., ; J.K.,
| | - Arianna Fornili
- Randall Division of Cell and Molecular Biophysics, King's College London, London, UK; and
| | - Franca Fraternali
- Randall Division of Cell and Molecular Biophysics, King's College London, London, UK; and ,The Thomas Young Centre for Theory and Simulation of Materials, London, UK
| | - Jens Kleinjung
- Division of Mathematical Biology, Medical Research Council National Institute for Medical Research, London, UK; , Correspondence: Division of Mathematical Biology, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, NW7 1AA London, UK. E-mail: A.P., ; J.K.,
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Kifer I, Nussinov R, Wolfson HJ. GOSSIP: a method for fast and accurate global alignment of protein structures. Bioinformatics 2011; 27:925-32. [PMID: 21296751 PMCID: PMC3065682 DOI: 10.1093/bioinformatics/btr044] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2010] [Revised: 12/04/2010] [Accepted: 01/21/2011] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION The database of known protein structures (PDB) is increasing rapidly. This results in a growing need for methods that can cope with the vast amount of structural data. To analyze the accumulating data, it is important to have a fast tool for identifying similar structures and clustering them by structural resemblance. Several excellent tools have been developed for the comparison of protein structures. These usually address the task of local structure alignment, an important yet computationally intensive problem due to its complexity. It is difficult to use such tools for comparing a large number of structures to each other at a reasonable time. RESULTS Here we present GOSSIP, a novel method for a global all-against-all alignment of any set of protein structures. The method detects similarities between structures down to a certain cutoff (a parameter of the program), hence allowing it to detect similar structures at a much higher speed than local structure alignment methods. GOSSIP compares many structures in times which are several orders of magnitude faster than well-known available structure alignment servers, and it is also faster than a database scanning method. We evaluate GOSSIP both on a dataset of short structural fragments and on two large sequence-diverse structural benchmarks. Our conclusions are that for a threshold of 0.6 and above, the speed of GOSSIP is obtained with no compromise of the accuracy of the alignments or of the number of detected global similarities. AVAILABILITY A server, as well as an executable for download, are available at http://bioinfo3d.cs.tau.ac.il/gossip/.
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Affiliation(s)
- I Kifer
- School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, Sackler Institute of Molecular Medicine, Tel Aviv University, Tel Aviv, Israel
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Vanhee P, Verschueren E, Baeten L, Stricher F, Serrano L, Rousseau F, Schymkowitz J. BriX: a database of protein building blocks for structural analysis, modeling and design. Nucleic Acids Res 2010; 39:D435-42. [PMID: 20972210 PMCID: PMC3013806 DOI: 10.1093/nar/gkq972] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
High-resolution structures of proteins remain the most valuable source for understanding their function in the cell and provide leads for drug design. Since the availability of sufficient protein structures to tackle complex problems such as modeling backbone moves or docking remains a problem, alternative approaches using small, recurrent protein fragments have been employed. Here we present two databases that provide a vast resource for implementing such fragment-based strategies. The BriX database contains fragments from over 7000 non-homologous proteins from the Astral collection, segmented in lengths from 4 to 14 residues and clustered according to structural similarity, summing up to a content of 2 million fragments per length. To overcome the lack of loops classified in BriX, we constructed the Loop BriX database of non-regular structure elements, clustered according to end-to-end distance between the regular residues flanking the loop. Both databases are available online (http://brix.crg.es) and can be accessed through a user-friendly web-interface. For high-throughput queries a web-based API is provided, as well as full database downloads. In addition, two exciting applications are provided as online services: (i) user-submitted structures can be covered on the fly with BriX classes, representing putative structural variation throughout the protein and (ii) gaps or low-confidence regions in these structures can be bridged with matching fragments.
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Affiliation(s)
- Peter Vanhee
- VIB SWITCH Laboratory, Flanders Institute of Biotechnology, Free University of Brussels, Pleinlaan 2, 1050 Brussels, Belgium
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