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Su J, Zhou P. Musical protein: Mapping the time sequence of music onto the spatial architecture of proteins. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2024; 252:108233. [PMID: 38781810 DOI: 10.1016/j.cmpb.2024.108233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 05/13/2024] [Accepted: 05/16/2024] [Indexed: 05/25/2024]
Abstract
BACKGROUND AND OBJECTIVE Music, the ubiquitous language across human cultures, is traditionally considered as a form of art but has been linked to biomolecules in recent years. However, previous efforts have only been addressed on sonification of nucleic acids and proteins to produce so-called life music, the soundscape from the basic building blocks of life. In this study, we attempted to, for the first time, conduct a reverse operation of this process, i.e. conversion of music to protein (CoMtP). METHODS A novel notion termed musical protein (MP) -- the protein defined by music -- was proposed and, on this basis, we described a computational strategy to map the time sequence of music onto the spatial architecture of proteins, which considered that each note in the stave of a music (target) can be simply characterized by two acoustical quantities and that each residue in the primary sequence of a protein (hit) was represented by amino acid descriptors. RESULTS A simulated annealing (SA) algorithm was applied to iteratively generate the best matched MP hit for a music target and structural bioinformatics was then used to model spatial advanced structure for the resulting MP. We also demonstrated that some small MPs derived from music segments may have potential biological functions, which, for example, can serve as antimicrobial peptides (AMPs) to inhibit clinical bacterial strains with moderate or high antibacterial potency. CONCLUSIONS This work may benefit many aspects; for example, it would open a door for the hearing-impaired persons to 'listen' music in a biological vision and could be a mean of exposing students to the concepts of biomolecules at an earlier age through the use of auditory characteristics. The CoMtP would also facilitate the rational design of proteins with biological and medicinal significance.
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Affiliation(s)
- Jun Su
- College of Music, Chengdu Normal University, No.99 Haike Road East Section, Wenjiang District, Chengdu 611130, China.
| | - Peng Zhou
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC), No.2006 Xiyuan Ave West Hi-Tech Zone, Chengdu 611731, China.
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2
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Shan Y, Chen Y, Gu H, Wang Y, Sun Y. Regulatory Basis of Adipokines Leptin and Adiponectin in Epilepsy: from Signaling Pathways to Glucose Metabolism. Neurochem Res 2023; 48:2017-2028. [PMID: 36797447 PMCID: PMC10181973 DOI: 10.1007/s11064-023-03891-2] [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: 12/21/2022] [Revised: 01/25/2023] [Accepted: 02/07/2023] [Indexed: 02/18/2023]
Abstract
Epilepsy is a common and severe neurological disorder in which impaired glucose metabolism leads to changes in neuronal excitability that slow or promote the development of epilepsy. Leptin and adiponectin are important mediators regulating glucose metabolism in the peripheral and central nervous systems. Many studies have reported a strong association between epilepsy and these two adipokines involved in multiple signaling cascades and glucose metabolism. Due to the complex regulatory mechanisms between them and various signal activation networks, their role in epilepsy involves many aspects, including the release of inflammatory mediators, oxidative damage, and neuronal apoptosis. This paper aims to summarize the signaling pathways involved in leptin and adiponectin and the regulation of glucose metabolism from the perspective of the pathogenesis of epilepsy. In particular, we discuss the dual effects of leptin in epilepsy and the relationship between antiepileptic drugs and changes in the levels of these two adipokines. Clinical practitioners may need to consider these factors in evaluating clinical drugs. Through this review, we can better understand the specific involvement of leptin and adiponectin in the pathogenesis of epilepsy, provide ideas for further exploration, and bring about practical significance for the treatment of epilepsy, especially for the development of personalized treatment according to individual metabolic characteristics.
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Affiliation(s)
- Yisi Shan
- Department of Neurology, Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Zhangjiagang, 215600, China.,Translational Medical Innovation Center, Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Zhangjiagang, 215600, China
| | - Yeting Chen
- Department of Acupuncture, Zhangjiagang Second People's Hospital, Zhangjiagang, 215600, China
| | - Haiping Gu
- Department of Neurology, Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Zhangjiagang, 215600, China
| | - Yadong Wang
- Department of Neurology, Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Zhangjiagang, 215600, China
| | - Yaming Sun
- Department of Neurology, Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Zhangjiagang, 215600, China.
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3
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Chen F, Wang Q, Mu Y, Sun S, Yuan X, Shang P, Ji B. Systematic profiling and identification of the peptide-mediated interactions between human Yes-associated protein and its partners in esophageal cancer. J Mol Recognit 2021; 35:e2947. [PMID: 34964176 DOI: 10.1002/jmr.2947] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/26/2021] [Accepted: 12/10/2021] [Indexed: 11/07/2022]
Abstract
Human Yes-associated protein (YAP) is involved in the Hippo signaling pathway and serves as a coactivator to modulate gene expression, which contains a transactivation domain (TD) responsible for binding to the downstream TEA domain family (TEAD) of transcription factors and two WW1/2 domains that recognize the proline-rich motifs (PRMs) present in a variety of upstream protein partners through peptide-mediated interactions (PMIs). The downstream YAP TD-TEAD interactions are closely associated with gastric cancer, and a number of therapeutic agents have been developed to target the interactions. In contrast, the upstream YAP WW1/2-partner interactions are thought to be involved in esophageal cancer but still remain largely unexplored. Here, we attempted to elucidate the complicated PMIs between the YAP WW1/2 domains and various PRMs of YAP-interacting proteins. A total of 106 peptide segments carrying the class I WW-binding motif [P/L]Px[Y/P] were extracted from 22 partner candidates, which are potential recognition sites of YAP WW1/2 domains. Structural and energetic analyses of the intermolecular interactions between the domains and peptides created a systematic domain-peptide binding profile, from which a number of biologically functional PMIs were identified and then substantiated in vitro using fluorescence spectroscopy assays. It is revealed that: (a) The sequence requirement for the partner recognition site binding to YAP WW1/2 domains is a decapeptide segment that contains a core PRM motif as well as two three-residue extensions from each side of the motif; the core motif and extended sections are responsible for the binding stability and recognition specificity of domain-peptide interaction, respectively. (b) There is an exquisite difference in the recognition specificity of the two domains; the LPxP and PPxP appear to more prefer WW1 than WW2, whereas the WW2 can bind more effectively to LPxY and PPxY than WW1. (c) WW2 generally exhibits a higher affinity to the panel of recognition site candidates than WW1. In addition, a number of partner peptides were found as promising recognition sites of the two domains and/or to have a good selectivity between the two domains. For example, the DVL1 peptide was determined to have moderate affinity to WW2 and strong selectivity for WW2 over WW1. Hydrogen bonds play a central role in selectivity.
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Affiliation(s)
- Fei Chen
- Department of Gastroenterology, the Second Affiliated Hospital of Shandong First Medical University, Taian, China
| | - Qifei Wang
- Department of Thoracic Medicine, the Second Affiliated Hospital of Shandong First Medical University, Taian, China
| | - Yushu Mu
- Department of Thoracic Medicine, the Second Affiliated Hospital of Shandong First Medical University, Taian, China
| | - Shibin Sun
- Department of Thoracic Medicine, the Second Affiliated Hospital of Shandong First Medical University, Taian, China
| | - Xulong Yuan
- Department of Thoracic Medicine, the Second Affiliated Hospital of Shandong First Medical University, Taian, China
| | - Pan Shang
- Department of Thoracic Medicine, the Second Affiliated Hospital of Shandong First Medical University, Taian, China
| | - Bo Ji
- Department of Thoracic Medicine, the Second Affiliated Hospital of Shandong First Medical University, Taian, China
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4
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Musi CA, Castaldo AM, Valsecchi AE, Cimini S, Morello N, Pizzo R, Renieri A, Meloni I, Bonati M, Giustetto M, Borsello T. JNK signaling provides a novel therapeutic target for Rett syndrome. BMC Biol 2021; 19:256. [PMID: 34911542 PMCID: PMC8675514 DOI: 10.1186/s12915-021-01190-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 11/11/2021] [Indexed: 11/24/2022] Open
Abstract
Background Rett syndrome (RTT) is a monogenic X-linked neurodevelopmental disorder characterized by loss-of-function mutations in the MECP2 gene, which lead to structural and functional changes in synapse communication, and impairments of neural activity at the basis of cognitive deficits that progress from an early age. While the restoration of MECP2 in animal models has been shown to rescue some RTT symptoms, gene therapy intervention presents potential side effects, and with gene- and RNA-editing approaches still far from clinical application, strategies focusing on signaling pathways downstream of MeCP2 may provide alternatives for the development of more effective therapies in vivo. Here, we investigate the role of the c-Jun N-terminal kinase (JNK) stress pathway in the pathogenesis of RTT using different animal and cell models and evaluate JNK inhibition as a potential therapeutic approach. Results We discovered that the c-Jun N-terminal kinase (JNK) stress pathway is activated in Mecp2-knockout, Mecp2-heterozygous mice, and in human MECP2-mutated iPSC neurons. The specific JNK inhibitor, D-JNKI1, promotes recovery of body weight and locomotor impairments in two mouse models of RTT and rescues their dendritic spine alterations. Mecp2-knockout presents intermittent crises of apnea/hypopnea, one of the most invalidating RTT pathological symptoms, and D-JNKI1 powerfully reduces this breathing dysfunction. Importantly, we discovered that also neurons derived from hiPSC-MECP2 mut show JNK activation, high-phosphorylated c-Jun levels, and cell death, which is not observed in the isogenic control wt allele hiPSCs. Treatment with D-JNKI1 inhibits neuronal death induced by MECP2 mutation in hiPSCs mut neurons. Conclusions As a summary, we found altered JNK signaling in models of RTT and suggest that D-JNKI1 treatment prevents clinical symptoms, with coherent results at the cellular, molecular, and functional levels. This is the first proof of concept that JNK plays a key role in RTT and its specific inhibition offers a new and potential therapeutic tool to tackle RTT. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01190-2.
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Affiliation(s)
- Clara Alice Musi
- Department of Pharmacological and Biomolecular Sciences, Milan University, Via Balzaretti 9, 20133, Milan, Italy.,Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri-IRCCS, Via Mario Negri 2, 20156, Milan, Italy
| | - Anna Maria Castaldo
- Department of Pharmacological and Biomolecular Sciences, Milan University, Via Balzaretti 9, 20133, Milan, Italy
| | | | - Sara Cimini
- Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri-IRCCS, Via Mario Negri 2, 20156, Milan, Italy
| | - Noemi Morello
- Department of Neuroscience and National Institute of Neuroscience, University of Turin, Turin, Italy
| | - Riccardo Pizzo
- Department of Neuroscience and National Institute of Neuroscience, University of Turin, Turin, Italy
| | | | | | - Maurizio Bonati
- Department of Public Heath, Istituto di Ricerche Farmacologiche Mario Negri-IRCCS, Milan, Italy
| | - Maurizio Giustetto
- Department of Neuroscience and National Institute of Neuroscience, University of Turin, Turin, Italy
| | - Tiziana Borsello
- Department of Pharmacological and Biomolecular Sciences, Milan University, Via Balzaretti 9, 20133, Milan, Italy. .,Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri-IRCCS, Via Mario Negri 2, 20156, Milan, Italy.
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5
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Lu G, Li X, Zhang J, Xu Q. Molecular insight into the affinity, specificity and cross-reactivity of systematic hepatocellular carcinoma RALT interaction profile with human receptor tyrosine kinases. Amino Acids 2021; 53:1715-1728. [PMID: 34618235 DOI: 10.1007/s00726-021-03083-8] [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: 03/28/2021] [Accepted: 09/22/2021] [Indexed: 11/28/2022]
Abstract
The ErbB family of receptor tyrosine kinases (RTKs) contains four members: EGFR, ErbB2, ErbB3 and ErbB4; they are involved in the tumorigenesis of diverse cancers and can be inhibited natively by receptor-associated late transducer (RALT), a negative feedback regulator of ErbB signaling in human hepatocytes and hepatocellular carcinoma. Although the biological effects of RALT on EGFR kinase have been widely documented previously, the binding behavior of RALT to other ErbB/RTK kinases still remains largely unexplored. Here, the intermolecular interactions of RALT ErbB-binding region (EBR) as well as its functional sections and peptide segments with ErbBs and other human RTKs were systematically investigated at molecular and structural levels, from which we were able to identify those potential kinase targets of RALT protein, and to profile the affinity, specificity and cross-reactivity of RALT EBR domain and its sub-regions against various RTKs. It is revealed that RALT can target all the four ErbB kinases with high affinity for EGFR/ErbB2/ErbB4 and moderate affinity for ErbB3, but generally exhibits modest affinity to other RTKs, albeit few kinases such as LTK, EPHB6, MET and MUSK were also top-ranked as the unexpected targets of RALT. Peptide segments covering the key binding regions of RALT EBR domain were identified with computational alanine scanning, which were then optimized to obtain a number of designed peptide mutants with improved selectivity between different top-ranked RTKs.
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Affiliation(s)
- Guang Lu
- Department of General Surgery, Liyang People's Hospital, Liyang, 213300, China
| | - Xiaoping Li
- Department of General Surgery, Liyang People's Hospital, Liyang, 213300, China
| | - Jun Zhang
- Department of General Surgery, Liyang People's Hospital, Liyang, 213300, China
| | - Qinghua Xu
- Department of General Surgery, Liyang People's Hospital, Liyang, 213300, China.
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Qiao Z, Wang S. Directed Molecular Engineering of Mig6 Peptide Selectivity between Proto-oncogene ErbB Family Receptor Tyrosine Kinases. BIOTECHNOL BIOPROC E 2021. [DOI: 10.1007/s12257-020-0102-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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7
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Structure-Based Optimization of Therapeutic Peptide Selectivity Between Cerebrovascular Rho-1 and Rho-2 Kinase Isoforms. Int J Pept Res Ther 2020. [DOI: 10.1007/s10989-020-10032-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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8
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Yu X, Zhang A, Sun G, Li X. Molecular selectivity design of mitogen-inducible gene-derived phosphopeptides between oncogenic HER kinases. J Mol Graph Model 2020; 99:107661. [PMID: 32574989 DOI: 10.1016/j.jmgm.2020.107661] [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: 03/10/2020] [Revised: 05/23/2020] [Accepted: 05/29/2020] [Indexed: 11/28/2022]
Abstract
Mitogen-inducible gene (MIG) is a natural negative regulator of the oncogenic HER kinase signaling by binding at the activation interface of kinase domain to disrupt the kinase dimerization. In this study, we systematically examine the binding structures, dynamics and energetics of MIG region 2 to four HER kinases based on their crystal or modeled complex structures, and identify an 8-mer phosphopeptide segment pYpY from the core strand sequence of MIG region 2 as the binding hotspot of MIG protein to HER kinases. We demonstrate that the small pYpY phosphopeptide can partially restore the binding affinity of full-length MIG protein, but exhibit a moderate selectivity over different HER kinases (S = 2.3-fold). In addition, the two phosphotyrosine residues pTyr394 and pTyr395 play an essential role in MIG-HER binding; dephosphorylation of them would fully eliminate the binding capability. A machine evolution algorithm is used to optimize the wild-type pYpY phosphopeptide, aiming to simultaneously improve affinity for these kinases and to maximize the affinity gap between different kinases. Consequently, a population is computationally evolved as selective phosphopeptide candidates; the dissociation constants of four representatives with HER kinases are systematically determined using binding affinity analysis, from which their selectivity is derived. The designed pYpYp3 phosphopeptide possesses a high selectivity over different HER kinases (S = 4.8-fold) and satisfactory affinity profile to these kinase (KD = 140-1000 μM). Structural analysis observes that the global binding modes of pYpYp3 to different kinases are roughly consistent, but its local conformation may vary considerably, thus conferring specificity to the phosphopeptide.
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Affiliation(s)
- Xiuli Yu
- Department of Radiotherapy, Yidu Central Hospital Affiliated to Weifang Medical University, Weifang, 262500, China
| | - Aiying Zhang
- Orthopaedic Trauma, Yidu Central Hospital Affiliated to Weifang Medical University, Weifang, 262500, China
| | - Guoyu Sun
- Intensive Care Unit, Yidu Central Hospital Affiliated to Weifang Medical University, Weifang, 262500, China
| | - Xuebo Li
- Department of Radiotherapy, Yidu Central Hospital Affiliated to Weifang Medical University, Weifang, 262500, China.
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9
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JNK signaling activation in the Ube3a maternal deficient mouse model: its specific inhibition prevents post-synaptic protein-enriched fraction alterations and cognitive deficits in Angelman Syndrome model. Neurobiol Dis 2020; 140:104812. [PMID: 32087286 DOI: 10.1016/j.nbd.2020.104812] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 01/30/2020] [Accepted: 02/18/2020] [Indexed: 12/22/2022] Open
Abstract
Deficiency of the E3 ubiquitin ligase UBE3A leads to the neurodevelopmental disorder Angelman syndrome (AS), while higher levels are linked to autism spectrum disorder. The mechanisms underlying the downstream effects of UBE3A loss or gain of function in these disorders are still not well understood, and treatments are still lacking. Here, using the Ube3a maternal loss (Ube3am-/p+) mouse model, we report an important JNK signaling activation in the hippocampus, cortex and cerebellum correlating with the onset of behavioral defects and biochemical marker alterations in the post-synaptic element, suggesting important spine pathology. JNK activation occurs at 7 and persists up till 23 weeks in Ube3am-/p+ mice in two different cellular compartments: the nucleus and the post-synaptic protein-enriched fraction. To study JNK's role in Ube3am-/p+ pathology we treated mice with the specific JNK inhibitor peptide, D-JNKI1, from 7 to 23 weeks of age. Preventing JNK action in vivo restores the post-synaptic protein-enriched fraction defects and the cognitive impairment in these mice. Our results imply a critical role of UBE3A-JNK signaling in the pathogenesis of UBE3A-related disorders. In particular, it was clear that JNK is a key player in regulating AS synaptic alterations and the correlated cognitive impairments, in fact, its specific inhibition tackles Ube3am-/p+ pathology. This study sheds new light on the neuronal functions of UBE3A and offers new prospects for understanding the pathogenesis of UBE3A-related disorders.
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Gu Z, Yan T, Yan F. Rational design and improvement of the dimerization-disrupting peptide selectivity between ROCK-I and ROCK-II kinase isoforms in cerebrovascular diseases. J Mol Recognit 2020; 33:e2835. [PMID: 31995258 DOI: 10.1002/jmr.2835] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 12/17/2019] [Accepted: 12/25/2019] [Indexed: 02/05/2023]
Abstract
Human rho-associated coiled-coil forming kinases (ROCKs) ROCK-I and ROCK-II have been documented as attractive therapeutic targets for cerebrovascular diseases. Although ROCK-I and ROCK-II share a high degree of structural conservation and are both present in classic rho/ROCK signaling pathway, their downstream substrates and pathological functions may be quite different. Selective targeting of the two kinase isoforms with traditional small-molecule inhibitors is a great challenge due to their surprisingly high homology in kinase domain (~90%) and the full identity in kinase active site (100%). Here, instead of developing small-molecule drugs to selectively target the adenosine triphosphate (ATP) site of two isoforms, we attempt to design peptide agents to selectively disrupt the homo-dimerization event of ROCK kinases through their dimerization domains which have a relatively low conservation (~60%). Three helical peptides H1, H2, and H3 are split from the kinase dimerization domain, from which the isolated H2 peptide is found to have the best capability to rebind at the dimerization interface. A simulated annealing (SA) iteration method is used to improve the H2 peptide selectivity between ROCK-I and ROCK-II. The method accepts moderate degradation in peptide affinity in order to maximize the affinity difference between peptide binding to the two isoforms. Consequently, hundreds of parallel SA runs yielded six promising peptide candidates with ROCK-I over ROCK-II (I over II [IoII]) calculated selectivity and four promising peptide candidates with ROCK-II over ROCK-I (II over I [IIoI]) calculated selectivity. Subsequent anisotropy assays confirm that the selectivity values range between 13.2-fold and 83.9-fold for IoII peptides, and between 5.8-fold and 21.2-fold for IIoI peptides, which are considerably increased relative to wild-type H2 peptide (2.6-fold for IoII and 2.0-fold for IIoI). The molecular origin of the designed peptide selectivity is also analyzed at structural level; it is revealed that the peptide residues can be classified into conserved, non-conserved, and others, in which the non-conserved residues play a crucial role in defining peptide selectivity, while conserved residues confer stability to kinase-peptide binding.
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Affiliation(s)
- Zhengtian Gu
- Department of Neurology, Affiliated Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China
| | - Tingting Yan
- Department of Pediatrics, Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, China
| | - Fuling Yan
- Department of Neurology, Affiliated Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China
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Li Z, Miao Q, Yan F, Meng Y, Zhou P. Machine Learning in Quantitative Protein–peptide Affinity Prediction: Implications for Therapeutic Peptide Design. Curr Drug Metab 2019; 20:170-176. [DOI: 10.2174/1389200219666181012151944] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 11/07/2017] [Accepted: 08/20/2018] [Indexed: 01/03/2023]
Abstract
Background:Protein–peptide recognition plays an essential role in the orchestration and regulation of cell signaling networks, which is estimated to be responsible for up to 40% of biological interaction events in the human interactome and has recently been recognized as a new and attractive druggable target for drug development and disease intervention.Methods:We present a systematic review on the application of machine learning techniques in the quantitative modeling and prediction of protein–peptide binding affinity, particularly focusing on its implications for therapeutic peptide design. We also briefly introduce the physical quantities used to characterize protein–peptide affinity and attempt to extend the content of generalized machine learning methods.Results:Existing issues and future perspective on the statistical modeling and regression prediction of protein– peptide binding affinity are discussed.Conclusion:There is still a long way to go before establishment of general, reliable and efficient machine leaningbased protein–peptide affinity predictors.
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Affiliation(s)
- Zhongyan Li
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC), Chengdu 610054, China
| | - Qingqing Miao
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC), Chengdu 610054, China
| | - Fugang Yan
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC), Chengdu 610054, China
| | - Yang Meng
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC), Chengdu 610054, China
| | - Peng Zhou
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC), Chengdu 610054, China
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Han CL, Zhao XM, Liu YP, Wang KL, Chen N, Hu W, Zhang JG, Ge M, Meng FG. Gene Expression Profiling of Two Epilepsy Models Reveals the ECM/Integrin signaling Pathway is Involved in Epiletogenesis. Neuroscience 2018; 396:187-199. [PMID: 30452975 DOI: 10.1016/j.neuroscience.2018.10.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 10/09/2018] [Accepted: 10/10/2018] [Indexed: 12/11/2022]
Abstract
The molecular mechanisms underlying the development of epilepsy, i.e., epileptogenesis, are due to altered expression of a series of genes. Global expression profiling of temporal lobe epilepsy is confounded by a number of factors, including the variability among animal species, animal models, and tissue sampling time-points. In this study, we pooled two microarray datasets of the most used pilocarpine and kainic acid epilepsy models from the Gene Expression Omnibus database. A total of 567 known and novel genes were commonly differentially expressed across the two models. Pathway analyses demonstrated that the dysregulated genes were involved in 46 pathways. Real-time PCR and western blot analysis confirmed the activation of extracellular matrix (ECM)/integrin signaling pathways. Moreover, targeting ECM/integrin signaling inhibits astrocyte activation and promotes neuron injury in the hippocampus of epileptic mice. This study may provide a "gene/pathway database" that with further investigation can determine the mechanisms underlining epileptogenesis and the possible targets for neuron protection in the hippocampus after status epilepticus.
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Affiliation(s)
- Chun-Lei Han
- Department of Functional Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing 100050, China; Beijing Key Laboratory of Neuromodulation, Beijing Municipal Science and Technology Commission, Beijing 100050, China
| | - Xue-Min Zhao
- Department of Functional Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing 100050, China; Beijing Key Laboratory of Neuromodulation, Beijing Municipal Science and Technology Commission, Beijing 100050, China
| | - Yun-Peng Liu
- Department of Functional Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing 100050, China; Beijing Key Laboratory of Neuromodulation, Beijing Municipal Science and Technology Commission, Beijing 100050, China
| | - Kai-Liang Wang
- Department of Functional Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing 100050, China; Beijing Key Laboratory of Neuromodulation, Beijing Municipal Science and Technology Commission, Beijing 100050, China
| | - Ning Chen
- Beijing Key Laboratory of Neuromodulation, Beijing Municipal Science and Technology Commission, Beijing 100050, China; Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100050, China
| | - Wei Hu
- Department of Neurology, University of Florida, FL 32607, USA
| | - Jian-Guo Zhang
- Beijing Key Laboratory of Neuromodulation, Beijing Municipal Science and Technology Commission, Beijing 100050, China; Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100050, China
| | - Ming Ge
- Department of Neurosurgery, Beijing Children's Hospital, Capital Medical University, Beijing 100045, China
| | - Fan-Gang Meng
- Department of Functional Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing 100050, China; Beijing Key Laboratory of Neuromodulation, Beijing Municipal Science and Technology Commission, Beijing 100050, China.
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13
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Deng Y, Li J. Rational Optimization of Tumor Suppressor-Derived Peptide Inhibitor Selectivity between Oncogene Tyrosine Kinases ErbB1 and ErbB2. Arch Pharm (Weinheim) 2017; 350. [PMID: 29131383 DOI: 10.1002/ardp.201700181] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 09/23/2017] [Accepted: 10/04/2017] [Indexed: 02/04/2023]
Affiliation(s)
- Yilin Deng
- Weifang People's Hospital affiliated to Weifang Medical University; Weifang; China
| | - Jian Li
- The 89th Hospital of People's Liberation Army; Weifang; China
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Zhu L, Ding X. Molecular design of Stat3-derived peptide selectivity between BET proteins Brd2 and Brd4 in ovarian cancer. J Mol Recognit 2017; 31. [PMID: 28983974 DOI: 10.1002/jmr.2679] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 09/14/2017] [Accepted: 09/14/2017] [Indexed: 12/11/2022]
Abstract
Stat3 signaling has been recognized as a potential therapeutic target of human ovarian cancer. The signaling is transducted through the peptide-medicated interaction of Stat3 with BET family members Brd2 and Brd4 -- 2 highly homologous proteins involved in differential downstream pathways. Here, we reported a successful design of peptide selectivity between the Brd2 and Brd4. The design resulted in 3 linear peptides SMSLQCXYLGVA, QSKVLTXSYWGA, and RQCNLGXLYMNY with high or moderate selectivity for Brd2 over Brd4 (S = 3.3-fold, 6.8-fold, and 4.2-fold, respectively) as compared with the native Stat3 peptide 281 HNLLRIXQFLQS292 (S = 2.5-fold). Structural analysis revealed that peptide N-terminus and hydrogen bonds play important roles in the peptide interaction stability and specificity with Brd2 and Brd4. This study would help to establish an integrated in silico-in vitro method for rational molecular design of peptide ligand selectivity between homologous protein receptors.
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Affiliation(s)
- Lixia Zhu
- Department of Gynaecology and Obstetrics, the First People's Hospital of Kunshan, Kunshan, China
| | - Xi Ding
- Department of Pharmacy, the Affiliated Hospital of Nantong University, Dongtai, China
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15
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Ni H, Zhuang Y, Chen Z, Ji W. Molecular engineering of respiratory syncytial virus immunogen for rational redesign of prophylactic peptide vaccines against pediatric viral pneumonia. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2017.1383989] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Huiping Ni
- Department of Respiration, Children’s Hospital of Soochow University, Suzhou, China
- Department of Pediatrics, The Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Yibo Zhuang
- Department of Pediatrics, The Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Zhengrong Chen
- Department of Respiration, Children’s Hospital of Soochow University, Suzhou, China
| | - Wei Ji
- Department of Respiration, Children’s Hospital of Soochow University, Suzhou, China
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16
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Zhou J, Wang YS. Rational redesign of a cation···π···π stacking at cardiovascular Fbw7–Skp1 complex interface and its application for deriving self-inhibitory peptides to disrupt the complex interaction. J Mol Model 2017; 23:296. [DOI: 10.1007/s00894-017-3456-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 09/05/2017] [Indexed: 12/19/2022]
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17
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Structure-based rational design of peptide inhibitors to disrupt the recognition and interaction between hepatitis B virus large envelope protein and human hepatocyte receptor γ2-adaptin. Med Chem Res 2017. [DOI: 10.1007/s00044-017-1981-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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18
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Yu J, Wang S, Yu J, Liu C, Xu F, Wang S, Yi Y, Yin Y. Structure-based rational design of self-inhibitory peptides to disrupt the intermolecular interaction between the troponin subunits C and I in neuropathic pain. Bioorg Chem 2017; 73:10-15. [PMID: 28525735 DOI: 10.1016/j.bioorg.2017.05.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Revised: 04/08/2017] [Accepted: 05/01/2017] [Indexed: 11/26/2022]
Abstract
The troponin (Tn) is a ternary complex consisting of three subunits TnC, TnI and TnT; molecular disruption of the Tn complex has been recognized as an attractive strategy against neuropathic pain. Here, a self-inhibitory peptide is stripped from the switch region of TnI interaction interface with TnC, which is considered as a lead molecular entity and then used to generate potential peptide disruptors of TnC-TnI interaction based on a rational molecular design protocol. The region is a helical peptide segment capped by N- and C-terminal disorders. Molecular dynamics simulation and binding free energy analysis suggests that the switch peptide can interact with TnC in a structurally and energetically independent manner. Terminal truncation of the peptide results in a number of potent TnC binders with considerably simplified structure and moderately decreased activity relative to the native switch. We also employ fluorescence polarization assays to substantiate the computational findings; it is found that the rationally designed peptides exhibit moderate or high affinity to TnC with dissociation constants KD at micromolar level.
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Affiliation(s)
- Junmin Yu
- Department of Pain Management, The Affiliated Hospital of Qingdao University, Qingdao 266003, China
| | - Shilei Wang
- Department of Anesthesiology, The Affiliated Hospital of Qingdao University, Qingdao 266003, China
| | - Junjie Yu
- Chinese Traditional Patent Medicine Dispensary, The Affiliated Hospital of Qingdao University, Qingdao 266003, China
| | - Chuansheng Liu
- Department of Pain Management, The Affiliated Hospital of Qingdao University, Qingdao 266003, China
| | - Fenghe Xu
- Department of Pain Management, The Affiliated Hospital of Qingdao University, Qingdao 266003, China
| | - Shijie Wang
- Department of Pain Management, The Affiliated Hospital of Qingdao University, Qingdao 266003, China
| | - Yusheng Yi
- Department of Pain Management, The Affiliated Hospital of Qingdao University, Qingdao 266003, China
| | - Yanwei Yin
- Department of Pain Management, The Affiliated Hospital of Qingdao University, Qingdao 266003, China.
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Xiao X, He QH, Yu LY, Wang SQ, Li Y, Yang H, Zhang AH, Ma XH, Peng YJ, Chen B. Structure-based optimization of salt-bridge network across the complex interface of PTPN4 PDZ domain with its peptide ligands in neuroglioma. Comput Biol Chem 2016; 66:63-68. [PMID: 27923202 DOI: 10.1016/j.compbiolchem.2016.11.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 11/08/2016] [Accepted: 11/28/2016] [Indexed: 11/28/2022]
Abstract
The PTP non-receptor type 4 (PTPN4) is an important regulator protein in learning, spatial memory and cerebellar synaptic plasticity; targeting the PDZ domain of PTPN4 has become as attractive therapeutic strategy for human neuroglioma. Here, we systematically examined the complex crystal structures of PTPN4 PDZ domain with its known peptide ligands; a number of charged amino acid residues were identified in these ligands and in the peptide-binding pocket of PDZ domain, which can constitute a complicated salt-bridge network across the complex interface. Molecular dynamics (MD) simulations, binding free energy calculations and continuum model analysis revealed that the electrostatic effect plays a predominant role in domain-peptide binding, while other noncovalent interactions such as hydrogen bonds and hydrophobic forces are also responsible for the binding. The computational findings were then used to guide structure-based optimization of the interfacial salt-bridge network. Consequently, five peptides were rationally designed using the high-affinity binder Cyto8-RETEV (RETEV-COOH) as template, including four single-point mutants (i.e. Cyto8-mtxe0: RETEE-COOH, Cyto8-mtxd-1: RETDV-COOH, Cyto8-mtxd-3: RDTEV-COOH and Cyto8-mtxk-4: KETEV-COOH) and one double-point mutant (i.e. Cyto8-mtxd-1k-4: KETDV-COOH). Binding assays confirmed that three (Cyto8-mtxd-1, Cyto8-mtxk-4 and Cyto8-mtxd-1k-4) out of the five designed peptides exhibit moderately or considerably increased affinity as compared to the native peptide Cyto8-RETEV.
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Affiliation(s)
- Xian Xiao
- Department of Neurosurgery, No. 422 Hospital of PLA, Zhanjiang 524005, PR China
| | - Qiang-Hua He
- Department of Neurosurgery, No. 422 Hospital of PLA, Zhanjiang 524005, PR China
| | - Li-Yan Yu
- Department of Vascular, Thyroid, and Breast Surgery, Affiliated Hospital of Guangdong Medical University, Zhanjiang 524001, PR China
| | - Song-Qing Wang
- Department of Neurosurgery, No. 422 Hospital of PLA, Zhanjiang 524005, PR China
| | - Yang Li
- Department of Neurosurgery, No. 422 Hospital of PLA, Zhanjiang 524005, PR China
| | - Hua Yang
- Department of Neurosurgery, No. 422 Hospital of PLA, Zhanjiang 524005, PR China
| | - Ai-Hua Zhang
- Department of Neurosurgery, No. 422 Hospital of PLA, Zhanjiang 524005, PR China
| | - Xiao-Hong Ma
- Department of Neurosurgery, No. 422 Hospital of PLA, Zhanjiang 524005, PR China
| | - Yu-Jie Peng
- Department of Neurosurgery, No. 422 Hospital of PLA, Zhanjiang 524005, PR China
| | - Bing Chen
- Department of Neurosurgery, Affiliated Hospital of Guangdong Medical University, Zhanjiang 524001, PR China.
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Rational derivation, extension, and cyclization of self-inhibitory peptides to target TGF-β/BMP signaling in ONFH. Amino Acids 2016; 49:283-290. [DOI: 10.1007/s00726-016-2358-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 10/31/2016] [Indexed: 12/18/2022]
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