1
|
Li X, Zhang Y, Yang Z, Zhang S, Zhang L. The Inhibition Effect of Epigallocatechin-3-Gallate on the Co-Aggregation of Amyloid-β and Human Islet Amyloid Polypeptide Revealed by Replica Exchange Molecular Dynamics Simulations. Int J Mol Sci 2024; 25:1636. [PMID: 38338914 PMCID: PMC10855639 DOI: 10.3390/ijms25031636] [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: 01/04/2024] [Revised: 01/21/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
Alzheimer's disease and Type 2 diabetes are two epidemiologically linked diseases which are closely associated with the misfolding and aggregation of amyloid proteins amyloid-β (Aβ) and human islet amyloid polypeptide (hIAPP), respectively. The co-aggregation of the two amyloid proteins is regarded as the fundamental molecular mechanism underlying their pathological association. The green tea extract epigallocatechin-3-gallate (EGCG) has been extensively demonstrated to inhibit the amyloid aggregation of Aβ and hIAPP proteins. However, its potential role in amyloid co-aggregation has not been thoroughly investigated. In this study, we employed the enhanced-sampling replica exchange molecular dynamics simulation (REMD) method to investigate the effect of EGCG on the co-aggregation of Aβ and hIAPP. We found that EGCG molecules substantially diminish the β-sheet structures within the amyloid core regions of Aβ and hIAPP in their co-aggregates. Through hydrogen-bond, π-π and cation-π interactions targeting polar and aromatic residues of Aβ and hIAPP, EGCG effectively attenuates both inter-chain and intra-chain interactions within the co-aggregates. All these findings indicated that EGCG can effectively inhibit the co-aggregation of Aβ and hIAPP. Our study expands the potential applications of EGCG as an anti-amyloidosis agent and provides therapeutic options for the pathological association of amyloid misfolding disorders.
Collapse
Affiliation(s)
- Xuhua Li
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi’an Jiaotong University, Xi’an 710049, China (Z.Y.); (S.Z.); (L.Z.)
- State Key Laboratory of Surface Physics, Department of Physics, Fudan University, 2005 Songhu Road, Shanghai 200438, China
| | - Yu Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi’an Jiaotong University, Xi’an 710049, China (Z.Y.); (S.Z.); (L.Z.)
| | - Zhiwei Yang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi’an Jiaotong University, Xi’an 710049, China (Z.Y.); (S.Z.); (L.Z.)
| | - Shengli Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi’an Jiaotong University, Xi’an 710049, China (Z.Y.); (S.Z.); (L.Z.)
| | - Lei Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi’an Jiaotong University, Xi’an 710049, China (Z.Y.); (S.Z.); (L.Z.)
| |
Collapse
|
2
|
Potok P, Kola A, Valensin D, Capdevila M, Potocki S. Copper Forms a PPII Helix-Like Structure with the Catalytic Domains of Bacterial Zinc Metalloproteases. Inorg Chem 2023; 62:18425-18439. [PMID: 37909295 PMCID: PMC10647932 DOI: 10.1021/acs.inorgchem.3c02391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 10/11/2023] [Accepted: 10/11/2023] [Indexed: 11/03/2023]
Abstract
The rapid spread of antibiotic-resistant bacteria continuously raises concerns about the future ineffectiveness of current antimicrobial treatments against infectious diseases. To address this problem, new therapeutic strategies and antimicrobial drugs with unique modes of action are urgently needed. Inhibition of metalloproteases, bacterial virulence factors, is a promising target for the development of antibacterial treatments. In this study, the interaction among Zn(II), Cu(II), and the metal-binding domains of two metalloproteases, AprA (Pseudomonas aureginosa) and CpaA (Acinetobacter baumanii), was investigated. The objective was to determine the coordination sphere of Zn(II) with a peptide model of two zinc-dependent metalloproteases. Additionally, the study explored the formation of Cu(II) complexes with the domains, as Cu(II) has been shown to inhibit metalloproteases. The third aim was to understand the role of nonbinding amino acids in stabilizing the metal complexes formed by these proteases. This work identified specific coordination patterns (HExxHxxxxxH) for both Zn(II) and Cu(II) complexes, with AprA and CpaA exhibiting a higher affinity for Cu(II) compared to Zn(II). The study also found that the CpaA domain has greater stability for both Zn(II) and Cu(II) complexes compared to AprA. The nonbinding amino acids of CpaA surrounding the metal ion contribute to the increased thermodynamic stability of the metal-peptide complex through various intramolecular interactions. These interactions can also influence the secondary structures of the peptides. The presence of certain amino acids, such as tyrosine, arginine, and glutamic acid, and their interactions contribute to the stability and, only in the case of Cu(II) complexes, the formation of a rare protein structure called a left-handed polyproline II helix (PPII), which is known to play a role in the stability and function of various proteins. These findings provide valuable insights into the coordination chemistry of bacterial metalloproteases and expand our understanding of potential mechanisms for inhibiting these enzymes.
Collapse
Affiliation(s)
- Paulina Potok
- Faculty
of Chemistry, University of Wroclaw, 50-383 Wroclaw, Poland
| | - Arian Kola
- Department
of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Daniela Valensin
- Department
of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Merce Capdevila
- Departament
de Química, Universitat Autònoma
de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Sławomir Potocki
- Faculty
of Chemistry, University of Wroclaw, 50-383 Wroclaw, Poland
| |
Collapse
|
3
|
Choudhari S, Patil SK, Rathod S. Identification of hits as anti-obesity agents against human pancreatic lipase via docking, drug-likeness, in-silico ADME(T), pharmacophore, DFT, molecular dynamics, and MM/PB(GB)SA analysis. J Biomol Struct Dyn 2023:1-23. [PMID: 37735906 DOI: 10.1080/07391102.2023.2258407] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 09/07/2023] [Indexed: 09/23/2023]
Abstract
Obesity, characterized by excessive fat accumulation, is a major health concern. Inhibition of human pancreatic lipase, an enzyme involved in fat digestion, offers a potential strategy for weight loss and obesity treatment. This study aimed to identify polyphenols capable of forming stable complexes with human pancreatic lipase to block its activity. Molecular docking, density functional theory (DFT), molecular dynamics (MD) simulations, and MMPBGBSA calculations were employed to evaluate ligand binding, stability, and energy profiles. Pharmacophore modeling was also performed to identify key structural features for effective inhibition. Virtual screening identified ZINC000015120539, ZINC000000899200, ZINC000001531702, and ZINC000013340267 as potential candidates, exhibiting favorable binding and stable interactions over 100 ns MD simulations. These findings provide insights into the inhibitory potential of selected polyphenols on human pancreatic lipase and support further experimental investigations for obesity treatment.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Sujata Choudhari
- Department of Pharmaceutical Chemistry, Sarojini College of Pharmacy, Kolhapur, MS, India
- Department of Pharmaceutics, Ashokrao Mane College of Pharmacy, Peth Vadgaon, MS, India
| | - Sachin Kumar Patil
- Department of Pharmaceutics, Ashokrao Mane College of Pharmacy, Peth Vadgaon, MS, India
| | - Sanket Rathod
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur, MS, India
| |
Collapse
|
4
|
Abstract
Multivalent proteins and nucleic acids, collectively referred to as multivalent associative biomacromolecules, provide the driving forces for the formation and compositional regulation of biomolecular condensates. Here, we review the key concepts of phase transitions of aqueous solutions of associative biomacromolecules, specifically proteins that include folded domains and intrinsically disordered regions. The phase transitions of these systems come under the rubric of coupled associative and segregative transitions. The concepts underlying these processes are presented, and their relevance to biomolecular condensates is discussed.
Collapse
Affiliation(s)
- Rohit V Pappu
- Department of Biomedical Engineering, Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Samuel R Cohen
- Department of Biomedical Engineering, Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, Missouri 63130, United States.,Center of Regenerative Medicine, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Furqan Dar
- Department of Biomedical Engineering, Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Mina Farag
- Department of Biomedical Engineering, Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Mrityunjoy Kar
- Max Planck Institute of Cell Biology and Genetics, 01307 Dresden, Germany
| |
Collapse
|
5
|
Yamada M, Kurihara Y, Koizumi M, Tsuji K, Maeda Y, Suzuki M. Understanding the Nature and Strength of Noncovalent Face‐to‐Face Arene–Fullerene Interactions. Angew Chem Int Ed Engl 2022; 61:e202212279. [DOI: 10.1002/anie.202212279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Indexed: 11/07/2022]
Affiliation(s)
- Michio Yamada
- Department of Chemistry Tokyo Gakugei University Nukuikitamachi 4-1-1, Koganei Tokyo 184-8501 Japan
| | - Yukiyo Kurihara
- Department of Chemistry Tokyo Gakugei University Nukuikitamachi 4-1-1, Koganei Tokyo 184-8501 Japan
| | - Masaaki Koizumi
- Department of Chemistry Tokyo Gakugei University Nukuikitamachi 4-1-1, Koganei Tokyo 184-8501 Japan
| | - Kasumi Tsuji
- Department of Chemistry Tokyo Gakugei University Nukuikitamachi 4-1-1, Koganei Tokyo 184-8501 Japan
| | - Yutaka Maeda
- Department of Chemistry Tokyo Gakugei University Nukuikitamachi 4-1-1, Koganei Tokyo 184-8501 Japan
| | - Mitsuaki Suzuki
- Department of Chemistry Josai University Sakado Saitama 350-0295 Japan
| |
Collapse
|
6
|
Kumar S, Venkatesha MA, Balaram P. Mechanistic Investigations on N-C α Bond Cleavages in Dibasic Peptides Containing Internal Lys and Arg Residues. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1598-1606. [PMID: 35880778 DOI: 10.1021/jasms.2c00055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The model nonapeptide AAARAAKAG* (* indicates amide) is used to explore N-Cα bond fragmentation under CID-MS conditions. Neighboring group participation and the effect of positioning of Lys and Arg residues on N-Cα bond cleavage is established using a library of synthetic peptide analogues. The importance of the Arg residue at position 4 and the i to i+3 spacing between Arg and Lys residues in determining the formation of the N-Cα bond cleaved product ions (cn) is demonstrated by a comparative MS study of positional variants in analogue peptides. The effect of shortening of the Lys side chain has been established using ornithine (Orn) and diaminobutyric acid (Dab) analogues. The involvement of the Lys residue in mediating the N-Cα bond cleavage is further probed using Nε-dimethyl and isotopically labeled 15Nα, ε lysine residues. MSn experiments reveal that the c6 ion originates from a doubly charged dehydrated b8 ion [b8-18]2+. The mechanism of this unusual fragmentation process has been probed by using position 8 analogues (Gly, Ala, and Aib). A plausible mechanism is proposed for the origin of the c6 ion, which involves C-terminus lactam formation followed by transannular cyclization and dehydration. The results presented in this study highlight the role of reactive side chain functionalities in promoting noncanonical fragmentation pathways.
Collapse
Affiliation(s)
- Sanjeev Kumar
- National Center for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - M Achanna Venkatesha
- National Center for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Padmanabhan Balaram
- National Center for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| |
Collapse
|
7
|
Yamada M, Kurihara Y, Koizumi M, Tsuji K, Maeda Y, Suzuki M. Understanding the Nature and Strength of Noncovalent Face‐to‐Face Arene–Fullerene Interactions. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202212279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Michio Yamada
- Tokyo Gakugei University Department of Chemistry 4-1-1 Nukuikitamachi 184-8501 Koganei, Tokyo JAPAN
| | - Yukiyo Kurihara
- Tokyo Gakugei University: Tokyo Gakugei Daigaku Department of Chemistry JAPAN
| | - Masaaki Koizumi
- Tokyo Gakugei University: Tokyo Gakugei Daigaku Department of Chemistry JAPAN
| | - Kasumi Tsuji
- Tokyo Gakugei University: Tokyo Gakugei Daigaku Department of Chemistry JAPAN
| | - Yutaka Maeda
- Tokyo Gakugei University: Tokyo Gakugei Daigaku Department of Chemistry JAPAN
| | - Mitsuaki Suzuki
- Josai University: Josai Daigaku Department of Chemistry JAPAN
| |
Collapse
|
8
|
Wang C, Liu Y, Qu X, Shi B, Zheng Q, Lin X, Chao S, Wang C, Zhou J, Sun Y, Mao G, Li Z. Ultra-Stretchable and Fast Self-Healing Ionic Hydrogel in Cryogenic Environments for Artificial Nerve Fiber. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2105416. [PMID: 35103354 DOI: 10.1002/adma.202105416] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 01/15/2022] [Indexed: 06/14/2023]
Abstract
Self-healing materials behave with irreplaceable advantages in biomimetic intelligent robots (BIR) for avoiding or reducing safety hazards and economic losses from accidental damage during service. However, the self-healing ability is unreservedly lost and even becomes rigid and fragile in the cryogenic environment where BIR are precisely needed. Here, the authors report a versatile ionic hydrogel with fast self-healing ability, ultra-stretchability, and stable conductivity, even at -80 °C. The hydrogel is systematically optimized to improve a hydrogen-bonded network nanostructure, coordinated achieving a quick self-healing ability within 10 min, large deformation tolerance of over 7000%, superior conductivity of 11.76 S cm-1 and anti-freezing ability, which is difficult to obtain simultaneously. Such a hydrogel provides new opportunities for artificial electronic devices in harsh environments. As a prospective application, they fabricate an artificial nerve fiber by mimicking the structure and functions of the myelinated axon, exhibiting the property of fast and potential-gated signal transmission. This artificial nerve fiber is integrated into a robot for demonstrating a real-time high fidelity and high throughput information interaction under big deformation and cryogenic temperature. The hydrogel and bionic device will bring pioneering functions for robots and open a broad application scenario in extreme conditions.
Collapse
Affiliation(s)
- Chan Wang
- CAS Center for Excellence in Nanoscience, Beijing Key Laboratory of Micro-Nano Energy and Sensor, Beijing Institute of Nanoenergy and Nanosystems, Chinese Academy of Sciences, Beijing, 101400, China
- School of Nanoscience and Technology, University of Chinese Academy of Sciences, Beijing, 101400, China
| | - Ying Liu
- CAS Center for Excellence in Nanoscience, Beijing Key Laboratory of Micro-Nano Energy and Sensor, Beijing Institute of Nanoenergy and Nanosystems, Chinese Academy of Sciences, Beijing, 101400, China
- School of Nanoscience and Technology, University of Chinese Academy of Sciences, Beijing, 101400, China
| | - Xuecheng Qu
- CAS Center for Excellence in Nanoscience, Beijing Key Laboratory of Micro-Nano Energy and Sensor, Beijing Institute of Nanoenergy and Nanosystems, Chinese Academy of Sciences, Beijing, 101400, China
- School of Nanoscience and Technology, University of Chinese Academy of Sciences, Beijing, 101400, China
| | - Bojing Shi
- CAS Center for Excellence in Nanoscience, Beijing Key Laboratory of Micro-Nano Energy and Sensor, Beijing Institute of Nanoenergy and Nanosystems, Chinese Academy of Sciences, Beijing, 101400, China
- Beijing Advanced Innovation Centre for Biomedical Engineering, Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China
| | - Qiang Zheng
- CAS Center for Excellence in Nanoscience, Beijing Key Laboratory of Micro-Nano Energy and Sensor, Beijing Institute of Nanoenergy and Nanosystems, Chinese Academy of Sciences, Beijing, 101400, China
- School of Biology and Engineering, Guizhou Medical University, Guiyang, 550025, China
| | - Xubo Lin
- Beijing Advanced Innovation Centre for Biomedical Engineering, Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China
| | - Shengyu Chao
- CAS Center for Excellence in Nanoscience, Beijing Key Laboratory of Micro-Nano Energy and Sensor, Beijing Institute of Nanoenergy and Nanosystems, Chinese Academy of Sciences, Beijing, 101400, China
- School of Nanoscience and Technology, University of Chinese Academy of Sciences, Beijing, 101400, China
| | - Changyong Wang
- Beijing Institute of Basic Medical Sciences, Beijing, 100850, China
| | - Jin Zhou
- Beijing Institute of Basic Medical Sciences, Beijing, 100850, China
| | - Yu Sun
- Department of Neurovascular Surgery, The Third Medical Centre Chinese People's Liberation Army General Hospital, Beijing, 100036, China
| | - Gengsheng Mao
- Department of Neurovascular Surgery, The Third Medical Centre Chinese People's Liberation Army General Hospital, Beijing, 100036, China
| | - Zhou Li
- CAS Center for Excellence in Nanoscience, Beijing Key Laboratory of Micro-Nano Energy and Sensor, Beijing Institute of Nanoenergy and Nanosystems, Chinese Academy of Sciences, Beijing, 101400, China
- School of Nanoscience and Technology, University of Chinese Academy of Sciences, Beijing, 101400, China
- Center on Nanoenergy Research, School of Physical Science and Technology, Guangxi University, Nanning, 530004, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
| |
Collapse
|
9
|
π-π Stacking Interaction of Metal Phenoxyl Radical Complexes. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27031135. [PMID: 35164397 PMCID: PMC8840625 DOI: 10.3390/molecules27031135] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/29/2022] [Accepted: 02/02/2022] [Indexed: 11/17/2022]
Abstract
π-π stacking interaction is well-known to be one of the weak interactions. Its importance in the stabilization of protein structures and functionalization has been reported for various systems. We have focused on a single copper oxidase, galactose oxidase, which has the π-π stacking interaction of the alkylthio-substituted phenoxyl radical with the indole ring of the proximal tryptophan residue and catalyzes primary alcohol oxidation to give the corresponding aldehyde. This stacking interaction has been considered to stabilize the alkylthio-phenoxyl radical, but further details of the interaction are still unclear. In this review, we discuss the effect of the π-π stacking interaction of the alkylthio-substituted phenoxyl radical with an indole ring.
Collapse
|
10
|
The fluorescent aptamer Squash extensively repurposes the adenine riboswitch fold. Nat Chem Biol 2022; 18:191-198. [PMID: 34937911 PMCID: PMC9812287 DOI: 10.1038/s41589-021-00931-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 10/21/2021] [Indexed: 01/07/2023]
Abstract
Squash is an RNA aptamer that strongly activates the fluorescence of small-molecule analogs of the fluorophore of green fluorescent protein (GFP). Unlike other fluorogenic aptamers, isolated de novo from random-sequence RNA, Squash was evolved from the bacterial adenine riboswitch to leverage its optimized in vivo folding and stability. We now report the 2.7-Å resolution cocrystal structure of fluorophore-bound Squash, revealing that while the overall fold of the riboswitch is preserved, the architecture of the ligand-binding core is dramatically transformed. Unlike previously characterized aptamers that activate GFP-derived fluorophores, Squash does not harbor a G-quadruplex, sandwiching its fluorophore between a base triple and a noncanonical base quadruple in a largely apolar pocket. The expanded structural core of Squash allows it to recognize unnatural fluorophores that are larger than the simple purine ligand of the parental adenine riboswitch, and suggests that stable RNA scaffolds can tolerate larger variation than has hitherto been appreciated.
Collapse
|
11
|
Mehreen S, Ullah A, Nadeem H, Dege N, Naseer MM. Synthesis, solid state self-assembly driven by antiparallel π⋯π stacking and {⋯H-C-C-F} 2 dimer synthons, and in vitro acetyl cholinesterase inhibition activity of phenoxy pendant isatins. RSC Adv 2022; 12:1788-1796. [PMID: 35425213 PMCID: PMC8979220 DOI: 10.1039/d1ra08286h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 01/03/2022] [Indexed: 12/12/2022] Open
Abstract
A series of novel phenoxy pendant isatins PI1-12 have been synthesized in excellent yields by a simple nucleophilic substitution reaction involving isatins and 1-(2-bromoethoxy)-4-substituted benzenes, and characterized by their FT-IR, 1H NMR, 13C NMR and GC-MS data, and in the case of PI4 by its single crystal X-ray analysis. The solid-state structure of PI4 showed an intriguing and unique 1D-supramolecular chain-based self-assembled structure, the driving force of which is mainly the strong antiparallel π⋯π stacking and {⋯H-C-C-F}2 dimer synthons. This compound not only highlights the potential of the isatin moiety in forming strong antiparallel π⋯π stacking interactions but also provides a platform to have considerable insight into the nature, strength and directionality of much debated π-π and C-H⋯F-C interactions. The in vitro biological studies revealed that three phenoxy pendant isatins PI1, PI2 and PI4 are highly potent inhibitors of acetylcholinesterase enzyme with IC50 values of 0.52 ± 0.073 μg ml-1, 0.72 ± 0.012 μg ml-1 and 0.68 ± 0.011 μg ml-1, respectively, showing comparable activity to the standard drug, donepezil (IC50 = 0.73 ± 0.015 μg ml-1). A simple and efficient synthesis of phenoxy pendant isatins PI1-12 from inexpensive and commercially available starting materials, and their high potential of acetyl cholinesterase inhibition provide an attractive opportunity to find more effective medication for Alzheimer's disease (AD).
Collapse
Affiliation(s)
- Saba Mehreen
- Department of Chemistry, Quaid-i-Azam University Islamabad 45320 Pakistan
| | - Aman Ullah
- Department of Agricultural, Food and Nutritional Science, 4-10 Agriculture/Forestry Centre, University of Alberta Edmonton AB T6G 2P5 Canada
| | - Humaira Nadeem
- Department of Pharmaceutical Chemistry, Riphah Institute of Pharmaceutical Sciences, Riphah International University G-7/4 Islamabad Pakistan
| | - Necmi Dege
- Ondokuz Mayıs University, Faculty of Arts and Sciences, Department of Physics Kurupelit 55139 Samsun Turkey
| | | |
Collapse
|
12
|
Borodina T, Smirnov V, Serykh V, Rozentsveig I. π-Stacking interactions in new arylsulphonylamine-substituted derivatives of imidazo[2,1-b]thiazol. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
13
|
Mehreen S, Zia M, Khan A, Hussain J, Ullah S, Anwar MU, Al-Harrasi A, Naseer MM. Phenoxy pendant isatins as potent α-glucosidase inhibitors: reciprocal carbonyl⋯carbonyl interactions, antiparallel π⋯π stacking driven solid state self-assembly and biological evaluation. RSC Adv 2022; 12:20919-20928. [PMID: 35919179 PMCID: PMC9302069 DOI: 10.1039/d2ra03307k] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 07/02/2022] [Indexed: 11/28/2022] Open
Abstract
Carbonyl–carbonyl (CO⋯CO) interactions are recently explored noncovalent interactions of significant interest owing to their role in the stability of biomacromolecules. Currently, substantial efforts are being made to understand the nature of these interactions. In this study, twelve phenoxy pendant isatins 1–12 have been evaluated for their α-glucosidase inhibitory potential in addition to the analysis of X-ray single crystals of 4 and 9. Both compounds 4 and 9 showed intriguing and unique self-assembled structures. The CO⋯CO and antiparallel displaced π⋯π stacking interactions are mainly involved in the formation of 1D-stair like supramolecular chains of 4 whereas antiparallel π⋯π stacking interactions drive the formation of 1D-columnar stacks of 9. These compounds not only highlight the potential of the isatin moiety in forming strong CO⋯CO and antiparallel π⋯π stacking interactions but also are interesting models to provide considerable insight into the nature of these interactions. The in vitro biological studies revealed that all twelve phenoxy pendant isatins 1–12 are highly potent inhibitors of α-glucosidase enzyme with IC50 values ranging from 5.32 ± 0.17 to 150.13 ± 0.62 μM, showing many fold more potent activity than the standard drug, acarbose (IC50 = 873.34 ± 1.67). Easy access and high α-glucosidase inhibition potential of these phenoxy pendant isatins 1–12 provide an attractive platform for finding more effective medication for controlling postprandial hyperglycemia. Carbonyl–carbonyl (CO⋯CO) interactions are recently explored noncovalent interactions of significant interest owing to their role in the stability of biomacromolecules.![]()
Collapse
Affiliation(s)
- Saba Mehreen
- Department of Chemistry, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Mehwash Zia
- Department of Chemistry, Allama Iqbal Open University, Islamabad-44000, Pakistan
| | - Ajmal Khan
- Natural and Medical Sciences Research Centre, University of Nizwa, Birkat Almouz 616, Oman
| | - Javid Hussain
- Department of Biological Sciences & Chemistry, College of Arts and Sciences, University of Nizwa, Nizwa, Oman
| | - Saeed Ullah
- Natural and Medical Sciences Research Centre, University of Nizwa, Birkat Almouz 616, Oman
| | - Muhammad U. Anwar
- Natural and Medical Sciences Research Centre, University of Nizwa, Birkat Almouz 616, Oman
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Centre, University of Nizwa, Birkat Almouz 616, Oman
| | | |
Collapse
|
14
|
Fan C, Deng Q, Zhu TF. Bioorthogonal information storage in L-DNA with a high-fidelity mirror-image Pfu DNA polymerase. Nat Biotechnol 2021; 39:1548-1555. [PMID: 34326549 DOI: 10.1038/s41587-021-00969-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 05/31/2021] [Indexed: 02/07/2023]
Abstract
Natural DNA is exquisitely evolved to store genetic information. The chirally inverted L-DNA, possessing the same informational capacity but resistant to biodegradation, may serve as a robust, bioorthogonal information repository. Here we chemically synthesize a 90-kDa high-fidelity mirror-image Pfu DNA polymerase that enables accurate assembly of a kilobase-sized mirror-image gene. We use the polymerase to encode in L-DNA an 1860 paragraph by Louis Pasteur that first proposed a mirror-image world of biology. We realize chiral steganography by embedding a chimeric D-DNA/L-DNA key molecule in a D-DNA storage library, which conveys a false or secret message depending on the chirality of reading. Furthermore, we show that a trace amount of an L-DNA barcode preserved in water from a local pond remains amplifiable and sequenceable for 1 year, whereas a D-DNA barcode under the same conditions could not be amplified after 1 day. These next-generation mirror-image molecular tools may transform the development of advanced mirror-image biology systems and pave the way for the realization of the mirror-image central dogma and exploration of their applications.
Collapse
Affiliation(s)
- Chuyao Fan
- School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Ministry of Education Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China
| | - Qiang Deng
- School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Ministry of Education Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China
| | - Ting F Zhu
- School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Ministry of Education Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China.
| |
Collapse
|
15
|
Pachisia S, Gupta R. Supramolecular catalysis: the role of H-bonding interactions in substrate orientation and activation. Dalton Trans 2021; 50:14951-14966. [PMID: 34617524 DOI: 10.1039/d1dt02131a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hydrogen bonding plays significant roles in various biological processes during substrate orientation and binding and therefore assists in assorted organic transformations. However, replicating the intricate selection of hydrogen bonds, as observed in nature, in synthetic complexes has met with only limited success. Despite this fact, recent times have seen the emergence of several notable examples where hydrogen bonds have been introduced in synthetic complexes. A few such examples have also illustrated the substantial role played by the hydrogen bonds in influencing and often controlling the catalytic outcome. This perspective presents selected examples illustrating the significance of hydrogen bonds offered by the coordination and the organometallic complexes that aid in providing the desired orientation to a substrate adjacent to a catalytic metal center and remarkably assisting in the catalysis.
Collapse
Affiliation(s)
- Sanya Pachisia
- Department of Chemistry, University of Delhi, Delhi - 110007, India.
| | - Rajeev Gupta
- Department of Chemistry, University of Delhi, Delhi - 110007, India.
| |
Collapse
|
16
|
Boudouh I, González JA, Coto B, Moussaoui A, Kasmi A, Djemai I, Hadj-Kali MK. Solid-liquid equilibria for dibenzofuran or Xanthene + Heavy Hydrocarbons: Experimental measurements and modelling. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
17
|
Justino GC, Nascimento CP, Justino MC. Molecular dynamics simulations and analysis for bioinformatics undergraduate students. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2021; 49:570-582. [PMID: 33844418 DOI: 10.1002/bmb.21512] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 02/21/2021] [Accepted: 03/30/2021] [Indexed: 06/12/2023]
Abstract
A computational biochemistry laboratory, fitted for bioinformatics students, is presented. The molecular dynamics package GROMACS is used to prepare and simulate a solvated protein. Students analyze the trajectory with different available tools (GROMACS and VMD) to probe the structural stability of the protein during the simulation. Students are also required to make use of Python libraries and write their own code to probe non-covalent interactions between the amino acid side chains. Based on these results, students characterize the system in a qualitatively approach but also assess the importance of each specific interaction through time. This work mobilizes biochemical concepts and programming skills, fostering critical thinking and group work and developing presenting skills.
Collapse
Affiliation(s)
- Gonçalo C Justino
- Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Escola Superior de Tecnologia do Barreiro, Instituto Politécnico de Setúbal, Lavradio, Portugal
| | - Catarina P Nascimento
- Escola Superior de Tecnologia do Barreiro, Instituto Politécnico de Setúbal, Lavradio, Portugal
| | - Marta C Justino
- Escola Superior de Tecnologia do Barreiro, Instituto Politécnico de Setúbal, Lavradio, Portugal
- Centro Interdisciplinar de Ciências Químicas e Biológicas, Instituto Politécnico de Setúbal, Lavradio, Portugal
| |
Collapse
|
18
|
Friedman AK, Boeynaems S, Baker LA. Synthetic hydrogel mimics of the nuclear pore complex for the study of nucleocytoplasmic transport defects in C9orf72 ALS/FTD. Anal Bioanal Chem 2021; 414:525-532. [PMID: 34170347 DOI: 10.1007/s00216-021-03478-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 06/08/2021] [Accepted: 06/14/2021] [Indexed: 11/29/2022]
Abstract
Dipeptide repeats (DPRs) associated with C9orf72 repeat expansions perturb nucleocytoplasmic transport and are implicated in the pathogenesis of amyotrophic lateral sclerosis. We present a synthetic hydrogel platform that can be used to analyze aspects of the molecular interaction of dipeptide repeats and the phenylalanine-glycine (FG) phase of the nuclear pore complex (NPC). Hydrogel scaffolds composed of acrylamide and copolymerized with FG monomers are first formed to recapitulate key FG interactions found in the NPC. With labeled probes, we find evidence that toxic arginine-rich DPRs (poly-GR and poly-PR), but not the non-toxic poly-GP, target NPC hydrogel mimics and block selective entry of a key nuclear transport receptor, importin beta (Impβ). The ease with which these synthetic hydrogel mimics can be adjusted/altered makes them an invaluable tool to dissect complex molecular interactions that underlie cellular transport processes and their perturbation in disease.
Collapse
Affiliation(s)
- Alicia K Friedman
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210, USA
| | - Steven Boeynaems
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA.
| | - Lane A Baker
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana, 47405, USA.
| |
Collapse
|
19
|
Merkulyeva YA, Shcherbakov DN, Sharlaeva EA, Chirkova VY. Phospholipases C from the Genus Bacillus: Biological Role, Properties, and Fields of Application. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2021. [DOI: 10.1134/s1068162021030134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
20
|
Abstract
Phycobilisomes (PBSs) are extremely large chromophore-protein complexes on the stromal side of the thylakoid membrane in cyanobacteria and red algae. The main function of PBSs is light harvesting, and they serve as antennas and transfer the absorbed energy to the reaction centers of two photosynthetic systems (photosystems I and II). PBSs are composed of phycobiliproteins and linker proteins. How phycobiliproteins and linkers are organized in PBSs and how light energy is efficiently harvested and transferred in PBSs are the fundamental questions in the study of photosynthesis. In this review, the structures of the red algae Griffithsia pacifica and Porphyridium purpureum are discussed in detail, along with the functions of linker proteins in phycobiliprotein assembly and in fine-tuning the energy state of chromophores.
Collapse
Affiliation(s)
- Sen-Fang Sui
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology and Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China;
| |
Collapse
|
21
|
Maué D, Strebert PH, Bernhard D, Rösel S, Schreiner PR, Gerhards M. Dispersionsgebundene, isolierte Dimere in der Gasphase: Beobachtung des kürzesten intermolekularen C‐H⋅⋅⋅H‐C Abstands mittels stimulierter Raman‐Spektroskopie. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202016020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Dominique Maué
- Fachbereich Chemie und Forschungszentrum Optimas TU Kaiserslautern Erwin-Schrödinger-Str. 52 67663 Kaiserslautern Deutschland
| | - Patrick H. Strebert
- Fachbereich Chemie und Forschungszentrum Optimas TU Kaiserslautern Erwin-Schrödinger-Str. 52 67663 Kaiserslautern Deutschland
| | - Dominic Bernhard
- Fachbereich Chemie und Forschungszentrum Optimas TU Kaiserslautern Erwin-Schrödinger-Str. 52 67663 Kaiserslautern Deutschland
| | - Sören Rösel
- Institut für organische Chemie Justus-Liebig-Universität Gießen Heinrich-Buff-Ring 17 35392 Gießen Deutschland
| | - Peter R. Schreiner
- Institut für organische Chemie Justus-Liebig-Universität Gießen Heinrich-Buff-Ring 17 35392 Gießen Deutschland
| | - Markus Gerhards
- Fachbereich Chemie und Forschungszentrum Optimas TU Kaiserslautern Erwin-Schrödinger-Str. 52 67663 Kaiserslautern Deutschland
| |
Collapse
|
22
|
Maué D, Strebert PH, Bernhard D, Rösel S, Schreiner PR, Gerhards M. Dispersion-Bound Isolated Dimers in the Gas Phase: Observation of the Shortest Intermolecular CH⋅⋅⋅H-C Distance via Stimulated Raman Spectroscopy. Angew Chem Int Ed Engl 2021; 60:11305-11309. [PMID: 33709534 PMCID: PMC8252503 DOI: 10.1002/anie.202016020] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 02/13/2021] [Indexed: 11/30/2022]
Abstract
The triphenylmethane and all‐meta tert‐butyl triphenylmethane dimers, (TPM)2 and (T tBuPM)2, respectively, were studied with ionization loss stimulated Raman spectroscopy in molecular beam experiments to resolve structure sensitive vibrations. This answers the question whether the recently reported linear head‐to‐head arrangement in (T tBuPM)2 results from crystal packing or prevails also in the gas phase, and therefore must result from extraordinarily strong London dispersion (LD) interactions. Our study clearly demonstrates that the head‐to‐head arrangement is maintained even under isolated molecular beam conditions in the absence of crystal packing effects. The central Raman‐active aliphatic C−D vibration of appropriately deuterated (T tBuPM)2 associated with an unusually short C−D⋅⋅⋅D−C distance exhibits a strong blue‐shift compared to the undisturbed case. As the LD stabilizing tert‐butyl groups are absent in (TPM)2, it displays an approximately S6‐symmetric tail‐to‐tail arrangement.
Collapse
Affiliation(s)
- Dominique Maué
- Fachbereich Chemie and Research Center Optimas, TU Kaiserslautern, Erwin-Schrödinger-Str. 52, 67663, Kaiserslautern, Germany
| | - Patrick H Strebert
- Fachbereich Chemie and Research Center Optimas, TU Kaiserslautern, Erwin-Schrödinger-Str. 52, 67663, Kaiserslautern, Germany
| | - Dominic Bernhard
- Fachbereich Chemie and Research Center Optimas, TU Kaiserslautern, Erwin-Schrödinger-Str. 52, 67663, Kaiserslautern, Germany
| | - Sören Rösel
- Institute of Organic Chemistry, Justus-Liebig University, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
| | - Peter R Schreiner
- Institute of Organic Chemistry, Justus-Liebig University, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
| | - Markus Gerhards
- Fachbereich Chemie and Research Center Optimas, TU Kaiserslautern, Erwin-Schrödinger-Str. 52, 67663, Kaiserslautern, Germany
| |
Collapse
|
23
|
Hastings RL, Boeynaems S. Designer Condensates: A Toolkit for the Biomolecular Architect. J Mol Biol 2021; 433:166837. [PMID: 33539874 DOI: 10.1016/j.jmb.2021.166837] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 01/06/2021] [Accepted: 01/16/2021] [Indexed: 12/19/2022]
Abstract
Protein phase separation has emerged as a novel paradigm to explain the biogenesis of membraneless organelles and other so-called biomolecular condensates. While the implication of this physical phenomenon within cell biology is providing us with novel ways for understanding how cells compartmentalize biochemical reactions and encode function in such liquid-like assemblies, the newfound appreciation of this process also provides immense opportunities for designing and sculpting biological matter. Here, we propose that understanding the cell's instruction manual of phase separation will enable bioengineers to begin creating novel functionalized biological materials and unprecedented tools for synthetic biology. We present FASE as the synthesis of the existing sticker-spacer framework, which explains the physical driving forces underlying phase separation, with quintessential principles of Scandinavian design. FASE serves both as a designer condensates catalogue and construction manual for the aspiring (membraneless) biomolecular architect. Our approach aims to inspire a new generation of bioengineers to rethink phase separation as an opportunity for creating reactive biomaterials with unconventional properties and to encode novel biological function in living systems. Although still in its infancy, several studies highlight how designer condensates have immediate and widespread potential applications in industry and medicine.
Collapse
Affiliation(s)
- Renee L Hastings
- Program in Biophysics, Stanford University, Stanford, CA 94305, USA
| | - Steven Boeynaems
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
| |
Collapse
|
24
|
Dechan P, Bajju GD, Sood P. Crystal Structure, Hirschfeld Surface Analysis, and Absorption Spectra of a New Polymorph of Highly Symmetric Tetraphenylporphyrinato Zn(II), ZnTPP. CRYSTALLOGR REP+ 2020. [DOI: 10.1134/s1063774520060127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
25
|
Merski M, Skrzeczkowski J, Roth JK, Górna MW. A Geometric Definition of Short to Medium Range Hydrogen-Mediated Interactions in Proteins. Molecules 2020; 25:E5326. [PMID: 33203097 PMCID: PMC7696500 DOI: 10.3390/molecules25225326] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/08/2020] [Accepted: 11/10/2020] [Indexed: 11/30/2022] Open
Abstract
We present a method to rapidly identify hydrogen-mediated interactions in proteins (e.g., hydrogen bonds, hydrogen bonds, water-mediated hydrogen bonds, salt bridges, and aromatic π-hydrogen interactions) through heavy atom geometry alone, that is, without needing to explicitly determine hydrogen atom positions using either experimental or theoretical methods. By including specific real (or virtual) partner atoms as defined by the atom type of both the donor and acceptor heavy atoms, a set of unique angles can be rapidly calculated. By comparing the distance between the donor and the acceptor and these unique angles to the statistical preferences observed in the Protein Data Bank (PDB), we were able to identify a set of conserved geometries (15 for donor atoms and 7 for acceptor atoms) for hydrogen-mediated interactions in proteins. This set of identified interactions includes every polar atom type present in the Protein Data Bank except OE1 (glutamate/glutamine sidechain) and a clear geometric preference for the methionine sulfur atom (SD) to act as a hydrogen bond acceptor. This method could be readily applied to protein design efforts.
Collapse
Affiliation(s)
- Matthew Merski
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, 02-089 Warsaw, Poland;
| | - Jakub Skrzeczkowski
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, 02-089 Warsaw, Poland;
| | - Jennifer K. Roth
- Department of Psychology, Carlow University, Pittsburgh, PA 15213, USA;
| | - Maria W. Górna
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, 02-089 Warsaw, Poland;
| |
Collapse
|
26
|
|
27
|
Petrovic AG, Polavarapu PL, Łopusiński A, Krasowska D, Wieczorek W, Szyrej M, Błaszczyk J, Drabowicz J. Absolute Configuration and Conformation of (-)- R- t-Butylphenylphosphinoamidate: Chiroptical Spectroscopy and X-ray Analysis. J Org Chem 2020; 85:14456-14466. [PMID: 32786637 PMCID: PMC7684576 DOI: 10.1021/acs.joc.0c00756] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
![]()
The
absolute configuration and conformations of (−)-tert-butylphenylphosphinoamidate were determined using three
different chiroptical spectroscopic methods, namely vibrational circular
dichroism (VCD), electronic circular dichroism (ECD), and optical
rotatory dispersion (ORD). In each of the spectroscopic methods used,
experimental data for the (−)-enantiomer of tert-butylphenylphosphinoamidate were measured in the solution phase.
Using the concentration-dependent experimental infrared spectra, the
existence of dimers in the solution was investigated, and the monomer–dimer
equilibrium constant was determined. Concomitant quantum mechanical
predictions of the VCD, ECD, and ORD for monomeric tert-butylphenylphosphinoamidate were carried out using density functional
theory (DFT) calculations using the B3LYP functional and the 6-31G(d),
6-311G(2d,2p) and aug-cc-pVDZ basis sets. Similar predictions for
dimeric tert-butylphenylphosphinoamidate were also
obtained using the B3LYP/6-31G(d) method. A comparison of theoretically
predicted data with the corresponding experimental data led to the
elucidation of the absolute configuration as (−)-(R)-tert-butylphenylphosphinoamidate with one predominant
conformation in the solution. This conclusion was independently supported
by X-ray analysis of the complex with (+)-R-2,2′-dihydroxy-1,1′-binaphthol
((+)-R- BINOL).
Collapse
Affiliation(s)
- Ana G Petrovic
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Prasad L Polavarapu
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Andrzej Łopusiński
- Center of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Łódź, Poland
| | - Dorota Krasowska
- Center of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Łódź, Poland
| | - Wanda Wieczorek
- Institute of General and Ecological Chemistry, Technical University of Łódź, Żeromskiego 116, 90-924 Łódź, Poland
| | - Małgorzata Szyrej
- Institute of Chemistry, Jan Długosz University in Częstochowa, Armii Krajowej 13/15, 42-200 Częstochowa, Poland
| | - Jarosław Błaszczyk
- Center of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Łódź, Poland
| | - Józef Drabowicz
- Center of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Łódź, Poland.,Institute of Chemistry, Jan Długosz University in Częstochowa, Armii Krajowej 13/15, 42-200 Częstochowa, Poland
| |
Collapse
|
28
|
Abstract
Many biomolecular condensates appear to form via spontaneous or driven processes that have the hallmarks of intracellular phase transitions. This suggests that a common underlying physical framework might govern the formation of functionally and compositionally unrelated biomolecular condensates. In this review, we summarize recent work that leverages a stickers-and-spacers framework adapted from the field of associative polymers for understanding how multivalent protein and RNA molecules drive phase transitions that give rise to biomolecular condensates. We discuss how the valence of stickers impacts the driving forces for condensate formation and elaborate on how stickers can be distinguished from spacers in different contexts. We touch on the impact of sticker- and spacer-mediated interactions on the rheological properties of condensates and show how the model can be mapped to known drivers of different types of biomolecular condensates.
Collapse
Affiliation(s)
- Jeong-Mo Choi
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, 63130, USA; , ,
- Center for Science & Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, Missouri, 63130, USA
- Natural Science Research Institute, Korea Advanced Institute of Science and Technology (KAIST), Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Alex S Holehouse
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, 63130, USA; , ,
- Center for Science & Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, Missouri, 63130, USA
| | - Rohit V Pappu
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, 63130, USA; , ,
- Center for Science & Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, Missouri, 63130, USA
| |
Collapse
|
29
|
Khalilinia E, Ebrahimi A. π-Stacking effects on acid capacity of p-aminobenzoic acid. Struct Chem 2020. [DOI: 10.1007/s11224-020-01530-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
30
|
Kim K, Plapp BV. Substitutions of Amino Acid Residues in the Substrate Binding Site of Horse Liver Alcohol Dehydrogenase Have Small Effects on the Structures but Significantly Affect Catalysis of Hydrogen Transfer. Biochemistry 2020; 59:862-879. [PMID: 31994873 DOI: 10.1021/acs.biochem.9b01074] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Previous studies showed that the L57F and F93W alcohol dehydrogenases catalyze the oxidation of benzyl alcohol with some quantum mechanical hydrogen tunneling, whereas the V203A enzyme has diminished tunneling. Here, steady-state kinetics for the L57F and F93W enzymes were studied, and microscopic rate constants for the ordered bi-bi mechanism were estimated from simulations of transient kinetics for the S48T, F93A, S48T/F93A, F93W, and L57F enzymes. Catalytic efficiencies for benzyl alcohol oxidation (V1/EtKb) vary over a range of ∼100-fold for the less active enzymes up to the L57F enzyme and are mostly associated with the binding of alcohol rather than the rate constants for hydride transfer. In contrast, catalytic efficiencies for benzaldehyde reduction (V2/EtKp) are ∼500-fold higher for the L57F enzyme than for the less active enzymes and are mostly associated with the rate constants for hydride transfer. Atomic-resolution structures (1.1 Å) for the F93W and L57F enzymes complexed with NAD+ and 2,3,4,5,6-pentafluorobenzyl alcohol or 2,2,2-trifluoroethanol are almost identical to previous structures for the wild-type, S48T, and V203A enzymes. Least-squares refinement with SHELXL shows that the nicotinamide ring is slightly strained in all complexes and that the apparent donor-acceptor distances from C4N of NAD to C7 of pentafluorobenzyl alcohol range from 3.28 to 3.49 Å (±0.02 Å) and are not correlated with the rate constants for hydride transfer or hydrogen tunneling. How the substitutions affect the dynamics of reorganization during hydrogen transfer and the extent of tunneling remain to be determined.
Collapse
Affiliation(s)
- Keehyuk Kim
- Department of Biochemistry , The University of Iowa , Iowa City , Iowa 52242 , United States
| | - Bryce V Plapp
- Department of Biochemistry , The University of Iowa , Iowa City , Iowa 52242 , United States
| |
Collapse
|
31
|
Lemkul JA. Pairwise-additive and polarizable atomistic force fields for molecular dynamics simulations of proteins. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 170:1-71. [PMID: 32145943 DOI: 10.1016/bs.pmbts.2019.12.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Protein force fields have been undergoing continual development since the first complete parameter sets were introduced nearly four decades ago. The functional forms that underlie these models have many common elements for the treatment of bonded and nonbonded forces, which are reviewed here. The most widely used force fields to date use a fixed-charge convention in which electronic polarization effects are treated via a mean-field approximation during partial charge assignment. Despite success in modeling folded proteins over many years, the fixed-charge assumption has limitations that cannot necessarily be overcome within their potential energy equations. To overcome these limitations, several force fields have recently been derived that explicitly treat electronic polarization effects with straightforward extensions of the potential energy functions used by nonpolarizable force fields. Here, we review the history of the most popular nonpolarizable force fields (AMBER, CHARMM, OPLS, and GROMOS) as well as studies that have validated them and applied them to studies of protein folding and misfolding. Building upon these force fields are more recent polarizable interaction potentials, including fluctuating charge models, POSSIM, AMOEBA, and the classical Drude oscillator. These force fields differ in their implementations but all attempt to model electronic polarization in a computationally tractable manner. Despite their recent emergence in the field of protein folding, several studies have already applied these polarizable models to challenging problems in this domain, including the role of polarization in folding free energies and sequence-specific effects on the stability of α-helical structures.
Collapse
Affiliation(s)
- Justin A Lemkul
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, United States.
| |
Collapse
|
32
|
Giri A, Pant D. Carbonic anhydrase modification for carbon management. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:1294-1318. [PMID: 31797268 DOI: 10.1007/s11356-019-06667-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 10/01/2019] [Indexed: 06/10/2023]
Abstract
Carbonic anhydrase modification (chemical and biological) is an attractive strategy for its diverse application to accelerate the absorption of CO2 from a flue gas with improved activity and stability. This article reports various possibilities of CA modification using metal-ligand homologous chemistry, cross-linking agents, and residue- and group-specific and genetic modifications, and assesses their role in carbon management. Chemically modified carbonic anhydrase is able to improve the absorption of carbon dioxide from a gas stream into mediation compounds with enhanced sequestration and mineral formation. Genetically modified CA polypeptide can also increase carbon dioxide conversion. Chemical modification of CA can be categorized in terms of (i) residue-specific modification (involves protein-ligand interaction in terms of substitution/addition) and group-specific modifications (based on the functional groups of the target CA). For every sustainable change, there should be no/limited toxic or immunological response. In this review, several CA modification pathways and biocompatibility rules are proposed as a theoretical support for emerging research in this area.
Collapse
Affiliation(s)
- Anand Giri
- Department of Environmental Sciences, Central University of Himachal Pradesh, Kangra, India
| | - Deepak Pant
- School of Chemical Sciences, Central University of Haryana, Mahendragarh, Haryana, 123029, India.
| |
Collapse
|
33
|
Joshi S, Sharma P, Siddiqui R, Kaushal K, Sharma S, Verma G, Saini A. A review on peptide functionalized graphene derivatives as nanotools for biosensing. Mikrochim Acta 2019; 187:27. [PMID: 31811393 DOI: 10.1007/s00604-019-3989-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 10/28/2019] [Indexed: 12/20/2022]
Abstract
Peptides exhibit unique binding behavior with graphene and its derivatives by forming bonds on its edges and planes. This makes them useful for sensing and imaging applications. This review with (155 refs.) summarizes the advances made in the last decade in the field of peptide-GO bioconjugation, and the use of these conjugates in analytical sciences and imaging. The introduction emphasizes the need for understanding the biotic-abiotic interactions in order to construct controllable peptide-functionalized graphitic material-based nanotools. The next section covers covalent and non-covalent interactions between peptide and oxidized graphene derivatives along with a discussion of the adsorption events during interfacing. We then describe applications of peptide-graphene conjugates in bioassays, with subsections on (a) detection of cancer cells, (b) monitoring protease activity, (c) determination of environmental pollutants and (d) determination of pathogenic microorganisms. The concluding section describes the current status of peptide functionalized graphitic bioconjugates and addresses future perspectives. Graphical abstractSchematic representation depicting biosensing applications of peptide functionalized graphene oxide.
Collapse
Affiliation(s)
- Shubhi Joshi
- Energy Research Centre, Panjab University, Sector 14, Chandigarh, 160014, India
| | - Pratibha Sharma
- Department of Biophysics, Panjab University, Sector 25, Chandigarh, 160014, India
| | - Ruby Siddiqui
- Department of Biophysics, Panjab University, Sector 25, Chandigarh, 160014, India
| | - Kanica Kaushal
- Department of Biophysics, Panjab University, Sector 25, Chandigarh, 160014, India
| | - Shweta Sharma
- Institute of Forensic Science & Criminology (UIEAST), Panjab University, Sector 14, Chandigarh, 160014, India
| | - Gaurav Verma
- Dr. S.S. Bhatnagar University Institute of Chemical Engineering & Technology (Dr.SSBUICET), Panjab University, Sector 14, Chandigarh, 160014, India
- Centre for Nanoscience and Nanotechnology (UIEAST), Panjab University, Sector 14, Chandigarh, 160014, India
| | - Avneet Saini
- Department of Biophysics, Panjab University, Sector 25, Chandigarh, 160014, India.
| |
Collapse
|
34
|
Taborosi A, Yamaguchi T, Odani A, Yamauchi O, Kohzuma T. The Role for the Weak Interaction on the Stabilization of Copper-Containing Complex: DFT Investigation of Noncovalent Interactions in Ternary-Cu(II) (DA)(AA) Complexes (DA = Diamine and AA = Amino Acids) as a Model of Metalloprotein. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2019. [DOI: 10.1246/bcsj.20190197] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Attila Taborosi
- Institute of Quantum Beam Science, Graduate School of Science and Engineering, Ibaraki University, 2-1-1 Bunkyo, Mito, Ibaraki 310-8512, Japan
| | - Takahide Yamaguchi
- Institute of Quantum Beam Science, Graduate School of Science and Engineering, Ibaraki University, 2-1-1 Bunkyo, Mito, Ibaraki 310-8512, Japan
- Frontier Research Center for Applied Atomic Science, 162-1 Shirakata, Tokai, Naka, Ibaraki 319-1106, Japan
| | - Akira Odani
- Graduate School of Pharmaceutical Sciences, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Osamu Yamauchi
- Graduate School of Science, Nagoya University, Furou-cho, Chikusa, Nagoya, Aichi 464-8601, Japan
| | - Takamitsu Kohzuma
- Institute of Quantum Beam Science, Graduate School of Science and Engineering, Ibaraki University, 2-1-1 Bunkyo, Mito, Ibaraki 310-8512, Japan
- Frontier Research Center for Applied Atomic Science, 162-1 Shirakata, Tokai, Naka, Ibaraki 319-1106, Japan
| |
Collapse
|
35
|
Altered dynamics may drift pathological fibrillization in membraneless organelles. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:988-998. [DOI: 10.1016/j.bbapap.2019.04.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 04/08/2019] [Accepted: 04/09/2019] [Indexed: 12/12/2022]
|
36
|
Bhosale S, Nikte SV, Sengupta D, Joshi M. Differential Dynamics Underlying the Gln27Glu Population Variant of the β 2-Adrenergic Receptor. J Membr Biol 2019; 252:499-507. [PMID: 31520159 DOI: 10.1007/s00232-019-00093-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Accepted: 08/23/2019] [Indexed: 12/21/2022]
Abstract
The β2-adrenergic receptor (β2AR) is a membrane-bound G-protein-coupled receptor and an important drug target for asthma. Clinical studies report that the population variant Gln27Glu is associated with a differential response to common asthma drugs, such as albuterol, isoproterenol and terbutaline. Interestingly, the 27th amino acid is positioned on the N-terminal region that is the most flexible and consequently the least studied part of the receptor. In this study, we probe the molecular origin of the differential drug binding by performing structural modeling and simulations of the wild-type (Gln) and variant (Glu) receptors followed by ensemble docking with the ligands, albuterol, isoproterenol and terbutaline. In line with clinical studies, the ligands were observed to interact preferentially with the Glu variant. Our results indicate that the Glu residue at the 27th position perturbs the network of electrostatic interactions that connects the N-terminal region to the binding site in the wild-type receptor. As a result, the Glu variant is observed to bind better to the three ligands tested in this study. Our study provides a structural basis to explain the variable drug response associated with the 27th position polymorphism in the β2AR and is a starting step to identify genotype-specific therapeutics.
Collapse
Affiliation(s)
- Sumedha Bhosale
- Bioinformatics Centre, S. P. University, Pune, 411 007, India
| | - Siddhanta V Nikte
- Physical Chemistry Division, National Chemical Laboratory, Pune, 411 008, India
| | - Durba Sengupta
- Physical Chemistry Division, National Chemical Laboratory, Pune, 411 008, India.
| | - Manali Joshi
- Bioinformatics Centre, S. P. University, Pune, 411 007, India.
| |
Collapse
|
37
|
Alshareedah I, Kaur T, Ngo J, Seppala H, Kounatse LAD, Wang W, Moosa MM, Banerjee PR. Interplay between Short-Range Attraction and Long-Range Repulsion Controls Reentrant Liquid Condensation of Ribonucleoprotein-RNA Complexes. J Am Chem Soc 2019; 141:14593-14602. [PMID: 31437398 DOI: 10.1021/jacs.9b03689] [Citation(s) in RCA: 113] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In eukaryotic cells, ribonucleoproteins (RNPs) form mesoscale condensates by liquid-liquid phase separation that play essential roles in subcellular dynamic compartmentalization. The formation and dissolution of many RNP condensates are finely dependent on the RNA-to-RNP ratio, giving rise to a windowlike phase separation behavior. This is commonly referred to as reentrant liquid condensation (RLC). Here, using ribonucleoprotein-inspired polypeptides with low-complexity RNA-binding sequences as well as an archetypal disordered RNP, fused in sarcoma, as model systems, we investigate the molecular driving forces underlying this nonmonotonous phase transition. We show that an interplay between short-range cation-π attractions and long-range electrostatic forces governs the heterotypic RLC behavior of RNP-RNA complexes. Short-range attractions, which can be encoded by both polypeptide chain primary sequence and nucleic acid base sequence, control the two-phase coexistence regime, regulate material properties of polypeptide-RNA condensates, and oppose condensate reentrant dissolution. In the presence of excess RNA, a competition between short-range attraction and long-range electrostatic repulsion drives the formation of a colloidlike cluster phase. With increasing short-range attraction, the fluid dynamics of the cluster phase is arrested, leading to the formation of a colloidal gel. Our results reveal that phase behavior, supramolecular organization, and material states of RNP-RNA assemblies are controlled by a dynamic interplay between molecular interactions at different length scales.
Collapse
Affiliation(s)
- Ibraheem Alshareedah
- Department of Physics , University at Buffalo , Buffalo , New York 14260 , United States
| | - Taranpreet Kaur
- Department of Physics , University at Buffalo , Buffalo , New York 14260 , United States
| | - Jason Ngo
- Department of Physics , University at Buffalo , Buffalo , New York 14260 , United States
| | - Hannah Seppala
- Department of Physics , University at Buffalo , Buffalo , New York 14260 , United States
| | | | - Wei Wang
- Department of Physics , University at Buffalo , Buffalo , New York 14260 , United States
| | - Mahdi Muhammad Moosa
- Department of Physics , University at Buffalo , Buffalo , New York 14260 , United States
| | - Priya R Banerjee
- Department of Physics , University at Buffalo , Buffalo , New York 14260 , United States
| |
Collapse
|
38
|
Oshita H, Suzuki T, Kawashima K, Abe H, Tani F, Mori S, Yajima T, Shimazaki Y. The effect of π-π stacking interaction of the indole ring with the coordinated phenoxyl radical in a nickel(ii)-salen type complex. Comparison with the corresponding Cu(ii) complex. Dalton Trans 2019; 48:12060-12069. [PMID: 31250847 DOI: 10.1039/c9dt01887e] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In order to gain new insights into the effect of the π-π stacking interaction of the indole ring with the phenoxyl radical moiety as seen in the active form of galactose oxidase, we have prepared Ni(ii) complexes of a methoxy substituted salen-type ligand containing a pendent indole ring on the dinitrogen chelate backbone and characterized their one-electron oxidized forms. The X-ray crystal structure analysis and the other physicochemical experiments of the Ni(ii) complex revealed no significant intramolecular interaction of the indole ring with the coordination plane. On the other hand, the X-ray crystal structures of the oxidized Ni(ii) complex exhibited the π-π stacking interaction of the indole ring mainly with one of the two phenolate moieties. While the phenoxyl radical electron was delocalized on the two phenolate moieties in the Ni(ii)-salen coordination plane, the phenolate moiety in close contact with the indole moiety was considered to be the initial oxidation locus, indicating that the indole ring interacted with the phenoxyl radical by π-π stacking. The UV-vis-NIR spectrum of the oxidized Ni(ii) complex with the pendent indole ring was different from that of the complex without the side chain indole ring, but the differences were rather small in comparison with the oxidized Cu(ii)-salen complexes with the π-π stacking interaction of the indole ring. Such differences are due to the electronic structure difference, the localized radical electron on one of the phenolate moieties in the oxidized Cu(ii) complexes being more favorable for the π-π stacking interaction.
Collapse
Affiliation(s)
- Hiromi Oshita
- Department of Chemistry of Functional Molecules, Konan University, Higashinada-ku, Kobe 658-8501, Japan
| | - Takashi Suzuki
- Graduate School of Science and Engineering, Ibaraki University, Bunkyo, Mito 310-8512, Japan.
| | - Kyohei Kawashima
- Graduate School of Science and Engineering, Ibaraki University, Bunkyo, Mito 310-8512, Japan.
| | - Hitoshi Abe
- Institute of Materials Structure Science (IMSS), High Energy Accelerator Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan and Department of Materials Structure Science, School of High Energy Accelerator Science, SOKENDAI (the Graduate University for Advanced Studies), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Fumito Tani
- Institute for Materials Chemistry and Engineering, Kyushu University, Nishi-ku, Fukuoka 819-0395, Japan
| | - Seiji Mori
- Graduate School of Science and Engineering, Ibaraki University, Bunkyo, Mito 310-8512, Japan.
| | - Tatsuo Yajima
- Faculty of Chemistry, Materials and Bioengineering, Kansai University, Suita, Osaka 564-8680, Japan
| | - Yuichi Shimazaki
- Graduate School of Science and Engineering, Ibaraki University, Bunkyo, Mito 310-8512, Japan.
| |
Collapse
|
39
|
Lysine/RNA-interactions drive and regulate biomolecular condensation. Nat Commun 2019; 10:2909. [PMID: 31266957 PMCID: PMC6606616 DOI: 10.1038/s41467-019-10792-y] [Citation(s) in RCA: 149] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 05/28/2019] [Indexed: 02/08/2023] Open
Abstract
Cells form and use biomolecular condensates to execute biochemical reactions. The molecular properties of non-membrane-bound condensates are directly connected to the amino acid content of disordered protein regions. Lysine plays an important role in cellular function, but little is known about its role in biomolecular condensation. Here we show that protein disorder is abundant in protein/RNA granules and lysine is enriched in disordered regions of proteins in P-bodies compared to the entire human disordered proteome. Lysine-rich polypeptides phase separate into lysine/RNA-coacervates that are more dynamic and differ at the molecular level from arginine/RNA-coacervates. Consistent with the ability of lysine to drive phase separation, lysine-rich variants of the Alzheimer's disease-linked protein tau undergo coacervation with RNA in vitro and bind to stress granules in cells. Acetylation of lysine reverses liquid-liquid phase separation and reduces colocalization of tau with stress granules. Our study establishes lysine as an important regulator of cellular condensation.
Collapse
|
40
|
Trinh HN, Jang SH, Lee C. Functional characterization of a SNP (F51S) found in human alpha 1-antitrypsin. Mol Genet Genomic Med 2019; 7:e819. [PMID: 31251477 PMCID: PMC6687665 DOI: 10.1002/mgg3.819] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 03/16/2019] [Accepted: 05/29/2019] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND Alpha 1-antitrypsin (A1AT) deficiency is related to lung and liver diseases, including pulmonary emphysema and liver cirrhosis in humans. Genetic variations including single nucleotide polymorphisms (SNPs) of SERPINA1 are responsible for A1AT deficiency, but the characteristics of the SNPs are not well-understood. Here, we investigated the features of a rare SNP (F51S) of A1AT, which introduces an additional N-glycosylation site in the N-terminal region of A1AT. METHODS We evaluated the F51S variant compared with the wild-type (WT) A1AT with regard to expression in CHO-K1 cells, trypsin inhibitory activity, polymerization, and thermal stability. RESULTS The recombinant F51S protein expressed in CHO-K1 cells was mostly retained inside cells. The F51S variant had trypsin inhibitory activity, but reduced thermal stability compared with the WT A1AT. The native acrylamide gel data showed that F51S tended to prevent polymerization of A1AT. CONCLUSION The results of this study indicate that Phe51 and the surrounding hydrophobic residue cluster plays an important role in the conformation and secretion of A1AT and suggest the harmful effects of a rare F51S SNP in human health.
Collapse
Affiliation(s)
- Hong-Nhung Trinh
- Department of Biomedical Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan, South Korea
| | - Sei-Heon Jang
- Department of Biomedical Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan, South Korea
| | - ChangWoo Lee
- Department of Biomedical Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan, South Korea
| |
Collapse
|
41
|
Oshita H, Suzuki T, Kawashima K, Abe H, Tani F, Mori S, Yajima T, Shimazaki Y. π-π Stacking Interaction in an Oxidized Cu II -Salen Complex with a Side-Chain Indole Ring: An Approach to the Function of the Tryptophan in the Active Site of Galactose Oxidase. Chemistry 2019; 25:7649-7658. [PMID: 30912194 DOI: 10.1002/chem.201900733] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Indexed: 11/07/2022]
Abstract
In order to gain new insights into the effect of the π-π stacking interaction of the indole ring with the CuII -phenoxyl radical as seen in the active form of galactose oxidase, we have prepared a CuII complex of a methoxy-substituted salen-type ligand, containing a pendent indole ring on the dinitrogen chelate backbone, and characterized its one-electron-oxidized forms. The X-ray crystal structures of the oxidized CuII complex exhibited the π-π stacking interaction of the indole ring mainly with one of the two phenolate moieties. The phenolate moiety in close contact with the indole moiety showed the characteristic phenoxyl radical structural features, indicating that the indole ring favors the π-π stacking interaction with the phenoxyl radical. The UV/Vis/NIR spectra of the oxidized CuII complex with the pendent indole ring was significantly different from those of the complex without the side-chain indole ring, and the absorption and CD spectra exhibited a solvent dependence, which is in line with the phenoxyl radical-indole stacking interaction in solution. The other physicochemical results and theoretical calculations strongly support that the indole ring, as an electron donor, stabilizes the phenoxyl radical by the π-π stacking interaction.
Collapse
Affiliation(s)
- Hiromi Oshita
- Graduate School of Science and Engineering, Ibaraki University, Mito, Ibaraki, 310-8512, Japan.,Present address: Department of Chemistry of Functional Molecules, Konan University, Higashinada-ku, Kobe, 658-8501, Japan
| | - Takashi Suzuki
- Graduate School of Science and Engineering, Ibaraki University, Mito, Ibaraki, 310-8512, Japan
| | - Kyohei Kawashima
- Graduate School of Science and Engineering, Ibaraki University, Mito, Ibaraki, 310-8512, Japan
| | - Hitoshi Abe
- Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, Tsukuba, Ibaraki, 305-0801, Japan
| | - Fumito Tani
- Institute for Material Chemistry and Engineering, Kyushu University, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Seiji Mori
- Graduate School of Science and Engineering, Ibaraki University, Mito, Ibaraki, 310-8512, Japan
| | - Tatsuo Yajima
- Faculty of Chemistry, Materials and Bioengineering, Kansai University, Suita, Osaka, 564-8680, Japan
| | - Yuichi Shimazaki
- Graduate School of Science and Engineering, Ibaraki University, Mito, Ibaraki, 310-8512, Japan
| |
Collapse
|
42
|
Boeynaems S, Holehouse AS, Weinhardt V, Kovacs D, Van Lindt J, Larabell C, Van Den Bosch L, Das R, Tompa PS, Pappu RV, Gitler AD. Spontaneous driving forces give rise to protein-RNA condensates with coexisting phases and complex material properties. Proc Natl Acad Sci U S A 2019; 116:7889-7898. [PMID: 30926670 PMCID: PMC6475405 DOI: 10.1073/pnas.1821038116] [Citation(s) in RCA: 268] [Impact Index Per Article: 53.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Phase separation of multivalent protein and RNA molecules underlies the biogenesis of biomolecular condensates such as membraneless organelles. In vivo, these condensates encompass hundreds of distinct types of molecules that typically organize into multilayered structures supporting the differential partitioning of molecules into distinct regions with distinct material properties. The interplay between driven (active) versus spontaneous (passive) processes that are required for enabling the formation of condensates with coexisting layers of distinct material properties remains unclear. Here, we deploy systematic experiments and simulations based on coarse-grained models to show that the collective interactions among the simplest, biologically relevant proteins and archetypal RNA molecules are sufficient for driving the spontaneous emergence of multilayered condensates with distinct material properties. These studies yield a set of rules regarding homotypic and heterotypic interactions that are likely to be relevant for understanding the interplay between active and passive processes that control the formation of functional biomolecular condensates.
Collapse
Affiliation(s)
- Steven Boeynaems
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305;
| | - Alex S Holehouse
- Department of Biomedical Engineering, Washington University, St. Louis, MO 63130
- Center for Science & Engineering of Living Systems, Washington University, St. Louis, MO 63130
| | - Venera Weinhardt
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Department of Anatomy, University of California, San Francisco, CA 94143
| | - Denes Kovacs
- Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Vrije Universiteit Brussel, B-1050 Brussels, Belgium
| | - Joris Van Lindt
- Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Vrije Universiteit Brussel, B-1050 Brussels, Belgium
| | - Carolyn Larabell
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Department of Anatomy, University of California, San Francisco, CA 94143
| | - Ludo Van Den Bosch
- Laboratory of Neurobiology, Center for Brain & Disease Research, Vlaams Instituut voor Biotechnologie, 3000 Leuven, Belgium
- Experimental Neurology, Department of Neurosciences, KU Leuven, 3001 Leuven, Belgium
| | - Rhiju Das
- Department of Biochemistry, Stanford University, Stanford, CA 94305
- Department of Physics, Stanford University, Stanford, CA 94305
| | - Peter S Tompa
- Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Vrije Universiteit Brussel, B-1050 Brussels, Belgium
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1117 Budapest, Hungary
| | - Rohit V Pappu
- Department of Biomedical Engineering, Washington University, St. Louis, MO 63130;
- Center for Science & Engineering of Living Systems, Washington University, St. Louis, MO 63130
| | - Aaron D Gitler
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305;
| |
Collapse
|
43
|
Sharada D, Saha A, Saha BK. Charge transfer complexes as colour changing and disappearing–reappearing colour materials. NEW J CHEM 2019. [DOI: 10.1039/c9nj00823c] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Charge transfer complexes, made of suitably chosen electron-rich and electron-deficient components, can perform as vanishing colour, disappearing–reappearing colour and colour changing materials.
Collapse
Affiliation(s)
- Durgam Sharada
- Department of Chemistry
- Pondicherry University
- Pondicherry
- India
| | - Arijit Saha
- Department of Chemistry
- Pondicherry University
- Pondicherry
- India
| | - Binoy K. Saha
- Department of Chemistry
- Pondicherry University
- Pondicherry
- India
| |
Collapse
|
44
|
Mahalakshmi R. Aromatic interactions in β-hairpin scaffold stability: A historical perspective. Arch Biochem Biophys 2018; 661:39-49. [PMID: 30395808 DOI: 10.1016/j.abb.2018.11.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Revised: 10/31/2018] [Accepted: 11/01/2018] [Indexed: 01/21/2023]
Abstract
Non-covalent interactions between naturally occurring aromatic residues have been widely exploited as scaffold stabilizing agents in de novo designed peptides and in Nature - inspired structures. Our understanding of the factors driving aromatic interactions and their observed interaction geometries have advanced remarkably with improvements in conventional structural studies, availability of novel molecular methods and in silico studies, which have together provided atomistic information on aromatic interactions and interaction strengths. This review attempts to recapitulate the early advances in our understanding of aromatic interactions as stabilizing agents of peptide β-hairpins.
Collapse
Affiliation(s)
- Radhakrishnan Mahalakshmi
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, 462066, India.
| |
Collapse
|
45
|
Iwane M, Tada T, Osuga T, Murase T, Fujita M, Nishino T, Kiguchi M, Fujii S. Controlling stacking order and charge transport in π-stacks of aromatic molecules based on surface assembly. Chem Commun (Camb) 2018; 54:12443-12446. [PMID: 30280176 DOI: 10.1039/c8cc06430j] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Here, we report a facile procedure based on surface self-assembly for controlling the π-π stacking order and relevant rectified charge transport properties in stacks of aromatic molecules on a single-molecule scale. A high rectification ratio of 10 was achieved and the rectification direction was uniquely determined by the controlled stacking order of the aromatic molecules on the graphene layers of HOPG.
Collapse
Affiliation(s)
- Madoka Iwane
- Department of Chemistry, Tokyo Tech., 2-12-1 W4-10 Ookayama, Meguro-ku, Tokyo 152-8511, Japan.
| | | | | | | | | | | | | | | |
Collapse
|
46
|
De Filippis V, Pozzi N, Acquasaliente L, Artusi I, Pontarollo G, Peterle D. Protein engineering by chemical methods: Incorporation of nonnatural amino acids as a tool for studying protein folding, stability, and function. Pept Sci (Hoboken) 2018. [DOI: 10.1002/pep2.24090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Vincenzo De Filippis
- Laboratory of Protein Chemistry, Department of Pharmaceutical & Pharmacological SciencesUniversity of Padua Padua Italy
| | - Nicola Pozzi
- Laboratory of Protein Chemistry, Department of Pharmaceutical & Pharmacological SciencesUniversity of Padua Padua Italy
| | - Laura Acquasaliente
- Laboratory of Protein Chemistry, Department of Pharmaceutical & Pharmacological SciencesUniversity of Padua Padua Italy
| | - Ilaria Artusi
- Laboratory of Protein Chemistry, Department of Pharmaceutical & Pharmacological SciencesUniversity of Padua Padua Italy
| | - Giulia Pontarollo
- Laboratory of Protein Chemistry, Department of Pharmaceutical & Pharmacological SciencesUniversity of Padua Padua Italy
| | - Daniele Peterle
- Laboratory of Protein Chemistry, Department of Pharmaceutical & Pharmacological SciencesUniversity of Padua Padua Italy
| |
Collapse
|
47
|
Rege NK, Wickramasinghe NP, Tustan AN, Phillips NFB, Yee VC, Ismail-Beigi F, Weiss MA. Structure-based stabilization of insulin as a therapeutic protein assembly via enhanced aromatic-aromatic interactions. J Biol Chem 2018; 293:10895-10910. [PMID: 29880646 PMCID: PMC6052209 DOI: 10.1074/jbc.ra118.003650] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 05/30/2018] [Indexed: 12/18/2022] Open
Abstract
Key contributions to protein structure and stability are provided by weakly polar interactions, which arise from asymmetric electronic distributions within amino acids and peptide bonds. Of particular interest are aromatic side chains whose directional π-systems commonly stabilize protein interiors and interfaces. Here, we consider aromatic-aromatic interactions within a model protein assembly: the dimer interface of insulin. Semi-classical simulations of aromatic-aromatic interactions at this interface suggested that substitution of residue TyrB26 by Trp would preserve native structure while enhancing dimerization (and hence hexamer stability). The crystal structure of a [TrpB26]insulin analog (determined as a T3Rf3 zinc hexamer at a resolution of 2.25 Å) was observed to be essentially identical to that of WT insulin. Remarkably and yet in general accordance with theoretical expectations, spectroscopic studies demonstrated a 150-fold increase in the in vitro lifetime of the variant hexamer, a critical pharmacokinetic parameter influencing design of long-acting formulations. Functional studies in diabetic rats indeed revealed prolonged action following subcutaneous injection. The potency of the TrpB26-modified analog was equal to or greater than an unmodified control. Thus, exploiting a general quantum-chemical feature of protein structure and stability, our results exemplify a mechanism-based approach to the optimization of a therapeutic protein assembly.
Collapse
Affiliation(s)
| | | | - Alisar N Tustan
- Medicine, Case Western Reserve University, Cleveland, Ohio 44106 and
| | | | | | | | - Michael A Weiss
- From the Departments of Biochemistry and
- the Department of Biochemistry, Indiana University School of Medicine, Indianapolis, Indiana 46202
| |
Collapse
|
48
|
Wang J, Choi JM, Holehouse AS, Lee HO, Zhang X, Jahnel M, Maharana S, Lemaitre R, Pozniakovsky A, Drechsel D, Poser I, Pappu RV, Alberti S, Hyman AA. A Molecular Grammar Governing the Driving Forces for Phase Separation of Prion-like RNA Binding Proteins. Cell 2018; 174:688-699.e16. [PMID: 29961577 DOI: 10.1016/j.cell.2018.06.006] [Citation(s) in RCA: 1079] [Impact Index Per Article: 179.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 03/19/2018] [Accepted: 05/31/2018] [Indexed: 12/23/2022]
Abstract
Proteins such as FUS phase separate to form liquid-like condensates that can harden into less dynamic structures. However, how these properties emerge from the collective interactions of many amino acids remains largely unknown. Here, we use extensive mutagenesis to identify a sequence-encoded molecular grammar underlying the driving forces of phase separation of proteins in the FUS family and test aspects of this grammar in cells. Phase separation is primarily governed by multivalent interactions among tyrosine residues from prion-like domains and arginine residues from RNA-binding domains, which are modulated by negatively charged residues. Glycine residues enhance the fluidity, whereas glutamine and serine residues promote hardening. We develop a model to show that the measured saturation concentrations of phase separation are inversely proportional to the product of the numbers of arginine and tyrosine residues. These results suggest it is possible to predict phase-separation properties based on amino acid sequences.
Collapse
Affiliation(s)
- Jie Wang
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Jeong-Mo Choi
- Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Alex S Holehouse
- Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Hyun O Lee
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Xiaojie Zhang
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Marcus Jahnel
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Shovamayee Maharana
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Régis Lemaitre
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Andrei Pozniakovsky
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - David Drechsel
- Research Institute of Molecular Pathology, Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Ina Poser
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Rohit V Pappu
- Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Simon Alberti
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany.
| | - Anthony A Hyman
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany.
| |
Collapse
|
49
|
Gropp C, Quigley BL, Diederich F. Molecular Recognition with Resorcin[4]arene Cavitands: Switching, Halogen-Bonded Capsules, and Enantioselective Complexation. J Am Chem Soc 2018; 140:2705-2717. [DOI: 10.1021/jacs.7b12894] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Cornelius Gropp
- Laboratory of Organic Chemistry,
Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg
3, 8093 Zürich, Switzerland
| | - Brendan L. Quigley
- Laboratory of Organic Chemistry,
Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg
3, 8093 Zürich, Switzerland
| | - François Diederich
- Laboratory of Organic Chemistry,
Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg
3, 8093 Zürich, Switzerland
| |
Collapse
|
50
|
De Filippis V, Acquasaliente L, Pontarollo G, Peterle D. Noncoded amino acids in protein engineering: Structure-activity relationship studies of hirudin-thrombin interaction. Biotechnol Appl Biochem 2018; 65:69-80. [DOI: 10.1002/bab.1632] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Accepted: 12/06/2017] [Indexed: 11/12/2022]
Affiliation(s)
- Vincenzo De Filippis
- Laboratory of Protein Chemistry; Department of Pharmaceutical & Pharmacological Sciences; University of Padua; Padua Italy
| | - Laura Acquasaliente
- Laboratory of Protein Chemistry; Department of Pharmaceutical & Pharmacological Sciences; University of Padua; Padua Italy
| | - Giulia Pontarollo
- Laboratory of Protein Chemistry; Department of Pharmaceutical & Pharmacological Sciences; University of Padua; Padua Italy
| | - Daniele Peterle
- Laboratory of Protein Chemistry; Department of Pharmaceutical & Pharmacological Sciences; University of Padua; Padua Italy
| |
Collapse
|