AMINO ACIDS
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2020
·Vol. 52
·期 5
·831-839
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IF 3.063
Zhao Dongxin,Lu Kui,Liu Guangbin,Zhu Hanjing,Ma Li,Qi Jianzhao,Yuan Libo
BRCA2 is an important tumor suppressor gene that plays a critical role in preserving the stability of cellular genetic information, participating in DNA repair by engaging in binding interactions with RAD51 proteins. However, the lack of structural data on BRCA2 and RAD51 makes the study of their interaction mechanism still a great challenge. We characterize the structure of the BRC8–RAD51 complex using ZDOCK protein docking software and identify the potential non-conserved active site of BRC8 via virtual alanine scanning, utilizing the obtained results to synthesize BRC8, its six analogous peptides (BRC8-1 to BRC8-6), and critical peptide fragment of RAD51 (RAD51(231–260)) by Fmoc solid-phase synthesis. The analogous peptides are found to exhibit a secondary structure significantly different from that of BRC8 by circular dichroism spectroscopy, which indicates that mutation sites determined by computer-aided simulation correspond to key amino acid residues substantially affecting polypeptide structure. On the other hand, the secondary structure of RAD51(231–260) was also considerably influenced by its interaction with BRC8 and analogs, e.g., the fraction of the α-helical structure in RAD51(231–260) increased to 23.6, 15.1, and 13.5% upon interaction with BRC8-1, BRC8-3, and BRC8-6, respectively. The results show that the properties of C-terminal amino acid residues significantly influence peptide–peptide interactions, in agreement with the results of virtual alanine scanning. Therefore, computer-aided simulation was confirmed to be a technique that is useful for narrowing down the range of sites responsible for interactions between peptides or proteins, and provides new inspirations for the design of peptides with strong interactions.
研究领域:
生物化学
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分子生物学
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结构生物学
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SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
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2019
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IF 2.931
Dongxin Zhao,Kui Lu,Guangbin Liu,Juhong Hou,Libo Yuan,Li Ma,Jie Liu,Juan He
Polypeptides with finger-like structures can often intercalate into the grooves of DNA , thereby affecting DNA repair or activating gene transcription, both of which are crucial for the regulation of physiological processes. Their conserved amino acid sequence and simple structure have provided useful elements for the design and assembly of functional molecules. In this paper, using the C 2 H 2 zinc finger domain and the PEP-FOLD3 online simulation platform 11 polypeptides containing 22 amino acid residues were designed. In addition, the CD spectroscopy was combined with the fluorescence spectroscopy to study the polypeptide structures and their interaction with DNA. Results showed that although addition of zinc ions affected the polypeptide structure, particularly of the polypeptides A4, B1, and B3, zinc ion was not an essential factor for increasing polypeptide-DNA interactions. Our study revealed an increase in the interaction strength between mutated polypeptides and DNA, suggesting that mutations disrupt polypeptide structure, and polypeptides interact with DNA by groove and electrostatic binding. Mutations at the 12th and 15th amino acid residues had the greatest effect. The stronger binding between A2 or B2 and DNA indicates that the polypeptide has a spatial structure that can stably interact with DNA. The structure and characteristics of these polypeptide domains can provide information for the design and development of new polypeptide functional molecules, which could have potential significance and applications. However, this information also suggests that there are many challenges facing polypeptide design due to the synergistic effects between the side chains of amino acid residues.
研究领域:
生物化学
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分子生物学
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ANALYTICAL CHEMISTRY
·
2023
·
IF 7.4
Jia Kong,Jinyao Hu,Jia Li,Jiaxing Zhang,Yuhe Shen,Tianli Yue,Xihui Shen,Yuefei Wang,Zhonghong Li,Yinqiang Xia
Reconstruction of the miniaturized peptide to mimic the tailored functions of protein has been attractive but challenging. Herein, initialized from the crystal structure of redox-sensitive green fluorescent protein-2 (roGFP2), we propose a practical approach to construct the roGFP2 mimetic peptide by rethreading the aromatic residues adjacent to the chromophore fragment. By fine-tuning the residues of peptides, a mini tetrapeptide (Cys-Phe-Phe-His) was designed, which can act as a hydrogen peroxide sensor using its ratiometric fluorescence. The roGFP2 mimetic tetrapeptide is biocompatible and photostable and has competitive fluorescent properties with roGFP2 by the virtue of its assembly induced emissions. We expand the ratiometric tetrapeptide for sensing hydrogen peroxide in acidic chambers. The results provide a promising approach for the artificial design of miniaturized peptides with the desired function.
研究领域:
生物化学
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分子生物学
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ANALYTICAL CHEMISTRY
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2021
·
IF 6.986
Zhen Song,Yihui Ma,Min Chen,Adriano Ambrosi,Caifeng Ding,Xiliang Luo
Biofouling caused by the accumulation of biomolecules on sensing surfaces is one of the major problems and challenges to realize the practical application of electrochemical biosensors, and an effective way to counter this problem is the construction of antifouling biosensors. Herein, an antifouling electrochemical biosensor was constructed based on electropolymerized polyaniline (PANI) nanowires and newly designed peptides for the detection of the COVID-19 N-gene. The inverted Y-shaped peptides were designed with excellent antifouling properties and two anchoring branches, and their antifouling performances against proteins and complex biological media were investigated using different approaches. Based on the biotin–streptavidin affinity system, biotin-labeled probes specific to the N-gene (nucleocapsid phosphoprotein) of COVID-19 were immobilized onto the peptide-coated PANI nanowires, forming a highly sensitive and antifouling electrochemical sensing interface for the detection of COVID-19 nucleic acid. The antifouling genosensor demonstrated a wide linear range (10–14 to 10–9 M) and an exceptional low detection limit (3.5 fM). The remarkable performance of the genosensor derives from the high peak current of PANI, which is chosen as the sensing signal, and the extraordinary antifouling properties of designed peptides, which guarantee accurate detection in complex systems. These crucial features represent essential elements for future rapid and decentralized clinical testing.
研究领域:
生物医学工程
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分子生物学
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高影响因子
Acta Pharmaceutica Sinica B
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2025
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IF 14.6
Sanjiang Du,Hanlin Wang,Feiyang Geng,Zongxu Zhang,Chenghao Liu,Weiyue Lu,Gang Wei
Transdermal drug delivery relies heavily on the skin permeability of therapeutic agents. In order to develop a peptide-based delivery strategy for promoting transdermal absorption, the key physicochemical factors influencing skin permeability are first identified through cell-penetrating peptides (CPPs) screening and computational simulation. Penetratin exhibits the most outstanding permeability and safety among CPPs from various origins, and positive surface patch area emerges as the key property correlated with skin permeability of the peptides. Based on these findings, a precise model to predict skin permeability of the peptides is established, leading to the computational redesign of penetratin’s amino acid sequence. The transdermal delivery efficiency of optimized penetratin derivative (589WP) is significantly improved in vitro compared with wild-type penetratin and visualized through in vivo imaging. Furthermore, the anti-metabolic drug floxuridine (FUdR) is covalently conjugated with 589WP via ester linkage, leading to accelerated FUdR release due to esterase degradation. Subsequently, this conjugate is formulated into an anhydrous gel, which significantly inhibits melanoma growth with topical application, outperforming a higher dose of free FUdR without observed skin irritancy or toxicity. The peptide prediction and design approaches established herein hold great potential for advancing transdermal drug delivery.
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International Journal of Peptide Research and Therapeutics
·
2024
·Vol. 30
·期 5
·1-13
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IF 2
Liu Ziyang,Wei Yuping,Zhang Man,Zhu Xingyan,Liu Kun
Angiotensin-converting enzyme-2 (ACE2) is a important cell surface receptor of SARS-CoV-2 S protein. The initial stage of SARS-COV-2 cell infection involves the binding of the S protein to ACE2. Hence, this work presents an innovative strategy to designing ACE2-based peptide inhibitors by considering the surface property and morphology of the S protein RBD. The aim is to develop a short peptide inhibitor that can effectively inhibit S protein-ACE2 interaction Through computational analysis and molecular simulation, the surface properties and morphology of S protein receptor-binding structural domain (RBD) were investigated, while the key residues of ACE2 ligand-binding structural domain (LBD) were identified based on their contributions and non-covalent interactions. Then, peptide inhibitors, consisting of ACE2 key residues, were developed by fitting to the surface characteristics and topographical features of the S protein RBD. Molecular simulation showed that two novel short peptides, IEPFF (I5) and WIEPFF (W6) had high affinity for S protein RBD but a low affinity for the cell membrane. Cellular adsorption studies demonstrated that both I5 and W6 effectively blocked ACE2-S protein binding without significant cytotoxicity. Flow cytometry analysis revealed that both I5 and W6 effectively inhibited S protein binding to the ACE2, resulting in a significant reduction (75 and 79%, respectively) in fluorescence intensity after 30 min of incubation at a concentration of 200 μM. Both I5 and W6 were excellent potential anti SARS-COV-2 drugs. This work provides an innovative perspective for the development of functional peptides for the prevention and management of SARS-COV-2.
研究领域:
生物化学
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分子生物学
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病毒学
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药学
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计算生物学
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高影响因子
Journal of Chemical Information and Modeling
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2024
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IF 5.6
Xinpei Wang,Xu Chen,Zhidong Chen,Wanting Xu,Ruizhi Lai,Xiaohui Qiu,Zekai Zeng,Chenglin Wang,Zhe Wang,Junqing Wang
Despite recent success in the computational approaches of cyclic peptide design, current studies face challenges in modeling noncanonical amino acids and nonstandard cyclizations due to limited data. To address this challenge, we developed an integrated framework for the tailored design of stapled peptides (SPs) targeting the bromodomain of CREBBP (CREBBP-BrD). We introduce a powerful combination of anchored stapling and hierarchical molecular dynamics to design and optimize SPs by employing the MultiScale integrative conformational dynamics assessment (MSICDA) strategy, which involves an initial virtual screening of over 1.5 million SPs, followed by comprehensive simulations amounting to 154.54 μs across 5418 of instances. The MSICDA method provides a detailed and holistic stability view of peptide–protein interactions, systematically isolated optimized peptides and identified two leading candidates, DA#430 and DA#99409, characterized by their enhanced stability, optimized binding, and high affinity toward the CREBBP-BrD. In cell-free assays, DA#430 and DA#99409 exhibited 2- to 12-fold greater potency than inhibitor SGC-CBP30. Cell studies revealed higher peptide selectivity for cancerous versus normal cells over small molecules. DA#430 combined with (+)-JQ-1 showed promising synergistic effects. Our approach enables the identification of peptides with optimized binding, high affinity, and enhanced stability, leading to more precise and effective cyclic peptide design, thereby establishing MSICDA as a generalizable and transformative tool for uncovering novel targeted drug development in various therapeutic areas.
研究领域:
药学科学
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计算化学
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分子生物学
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癌症研究
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药物发现
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高影响因子
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