1
|
He S, Zhao L, Feng L, Zhao W, Liu Y, Hu T, Li J, Zhao Q, Wei L, You S. Mechanistic insight into the aggregation ability of anammox microorganisms: Roles of polarity, composition and molecular structure of extracellular polymeric substances. WATER RESEARCH 2024; 254:121438. [PMID: 38467096 DOI: 10.1016/j.watres.2024.121438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 01/25/2024] [Accepted: 03/06/2024] [Indexed: 03/13/2024]
Abstract
The chemical characteristics of extracellular polymeric substances (EPS) of anammox bacteria (AnAOB) play a crucial role in the rapid enrichment of AnAOB and the stable operation of wastewater anammox processes. To clarify the influential mechanisms of sludge EPS on AnAOB aggregation, multiple parameters, including the polarity distribution, composition, and molecular structure of EPS, were selected, and their quantitative relationship with AnAOB aggregation was analyzed. Compared to typical anaerobic sludge (anaerobic floc and granular sludge), the anammox sludge EPS exhibited higher levels of tryptophan-like substances (44.82-56.52 % vs. 2.57-39.81 %), polysaccharides (40.02-53.49 mg/g VSS vs. 30.22-41.69 mg/g VSS), and protein structural units including α-helices (20.70-23.98 % vs. 16.48-19.32 %), β-sheets (37.43-42.98 % vs. 25.78-36.72 %), and protonated nitrogen (Npr) (0.065-0.122 vs. 0.017-0.061). In contrast, it had lower contents of β-turns (20.95-27.39 % vs. 28.17-39.04 %). These biopolymers were found to originate from different genera of AnAOB. Specifically, the α-helix-rich proteins were mainly derived from Candidatus Kuenenia, whereas the extracellular proteins related to tryptophan and Npr were closely associated with Candidatus Brocadia. Critically, these EPS components could drive anammox aggregation through interactions. Substantial amounts of tryptophan-like substances facilitated the formation of β-sheet structures and the exposure of internal hydrophobic clusters, which benefited the anammox aggregation. Meanwhile, extracellular proteins with high Npr content played a pivotal role in the formation of mixed protein-polysaccharide gel networks with the electronegative regions of polysaccharides, which could be regarded as the key component in the maintenance of anammox sludge stability. These findings provide a comprehensive understanding of the multifaceted roles of EPS in driving anammox aggregation and offer valuable insights into the development of EPS regulation strategies aimed at optimizing the anammox process.
Collapse
Affiliation(s)
- Shufei He
- State Key Laboratory of Urban Water Resources and Environment (SKLUWRE), School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Lingxin Zhao
- State Key Laboratory of Urban Water Resources and Environment (SKLUWRE), School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Likui Feng
- State Key Laboratory of Urban Water Resources and Environment (SKLUWRE), School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Weixin Zhao
- State Key Laboratory of Urban Water Resources and Environment (SKLUWRE), School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Yu Liu
- State Key Laboratory of Urban Water Resources and Environment (SKLUWRE), School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Tianyi Hu
- State Key Laboratory of Urban Water Resources and Environment (SKLUWRE), School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Jianju Li
- State Key Laboratory of Urban Water Resources and Environment (SKLUWRE), School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Qingliang Zhao
- State Key Laboratory of Urban Water Resources and Environment (SKLUWRE), School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Liangliang Wei
- State Key Laboratory of Urban Water Resources and Environment (SKLUWRE), School of Environment, Harbin Institute of Technology, Harbin 150090, China.
| | - Shijie You
- State Key Laboratory of Urban Water Resources and Environment (SKLUWRE), School of Environment, Harbin Institute of Technology, Harbin 150090, China
| |
Collapse
|
2
|
Pham TL, Thomas F. Design of Functional Globular β-Sheet Miniproteins. Chembiochem 2024; 25:e202300745. [PMID: 38275210 DOI: 10.1002/cbic.202300745] [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: 10/31/2023] [Revised: 01/25/2024] [Accepted: 01/26/2024] [Indexed: 01/27/2024]
Abstract
The design of discrete β-sheet peptides is far less advanced than e. g. the design of α-helical peptides. The reputation of β-sheet peptides as being poorly soluble and aggregation-prone often hinders active design efforts. Here, we show that this reputation is unfounded. We demonstrate this by looking at the β-hairpin and WW domain. Their structure and folding have been extensively studied and they have long served as model systems to investigate protein folding and folding kinetics. The resulting fundamental understanding has led to the development of hyperstable β-sheet scaffolds that fold at temperatures of 100 °C or high concentrations of denaturants. These have been used to design functional miniproteins with protein or nucleic acid binding properties, in some cases with such success that medical applications are conceivable. The β-sheet scaffolds are not always completely rigid, but can be specifically designed to respond to changes in pH, redox potential or presence of metal ions. Some engineered β-sheet peptides also exhibit catalytic properties, although not comparable to those of natural proteins. Previous reviews have focused on the design of stably folded and non-aggregating β-sheet sequences. In our review, we now also address design strategies to obtain functional miniproteins from β-sheet folding motifs.
Collapse
Affiliation(s)
- Truc Lam Pham
- Truc Lam Pham, Prof. Dr. Franziska Thomas, Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
| | - Franziska Thomas
- Truc Lam Pham, Prof. Dr. Franziska Thomas, Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
| |
Collapse
|
3
|
Núñez-Villanueva D, Plata-Ruiz A, Romero-Muñiz I, Martín-Pérez I, Infantes L, González-Muñiz R, Martín-Martínez M. β-Turn Induction by a Diastereopure Azepane-Derived Quaternary Amino Acid. J Org Chem 2023; 88:14688-14696. [PMID: 37774108 PMCID: PMC10594656 DOI: 10.1021/acs.joc.3c01689] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Indexed: 10/01/2023]
Abstract
β-Turns are one of the most common secondary structures found in proteins. In the interest of developing novel β-turn inducers, a diastereopure azepane-derived quaternary amino acid has been incorporated into a library of simplified tetrapeptide models in order to assess the effect of the azepane position and peptide sequence on the stabilization of β-turns. The conformational analysis of these peptides by molecular modeling, NMR spectroscopy, and X-ray crystallography showed that this azepane amino acid is an effective β-turn inducer when incorporated at the i + 1 position. Moreover, the analysis of the supramolecular self-assembly of one of the β-turn-containing peptide models in the solid state reveals that it forms a supramolecular helical arrangement while maintaining the β-turn structure. The results here presented provide the basis for the use of this azepane quaternary amino acid as a strong β-turn inducer in the search for novel peptide-based bioactive molecules, catalysts, and biomaterials.
Collapse
Affiliation(s)
| | - Adrián Plata-Ruiz
- Instituto
de Química Médica (IQM-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
| | - Ignacio Romero-Muñiz
- Instituto
de Química Médica (IQM-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
- Universidad
Autónoma de Madrid, Química Orgánica, Francisco Tomás y Valiente,
7, 28049 Madrid, Spain
| | - Ignacio Martín-Pérez
- Instituto
de Química Médica (IQM-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
| | - Lourdes Infantes
- Instituto
de Química Física Rocasolano (IQFR-CSIC), Serrano 119, 28006 Madrid, Spain
| | | | | |
Collapse
|
4
|
Atkinson BC, Thomson AR. Structured cyclic peptide mimics by chemical ligation. Pept Sci (Hoboken) 2022. [DOI: 10.1002/pep2.24266] [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]
|
5
|
Zhang YN, Zhang Y, Su S, Zhu HY, Xu W, Wang L, Wu M, Chen K, Yu FQ, Xi TK, Zhou Q, Xie YH, Qin X, Ge H, Lu L, Qing J, Fang GM. Neutralizing SARS-CoV-2 by dimeric side chain-to-side chain cross-linked ACE2 peptide mimetics. Chem Commun (Camb) 2022; 58:1804-1807. [PMID: 35040445 DOI: 10.1039/d1cc06301d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present the finding of a dimeric ACE2 peptide mimetic designed through side chain cross-linking and covalent dimerization. It has a binding affinity of 16 nM for the SARS-CoV-2 spike RBD, and effectively inhibits the SARS-CoV-2 pseudovirus in Huh7-hACE2 cells with an IC50 of 190 nM and neutralizes the authentic SARS-CoV-2 in Caco2 cells with an IC50 of 2.4 μM. Our study should provide a new insight for the optimization of peptide-based anti-SARS-CoV-2 inhibitors.
Collapse
Affiliation(s)
- Yan-Ni Zhang
- Department of Health Sciences, Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, P. R. China.
| | - Yuwei Zhang
- National Traditional Chinese Medicine Clinical Research Base, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, 646000, P. R. China.
| | - Shan Su
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences and Biosafety Level 3 Laboratory, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 200032, P. R. China.
| | - Han-Ying Zhu
- Department of Health Sciences, Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, P. R. China.
| | - Wei Xu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences and Biosafety Level 3 Laboratory, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 200032, P. R. China.
| | - Lu Wang
- National Traditional Chinese Medicine Clinical Research Base, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, 646000, P. R. China.
| | - Meng Wu
- Department of Health Sciences, Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, P. R. China.
| | - Kai Chen
- Department of Health Sciences, Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, P. R. China.
| | - Fei-Qiang Yu
- Department of Health Sciences, Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, P. R. China.
| | - Tong-Kuai Xi
- Department of Health Sciences, Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, P. R. China.
| | - Qin Zhou
- Department of Health Sciences, Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, P. R. China.
| | - You-Hua Xie
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences and Biosafety Level 3 Laboratory, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 200032, P. R. China.
| | - Ximing Qin
- Department of Health Sciences, Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, P. R. China.
| | - Honghua Ge
- Department of Health Sciences, Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, P. R. China.
| | - Lu Lu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences and Biosafety Level 3 Laboratory, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 200032, P. R. China.
| | - Jie Qing
- National Traditional Chinese Medicine Clinical Research Base, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, 646000, P. R. China.
| | - Ge-Min Fang
- Department of Health Sciences, Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, P. R. China.
| |
Collapse
|
6
|
Debnath S, Ghosh S, Pandit G, Satpati P, Chatterjee S. Effect of Differential Geminal Substitution of γ Amino Acid Residues at the ( i + 2) Position of αγ Turn Segments on the Conformation of Template β-Hairpin Peptides. J Org Chem 2021; 86:11310-11323. [PMID: 34479402 DOI: 10.1021/acs.joc.1c00351] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The effect of insertion of three geminally dimethyl substituted γ amino acid residues [γ2,2 (4-amino-2,2-dimethylbutanoic acid), γ3,3 (4-amino-3,3-dimethylbutanoic acid), and γ4,4 (4-amino-4,4-dimethylbutanoic acid)] at the (i + 2) position of a two-residue αγ C12 turn segment in a model octapeptide sequence Leu-Phe-Val-Aib-Xxx-Leu-Phe-Val (where Xxx = γ amino acid residues) has been investigated in this study. Solution conformational studies (NMR, CD, and IR) and ab initio calculations indicated that γ3,3 and γ4,4 residues were well accommodated in the β-hairpin nucleating αγ C12 turns, which gave rise to well-registered hairpins, in contrast to γ2,2, which was unable to form a tight C12 β-hairpin nucleating turn and promote a well-registered β-hairpin. Geminal disubstitution at the Cα carbon in γ2,2 led to unfavorable steric contacts, disabling its accommodation in the αγ C12 hairpin nucleating turn unlike the γ3,3 and γ4,4 residues. Geminal substitutions at different carbons along the backbone constrained backbone torsion angles for the three γ amino acid residues differently, generating diverse conformational preferences in them. Folded hairpins were energetically more stable (∼8 to 9 kcal/mol) than the unfolded peptides. Conformational preference of the peptides was independent of the N-terminal protecting group. Such fundamental understanding will instrumentalize the future directed design of foldamers.
Collapse
Affiliation(s)
- Swapna Debnath
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam 781039, India
| | - Suvankar Ghosh
- Biosciences and Bioengineering Indian Institute of Technology, Guwahati, Assam 781039, India
| | - Gopal Pandit
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam 781039, India
| | - Priyadarshi Satpati
- Biosciences and Bioengineering Indian Institute of Technology, Guwahati, Assam 781039, India
| | - Sunanda Chatterjee
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam 781039, India
| |
Collapse
|