1
|
Ravichandran A, Araque JC, Lawson JW. Predicting the functional state of protein kinases using interpretable graph neural networks from sequence and structural data. Proteins 2024; 92:623-636. [PMID: 38083830 DOI: 10.1002/prot.26641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 10/13/2023] [Accepted: 11/09/2023] [Indexed: 04/13/2024]
Abstract
Protein kinases are central to cellular activities and are actively pursued as drug targets for several conditions including cancer and autoimmune diseases. Despite the availability of a large structural database for kinases, methodologies to elucidate the structure-function relationship of these proteins (without manual intervention) are lacking. Such techniques are essential in structural biology and to accelerate drug discovery efforts. Here, we implement an interpretable graph neural network (GNN) framework for classifying the functionally active and inactive states of a large set of protein kinases by only using their tertiary structure and amino acid sequence. We show that the GNN models can classify kinase structures with high accuracy (>97%). We implement the Gradient-weighted Class Activation Mapping for graphs (Graph Grad-CAM) to automatically identify structurally important residues and residue-residue contacts of the kinases without any a priori input. We show that the motifs identified through the Graph Grad-CAM methodology are functionally critical, consistent with the existing kinase literature. Notably, the highly conserved DFG and HRD motifs of the well-known hydrophobic spine are identified by the interpretable framework in addition to some of the lesser known motifs. Further, using Grad-CAM maps as the vector embedding of the protein structures, we identify the subtle differences in the crystal structures among different sub-classes of kinases in the Protein Data Bank (PDB). Frameworks such as the one implemented here, for high-throughput identification of protein structure-function relationships are essential in designing targeted small molecules therapies as well as in engineering new proteins for novel applications.
Collapse
Affiliation(s)
- Ashwin Ravichandran
- KBR Inc., Intelligent Systems Division, NASA Ames Research Center, Moffett Field, California, USA
| | - Juan C Araque
- KBR Inc., Intelligent Systems Division, NASA Ames Research Center, Moffett Field, California, USA
| | - John W Lawson
- Intelligent Systems Division, NASA Ames Research Center, Moffett Field, California, USA
| |
Collapse
|
2
|
Fischer M, Mylo MD, Lorenz LS, Böckenholt L, Beismann H. Stereo Camera Setup for 360° Digital Image Correlation to Reveal Smart Structures of Hakea Fruits. Biomimetics (Basel) 2024; 9:191. [PMID: 38534876 DOI: 10.3390/biomimetics9030191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 03/15/2024] [Accepted: 03/19/2024] [Indexed: 03/28/2024] Open
Abstract
About forty years after its first application, digital image correlation (DIC) has become an established method for measuring surface displacements and deformations of objects under stress. To date, DIC has been used in a variety of in vitro and in vivo studies to biomechanically characterise biological samples in order to reveal biomimetic principles. However, when surfaces of samples strongly deform or twist, they cannot be thoroughly traced. To overcome this challenge, different DIC setups have been developed to provide additional sensor perspectives and, thus, capture larger parts of an object's surface. Herein, we discuss current solutions for this multi-perspective DIC, and we present our own approach to a 360° DIC system based on a single stereo-camera setup. Using this setup, we are able to characterise the desiccation-driven opening mechanism of two woody Hakea fruits over their entire surfaces. Both the breaking mechanism and the actuation of the two valves in predominantly dead plant material are models for smart materials. Based on these results, an evaluation of the setup for 360° DIC regarding its use in deducing biomimetic principles is given. Furthermore, we propose a way to improve and apply the method for future measurements.
Collapse
Affiliation(s)
- Matthias Fischer
- Westfälische Hochschule, Münsterstraße 265, 46397 Bocholt, Germany
| | - Max D Mylo
- Cluster of Excellence livMatS @ FIT-Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg im Breisgau, Germany
- Department of Microsystems Engineering-IMTEK, University of Freiburg, Georges-Köhler-Allee 078, 79110 Freiburg im Breisgau, Germany
| | - Leon S Lorenz
- Westfälische Hochschule, Münsterstraße 265, 46397 Bocholt, Germany
| | - Lars Böckenholt
- Westfälische Hochschule, Münsterstraße 265, 46397 Bocholt, Germany
| | - Heike Beismann
- Westfälische Hochschule, Münsterstraße 265, 46397 Bocholt, Germany
| |
Collapse
|
3
|
Li Z, Wu Q, Huang G, Jin X, Li J, Pan X, Yan N. Dissection of the structure-function relationship of Na v channels. Proc Natl Acad Sci U S A 2024; 121:e2322899121. [PMID: 38381792 PMCID: PMC10907234 DOI: 10.1073/pnas.2322899121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 01/17/2024] [Indexed: 02/23/2024] Open
Abstract
Voltage-gated sodium channels (Nav) undergo conformational shifts in response to membrane potential changes, a mechanism known as the electromechanical coupling. To delineate the structure-function relationship of human Nav channels, we have performed systematic structural analysis using human Nav1.7 as a prototype. Guided by the structural differences between wild-type (WT) Nav1.7 and an eleven mutation-containing variant, designated Nav1.7-M11, we generated three additional intermediate mutants and solved their structures at overall resolutions of 2.9-3.4 Å. The mutant with nine-point mutations in the pore domain (PD), named Nav1.7-M9, has a reduced cavity volume and a sealed gate, with all voltage-sensing domains (VSDs) remaining up. Structural comparison of WT and Nav1.7-M9 pinpoints two residues that may be critical to the tightening of the PD. However, the variant containing these two mutations, Nav1.7-M2, or even in combination with two additional mutations in the VSDs, named Nav1.7-M4, failed to tighten the PD. Our structural analysis reveals a tendency of PD contraction correlated with the right shift of the static inactivation I-V curves. We predict that the channel in the resting state should have a "tight" PD with down VSDs.
Collapse
Affiliation(s)
- Zhangqiang Li
- Beijing Frontier Research Center for Biological Structures, State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing100084, China
| | - Qiurong Wu
- Beijing Frontier Research Center for Biological Structures, State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing100084, China
| | - Gaoxingyu Huang
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou310024, China
| | - Xueqin Jin
- Beijing Frontier Research Center for Biological Structures, State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing100084, China
| | - Jiaao Li
- Beijing Frontier Research Center for Biological Structures, State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing100084, China
| | - Xiaojing Pan
- Beijing Frontier Research Center for Biological Structures, State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing100084, China
- Institute of Bio-Architecture and Bio-Interactions, Shenzhen Medical Academy of Research and Translation, Shenzhen518107, China
| | - Nieng Yan
- Beijing Frontier Research Center for Biological Structures, State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing100084, China
- Institute of Bio-Architecture and Bio-Interactions, Shenzhen Medical Academy of Research and Translation, Shenzhen518107, China
| |
Collapse
|
4
|
Toucheteau C, Deffains V, Gaignard C, Rihouey C, Laroche C, Pierre G, Lépine O, Probert I, Le Cerf D, Michaud P, Arnaudin-Fruitier I, Bridiau N, Maugard T. Role of some structural features in EPS from microalgae stimulating collagen production by human dermal fibroblasts. Bioengineered 2023; 14:2254027. [PMID: 37700452 PMCID: PMC10498797 DOI: 10.1080/21655979.2023.2254027] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 09/14/2023] Open
Abstract
Exopolysaccharides (EPS) from the microalgae Porphyridium cruentum, Chrysotila dentata, Pavlova sp., Diacronema sp., Glossomastix sp., Phaeodactylum tricornutum, and Synechococcus sp. were isolated and depolymerized. First, EPS were submitted to a high pressure pre-treatment step, followed by a solid acid-catalyzed hydrolysis step carried out in a batch or recycle fixed-bed reactor, using a strong acidic cation-exchange resin. Twenty-eight different EPS forms were thus obtained. After characterization of their main structural features (weight- and number-averaged molecular weight, polydispersity index, sulfate and uronic acid contents), we investigated the structure-function relationship of their pro-collagen activity. We found that native microalgae EPS were able to inhibit until 27% of human matrix metalloproteinase-1 (MMP-1) activity while the depolymerized forms were able to enhance collagen production by two different human fibroblast lines, used as cell models due to their major role in dermal collagen biosynthesis. The most active EPS forms, obtained by depolymerization in the recycle fixed-bed reactor of D. ennorea and Glossomastix sp. EPS, led to 390% increase in collagen production. Finally, principal component (PCA) and Pearson analyses indicated that MMP-1 inhibition was strongly correlated to the sulfate group content of EPS whereas collagen production by fibroblasts was mostly related to their proportion of low molecular weight polysaccharides (<10 kDa). Uronic acid content of EPS was also shown essential but only if the size of EPS was reduced in the first place. Altogether, these results gave new insights of the dermo-cosmetic potential of microalgae EPS as well as the key parameters of their activity.
Collapse
Affiliation(s)
- Claire Toucheteau
- La Rochelle Université, UMR CNRS 7266 LIENSs, Equipe Biotechnologie et Chimie des Bioressources pour la Santé, La Rochelle, France
| | - Valentine Deffains
- La Rochelle Université, UMR CNRS 7266 LIENSs, Equipe Biotechnologie et Chimie des Bioressources pour la Santé, La Rochelle, France
| | - Clément Gaignard
- Université Clermont Auvergne, CNRS, Institut Pascal, Aubière, France
| | - Christophe Rihouey
- Université de Rouen Normandie, PBS Laboratory, Mont Saint Aignan, France
| | - Céline Laroche
- Université Clermont Auvergne, CNRS, Institut Pascal, Aubière, France
| | - Guillaume Pierre
- Université Clermont Auvergne, CNRS, Institut Pascal, Aubière, France
| | - Olivier Lépine
- Algosource Technologies, 37 Bd de l’Université, Saint-Nazaire, France
| | - Ian Probert
- Roscoff marine station, CNRS/Sorbonne Université, Roscoff, France
| | - Didier Le Cerf
- Université de Rouen Normandie, PBS Laboratory, Mont Saint Aignan, France
| | - Philippe Michaud
- Université Clermont Auvergne, CNRS, Institut Pascal, Aubière, France
| | - Ingrid Arnaudin-Fruitier
- La Rochelle Université, UMR CNRS 7266 LIENSs, Equipe Biotechnologie et Chimie des Bioressources pour la Santé, La Rochelle, France
| | - Nicolas Bridiau
- La Rochelle Université, UMR CNRS 7266 LIENSs, Equipe Biotechnologie et Chimie des Bioressources pour la Santé, La Rochelle, France
| | - Thierry Maugard
- La Rochelle Université, UMR CNRS 7266 LIENSs, Equipe Biotechnologie et Chimie des Bioressources pour la Santé, La Rochelle, France
| |
Collapse
|
5
|
Erokhin D, Popletaeva S, Sinelnikov I, Rozhkova A, Shcherbakova L, Dzhavakhiya V. Some Structural Elements of Bacterial Protein MF3 That Influence Its Ability to Induce Plant Resistance to Fungi, Viruses, and Other Plant Pathogens. Int J Mol Sci 2023; 24:16374. [PMID: 38003563 PMCID: PMC10671687 DOI: 10.3390/ijms242216374] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 11/01/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
The ability of the MF3 protein from Pseudomonas fluorescens to protect plants by inducing their resistance to pathogenic fungi, bacteria, and viruses is well confirmed both in greenhouses and in the field; however, the molecular basis of this phenomenon remains unexplored. To find a relationship between the primary (and spatial) structure of the protein and its target activity, we analyzed the inducing activity of a set of mutants generated by alanine scanning and an alpha-helix deletion (ahD) in the part of the MF3 molecule previously identified by our group as a 29-amino-acid peptide working as the inducer on its own. Testing the mutants' inducing activity using the "tobacco-tobacco mosaic virus" pathosystem revealed that some of them showed an almost threefold (V60A and V62A) or twofold (G51A, L58A, ahD) reduction in inducing activity compared to the wild-type MF3 type. Interestingly, these mutations demonstrated close proximity in the homology model, probably contributing to MF3 reception in a host plant.
Collapse
Affiliation(s)
- Denis Erokhin
- All-Russian Research Institute of Phytopathology, 143050 Bolshie Vyazemy, Russia; (D.E.); (S.P.); (V.D.)
| | - Sophya Popletaeva
- All-Russian Research Institute of Phytopathology, 143050 Bolshie Vyazemy, Russia; (D.E.); (S.P.); (V.D.)
| | - Igor Sinelnikov
- Federal Research Centre “Fundamentals of Biotechnology”, Russian Academy of Sciences, 119991 Moscow, Russia; (I.S.); (A.R.)
| | - Alexandra Rozhkova
- Federal Research Centre “Fundamentals of Biotechnology”, Russian Academy of Sciences, 119991 Moscow, Russia; (I.S.); (A.R.)
| | - Larisa Shcherbakova
- All-Russian Research Institute of Phytopathology, 143050 Bolshie Vyazemy, Russia; (D.E.); (S.P.); (V.D.)
| | - Vitaly Dzhavakhiya
- All-Russian Research Institute of Phytopathology, 143050 Bolshie Vyazemy, Russia; (D.E.); (S.P.); (V.D.)
| |
Collapse
|
6
|
Zhong J, Huang W, Zhou H. Multifunctionality in Nature: Structure-Function Relationships in Biological Materials. Biomimetics (Basel) 2023; 8:284. [PMID: 37504172 PMCID: PMC10807375 DOI: 10.3390/biomimetics8030284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/25/2023] [Accepted: 06/29/2023] [Indexed: 07/29/2023] Open
Abstract
Modern material design aims to achieve multifunctionality through integrating structures in a diverse range, resulting in simple materials with embedded functions. Biological materials and organisms are typical examples of this concept, where complex functionalities are achieved through a limited material base. This review highlights the multiscale structural and functional integration of representative natural organisms and materials, as well as biomimetic examples. The impact, wear, and crush resistance properties exhibited by mantis shrimp and ironclad beetle during predation or resistance offer valuable inspiration for the development of structural materials in the aerospace field. Investigating cyanobacteria that thrive in extreme environments can contribute to developing living materials that can serve in places like Mars. The exploration of shape memory and the self-repairing properties of spider silk and mussels, as well as the investigation of sensing-actuating and sensing-camouflage mechanisms in Banksias, chameleons, and moths, holds significant potential for the optimization of soft robot designs. Furthermore, a deeper understanding of mussel and gecko adhesion mechanisms can have a profound impact on medical fields, including tissue engineering and drug delivery. In conclusion, the integration of structure and function is crucial for driving innovations and breakthroughs in modern engineering materials and their applications. The gaps between current biomimetic designs and natural organisms are also discussed.
Collapse
Affiliation(s)
| | - Wei Huang
- State Key Laboratory of Materials Processing and Die and Mould Technology, School of Materials Science and Engineering, Huazhong University of Science and Technology, Wuhan 430074, China; (J.Z.); (H.Z.)
| | | |
Collapse
|
7
|
Ohlendorf R, Tan NYH, Nakayama N. Engineering Themes in Plant Forms and Functions. Annu Rev Plant Biol 2023; 74:777-801. [PMID: 37216204 DOI: 10.1146/annurev-arplant-061422-094751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Living structures constantly interact with the biotic and abiotic environment by sensing and responding via specialized functional parts. In other words, biological bodies embody highly functional machines and actuators. What are the signatures of engineering mechanisms in biology? In this review, we connect the dots in the literature to seek engineering principles in plant structures. We identify three thematic motifs-bilayer actuator, slender-bodied functional surface, and self-similarity-and provide an overview of their structure-function relationships. Unlike human-engineered machines and actuators, biological counterparts may appear suboptimal in design, loosely complying with physical theories or engineering principles. We postulate what factors may influence the evolution of functional morphology and anatomy to dissect and comprehend better the why behind the biological forms.
Collapse
Affiliation(s)
- Rahel Ohlendorf
- Department of Bioengineering, Imperial College London, London, United Kingdom;
| | | | - Naomi Nakayama
- Department of Bioengineering, Imperial College London, London, United Kingdom;
| |
Collapse
|
8
|
Ye X, Liu X, Luo X, Sun F, Qin C, Ding L, Zhu W, Zhang H, Zhou H, Chen Z. Characterization of the Molecular Diversity and Degranulation Activity of Mastoparan Family Peptides from Wasp Venoms. Toxins (Basel) 2023; 15:toxins15050331. [PMID: 37235365 DOI: 10.3390/toxins15050331] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 04/21/2023] [Accepted: 04/22/2023] [Indexed: 05/28/2023] Open
Abstract
Wasp stings have become an increasingly serious public health problem because of their high incidence and mortality rates in various countries and regions. Mastoparan family peptides are the most abundant natural peptides in hornet venoms and solitary wasp venom. However, there is a lack of systematic and comprehensive studies on mastoparan family peptides from wasp venoms. In our study, for the first time, we evaluated the molecular diversity of 55 wasp mastoparan family peptides from wasp venoms and divided them into four major subfamilies. Then, we established a wasp peptide library containing all 55 known mastoparan family peptides by chemical synthesis and C-terminal amidation modification, and we systematically evaluated their degranulation activities in two mast cell lines, namely the RBL-2H3 and P815 cell lines. The results showed that among the 55 mastoparans, 35 mastoparans could significantly induce mast cell degranulation, 7 mastoparans had modest mast cell degranulation activity, and 13 mastoparans had little mast cell degranulation activity, suggesting functional variation in mastoparan family peptides from wasp venoms. Structure-function relationship studies found that the composition of amino acids in the hydrophobic face and amidation in the C-terminal region are critical for the degranulation activity of mastoparan family peptides from wasp venoms. Our research will lay a theoretical foundation for studying the mechanism underlying the degranulation activity of wasp mastoparans and provide new evidence to support the molecular design and molecular optimization of natural mastoparan peptides from wasp venoms in the future.
Collapse
Affiliation(s)
- Xiangdong Ye
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, College of Basic Medicine, Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan 442000, China
- Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Hubei University of Medicine, Shiyan 442000, China
| | - Xin Liu
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, College of Basic Medicine, Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan 442000, China
| | - Xudong Luo
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, College of Basic Medicine, Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan 442000, China
- Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Hubei University of Medicine, Shiyan 442000, China
| | - Fang Sun
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, College of Basic Medicine, Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan 442000, China
- Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Hubei University of Medicine, Shiyan 442000, China
| | - Chenhu Qin
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, College of Basic Medicine, Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan 442000, China
- Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Hubei University of Medicine, Shiyan 442000, China
| | - Li Ding
- Department of Clinical Laboratory, Dongfeng Hospital, Hubei University of Medicine, Shiyan 442000, China
| | - Wen Zhu
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, College of Basic Medicine, Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan 442000, China
- Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Hubei University of Medicine, Shiyan 442000, China
| | - Huajun Zhang
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, College of Basic Medicine, Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan 442000, China
| | - Haimei Zhou
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, College of Basic Medicine, Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan 442000, China
| | - Zongyun Chen
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, College of Basic Medicine, Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan 442000, China
- Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Hubei University of Medicine, Shiyan 442000, China
| |
Collapse
|
9
|
Son J, Choi W, Kim H, Kim M, Lee JH, Shin SC, Kim HW. Structural and biochemical insights into PsEst3, a new GHSR-type esterase obtained from Paenibacillus sp. R4. IUCrJ 2023; 10:220-232. [PMID: 36862488 PMCID: PMC9980389 DOI: 10.1107/s2052252523001562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
PsEst3, a psychrophilic esterase obtained from Paenibacillus sp. R4, which was isolated from the permafrost of Alaska, exhibits relatively high activity at low temperatures. Here, crystal structures of PsEst3 complexed with various ligands were generated and studied at atomic resolution, and biochemical studies were performed to analyze the structure-function relationship of PsEst3. Certain unique characteristics of PsEst3 distinct from those of other classes of lipases/esterases were identified. Firstly, PsEst3 contains a conserved GHSRA/G pentapeptide sequence in the GxSxG motif around the nucleophilic serine. Additionally, it contains a conserved HGFR/K consensus sequence in the oxyanion hole, which is distinct from that in other lipase/esterase families, as well as a specific domain composition (for example a helix-turn-helix motif) and a degenerative lid domain that exposes the active site to the solvent. Secondly, the electrostatic potential of the active site in PsEst3 is positive, which may cause unintended binding of negatively charged chemicals in the active site. Thirdly, the last residue of the oxyanion hole-forming sequence, Arg44, separates the active site from the solvent by sealing the acyl-binding pocket, suggesting that PsEst3 is an enzyme that is customized to sense an unidentified substrate that is distinct from those of classical lipases/esterases. Collectively, this evidence strongly suggests that PsEst3 belongs to a distinct family of esterases.
Collapse
Affiliation(s)
- Jonghyeon Son
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of Korea
- New Drug Development Center, Daegu–Gyeongbuk Medical Innovation Foundation, Daegu 41061, Republic of Korea
| | - Woong Choi
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Hyun Kim
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Minseo Kim
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Jun Hyuck Lee
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of Korea
- Department of Polar Sciences, University of Science and Technology, Incheon 21990, Republic of Korea
| | - Seung Chul Shin
- Division of Life Sciences, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Han-Woo Kim
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of Korea
- Department of Polar Sciences, University of Science and Technology, Incheon 21990, Republic of Korea
| |
Collapse
|
10
|
Chuang KH, Li Z, Huang HH, Khorasani Gerdekoohi S, Athwal D. Hemodynamic transient and functional connectivity follow structural connectivity and cell type over the brain hierarchy. Proc Natl Acad Sci U S A 2023; 120:e2202435120. [PMID: 36693103 DOI: 10.1073/pnas.2202435120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The neural circuit of the brain is organized as a hierarchy of functional units with wide-ranging connections that support information flow and functional connectivity. Studies using MRI indicate a moderate coupling between structural and functional connectivity at the system level. However, how do connections of different directions (feedforward and feedback) and regions with different excitatory and inhibitory (E/I) neurons shape the hemodynamic activity and functional connectivity over the hierarchy are unknown. Here, we used functional MRI to detect optogenetic-evoked and resting-state activities over a somatosensory pathway in the mouse brain in relation to axonal projection and E/I distribution. Using a highly sensitive ultrafast imaging, we identified extensive activation in regions up to the third order of axonal projections following optogenetic excitation of the ventral posteriomedial nucleus of the thalamus. The evoked response and functional connectivity correlated with feedforward projections more than feedback projections and weakened with the hierarchy. The hemodynamic response exhibited regional and hierarchical differences, with slower and more variable responses in high-order areas and bipolar response predominantly in the contralateral cortex. Electrophysiological recordings suggest that these reflect differences in neural activity rather than neurovascular coupling. Importantly, the positive and negative parts of the hemodynamic response correlated with E/I neuronal densities, respectively. Furthermore, resting-state functional connectivity was more associated with E/I distribution, whereas stimulus-evoked effective connectivity followed structural wiring. These findings indicate that the structure-function relationship is projection-, cell-type- and hierarchy-dependent. Hemodynamic transients could reflect E/I activity and the increased complexity of hierarchical processing.
Collapse
|
11
|
Pandey KN. Guanylyl cyclase/natriuretic peptide receptor-A: Identification, molecular characterization, and physiological genomics. Front Mol Neurosci 2023; 15:1076799. [PMID: 36683859 PMCID: PMC9846370 DOI: 10.3389/fnmol.2022.1076799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 12/02/2022] [Indexed: 01/06/2023] Open
Abstract
The natriuretic peptides (NPs) hormone family, which consists mainly of atrial, brain, and C-type NPs (ANP, BNP, and CNP), play diverse roles in mammalian species, ranging from renal, cardiac, endocrine, neural, and vascular hemodynamics to metabolic regulations, immune responsiveness, and energy distributions. Over the last four decades, new data has transpired regarding the biochemical and molecular compositions, signaling mechanisms, and physiological and pathophysiological functions of NPs and their receptors. NPs are incremented mainly in eliciting natriuretic, diuretic, endocrine, vasodilatory, and neurological activities, along with antiproliferative, antimitogenic, antiinflammatory, and antifibrotic responses. The main locus responsible in the biological and physiological regulatory actions of NPs (ANP and BNP) is the plasma membrane guanylyl cyclase/natriuretic peptide receptor-A (GC-A/NPRA), a member of the growing multi-limbed GC family of receptors. Advances in this field have provided tremendous insights into the critical role of Npr1 (encoding GC-A/NPRA) in the reduction of fluid volume and blood pressure homeostasis, protection against renal and cardiac remodeling, and moderation and mediation of neurological disorders. The generation and use of genetically engineered animals, including gene-targeted (gene-knockout and gene-duplication) and transgenic mutant mouse models has revealed and clarified the varied roles and pleiotropic functions of GC-A/NPRA in vivo in intact animals. This review provides a chronological development of the biochemical, molecular, physiological, and pathophysiological functions of GC-A/NPRA, including signaling pathways, genomics, and gene regulation in both normal and disease states.
Collapse
|
12
|
An K, Zhu X, Bai C. The Nature of Functional Features of Different Classes of G-Protein-Coupled Receptors. Biology (Basel) 2022; 11:biology11121839. [PMID: 36552350 PMCID: PMC9775959 DOI: 10.3390/biology11121839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/14/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022]
Abstract
G-protein-coupled receptors (GPCRs) are a critical family in the human proteome and are involved in various physiological processes. They are also the most important drug target, with approximately 30% of approved drugs acting on such receptors. The members of the family are divided into six classes based on their structural and functional characteristics. Understanding their structural-functional relationships will benefit us in future drug development. In this article, we investigate the features of protein function, structure, and energy that describe the dynamics of the GPCR activation process between different families. GPCRs straddle the cell membrane and transduce signals from outside the membrane into the cell. During the process, the conformational change in GPCRs that is activated by the binding of signal molecules is essential. During the binding process, different types of signal molecules result in different signal transfer efficiencies. Therefore, the GPCR classes show a variety of structures and activation processes. Based on the experimental crystal structures, we modeled the activation process of the β2 adrenergic receptor (β2AR), glucagon receptor (GCGR), and metabotropic glutamate receptor 2 (mGluR2), which represent class A, B, and C GPCRs, respectively. We calculated their activation free-energy landscapes and analyzed the structure-energy-function relationship. The results show a consistent picture of the activation mechanisms between different types of GPCRs. This could also provide us a way to understand other signal transduction proteins.
Collapse
Affiliation(s)
- Ke An
- Warshel Institute for Computational Biology, School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen 518172, China
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, China
| | - Xiaohong Zhu
- Warshel Institute for Computational Biology, School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen 518172, China
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, China
| | - Chen Bai
- Warshel Institute for Computational Biology, School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen 518172, China
- Chenzhu (MoMeD) Biotechnology Co., Ltd., Hangzhou 310005, China
- Correspondence:
| |
Collapse
|
13
|
Siemer AB. What makes functional amyloids work? Crit Rev Biochem Mol Biol 2022; 57:399-411. [PMID: 35997712 PMCID: PMC9588633 DOI: 10.1080/10409238.2022.2113030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 06/29/2022] [Accepted: 08/10/2022] [Indexed: 01/27/2023]
Abstract
Although first described in the context of disease, cross-β (amyloid) fibrils have also been found as functional entities in all kingdoms of life. However, what are the specific properties of the cross-β fibril motif that convey biological function, make them especially suited for their particular purpose, and distinguish them from other fibrils found in biology? This review approaches these questions by arguing that cross-β fibrils are highly periodic, stable, and self-templating structures whose formation is accompanied by substantial conformational change that leads to a multimerization of their core and framing sequences. A discussion of each of these properties is followed by selected examples of functional cross-β fibrils that show how function is usually achieved by leveraging many of these properties.
Collapse
Affiliation(s)
- Ansgar B Siemer
- Department of Physiology and Neuroscience, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| |
Collapse
|
14
|
Wang L. Designing a Dual GLP-1R/GIPR Agonist from Tirzepatide: Comparing Residues Between Tirzepatide, GLP-1, and GIP. Drug Des Devel Ther 2022; 16:1547-1559. [PMID: 35651477 PMCID: PMC9149770 DOI: 10.2147/dddt.s358989] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 05/18/2022] [Indexed: 12/13/2022] Open
Abstract
Improving type 2 diabetes using incretin analogues is becoming increasingly plausible. Currently, tirzepatide is the most promising listed incretin analogue. Here, I briefly explain the evolution of drugs of this kind, analyze the residue discrepancies between tirzepatide and endogenous incretins, summarize some existing strategies for prolonging half-life, and present suggestions for future research, mainly involving biased functions. This review aims to present some useful information for designing a dual glucagon like peptide-1 receptor/glucose-dependent insulinotropic polypeptide receptor agonist. ![]()
Point your SmartPhone at the code above. If you have a QR code reader the video abstract will appear. Or use: https://youtu.be/yo_lgebnhRo
Collapse
Affiliation(s)
- Lijing Wang
- College of Life Sciences and Technology, China Pharmaceutical University, Nanjing, Jiangsu, People's Republic of China
| |
Collapse
|
15
|
Abstract
Mental terms—such as perception, cognition, action, emotion, as well as attention, memory, decision-making—are epistemically sterile. We support our thesis based on extensive comparative neuroanatomy knowledge of the organization of the vertebrate brain. Evolutionary pressures have moulded the central nervous system to promote survival. Careful characterization of the vertebrate brain shows that its architecture supports an enormous amount of communication and integration of signals, especially in birds and mammals. The general architecture supports a degree of ‘computational flexibility’ that enables animals to cope successfully with complex and ever-changing environments. Here, we suggest that the vertebrate neuroarchitecture does not respect the boundaries of standard mental terms, and propose that neuroscience should aim to unravel the dynamic coupling between large-scale brain circuits and complex, naturalistic behaviours. This article is part of the theme issue ‘Systems neuroscience through the lens of evolutionary theory’.
Collapse
Affiliation(s)
- Luiz Pessoa
- Department of Psychology, University of Maryland, College Park, MD 20742, USA
| | - Loreta Medina
- Department of Experimental Medicine, Institut de Recerca Biomèdica de Lleida Fundació Dr. Pifarré (IRBLleida), University of Lleida, 25198 Lleida, Spain
| | - Ester Desfilis
- Department of Experimental Medicine, Institut de Recerca Biomèdica de Lleida Fundació Dr. Pifarré (IRBLleida), University of Lleida, 25198 Lleida, Spain
| |
Collapse
|
16
|
Luikham S, Bhattacharyya J. Targeting Natural Polymeric DNAs with Harmane: An Insight into Binding and Thermodynamic Interaction Through Biophysical Approach. DNA Cell Biol 2022; 41:91-102. [PMID: 35049377 DOI: 10.1089/dna.2021.0132] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
DNA is one of the major molecular targets for a broad range of anticancer drugs. Hence, interaction studies involving cellular DNA and small molecules can be highly beneficial as they often lead to rational and efficient drug design. In this study, the binding interaction of Harmane (a naturally occurring, bioactive indole alkaloid) with two natural polymeric DNAs, that is, Calf thymus (CT) DNA and Herring testis (HT) DNA has been elucidated using biophysical techniques. A ground state, 1:1 complexation, was revealed by steady-state fluorescence spectroscopy. The thermodynamic profile and energetics of the associated reaction were evaluated by temperature-dependent fluorescence spectroscopy. The spontaneity of the binding was confirmed by the negative ΔG° values in both cases. Negative enthalpy change, along with stronger positive entropic contribution, indicated the dominant electrostatic nature of the interaction and finally the entropy-driven exothermic binding process throughout. Salt-dependent studies further demonstrated the significant contribution of electrostatic interactions in ligand binding toward DNA. Infrared data substantiated the structural information of the said interactions, leading to the exploration of the structure-function relationship.
Collapse
Affiliation(s)
- Soching Luikham
- Department of Chemistry, National Institute of Technology Nagaland, Chumukedima, Dimapur, India
| | - Jhimli Bhattacharyya
- Department of Chemistry, National Institute of Technology Nagaland, Chumukedima, Dimapur, India
| |
Collapse
|
17
|
Bäcklund FG, Schmuck B, Miranda GHB, Greco G, Pugno NM, Rydén J, Rising A. An Image-Analysis-Based Method for the Prediction of Recombinant Protein Fiber Tensile Strength. Materials (Basel) 2022; 15:ma15030708. [PMID: 35160653 PMCID: PMC8915176 DOI: 10.3390/ma15030708] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/11/2022] [Accepted: 01/13/2022] [Indexed: 01/27/2023]
Abstract
Silk fibers derived from the cocoon of silk moths and the wide range of silks produced by spiders exhibit an array of features, such as extraordinary tensile strength, elasticity, and adhesive properties. The functional features and mechanical properties can be derived from the structural composition and organization of the silk fibers. Artificial recombinant protein fibers based on engineered spider silk proteins have been successfully made previously and represent a promising way towards the large-scale production of fibers with predesigned features. However, for the production and use of protein fibers, there is a need for reliable objective quality control procedures that could be automated and that do not destroy the fibers in the process. Furthermore, there is still a lack of understanding the specifics of how the structural composition and organization relate to the ultimate function of silk-like fibers. In this study, we develop a new method for the categorization of protein fibers that enabled a highly accurate prediction of fiber tensile strength. Based on the use of a common light microscope equipped with polarizers together with image analysis for the precise determination of fiber morphology and optical properties, this represents an easy-to-use, objective non-destructive quality control process for protein fiber manufacturing and provides further insights into the link between the supramolecular organization and mechanical functionality of protein fibers.
Collapse
Affiliation(s)
- Fredrik G. Bäcklund
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo, 14186 Huddinge, Sweden; (B.S.); (A.R.)
- Correspondence:
| | - Benjamin Schmuck
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo, 14186 Huddinge, Sweden; (B.S.); (A.R.)
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
| | - Gisele H. B. Miranda
- Division of Computational Science and Technology, KTH Royal Institute of Technology, 10044 Stockholm, Sweden;
- BioImage Informatics Facility, Science for Life Laboratory, 17165 Solna, Sweden
| | - Gabriele Greco
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
- Laboratory for Bioinspired, Bionic, Nano, Meta, Materials & Mechanics, Department of Civil, Environmental and Mechanical Engineering, University of Trento, Via Mesiano, 77, 38123 Trento, Italy; (G.G.); (N.M.P.)
| | - Nicola M. Pugno
- Laboratory for Bioinspired, Bionic, Nano, Meta, Materials & Mechanics, Department of Civil, Environmental and Mechanical Engineering, University of Trento, Via Mesiano, 77, 38123 Trento, Italy; (G.G.); (N.M.P.)
- School of Engineering and Materials Science, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Jesper Rydén
- Department of Energy and Technology, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden;
| | - Anna Rising
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo, 14186 Huddinge, Sweden; (B.S.); (A.R.)
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
| |
Collapse
|
18
|
Kumar A, Paul M, Panda M, Jayaram S, Kalidindi N, Sale H, Vetrichelvan M, Gupta A, Mathur A, Beno B, Regueiro-Ren A, Cheng D, Ramarao M, Ghosh K. Molecular mechanism of interspecies differences in the binding affinity of TD139 to Galectin-3. Glycobiology 2021; 31:1390-1400. [PMID: 34228782 DOI: 10.1093/glycob/cwab072] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 05/26/2021] [Accepted: 06/29/2021] [Indexed: 01/07/2023] Open
Abstract
Galectin-3 (Gal-3), a β-galactoside-binding lectin, has been implicated in a plethora of pathological disorders including fibrosis, inflammation, cancer and metabolic diseases. TD139-a thio-digalactoside inhibitor developed by Galecto Biotech as a potential therapeutic for idiopathic pulmonary fibrosis-is the most advanced small-molecule Gal-3 inhibitor in clinical studies. It binds to human Gal-3 with high affinity but has lower affinity towards mouse and rat homologs, which is also manifested in the differential inhibition of Gal-3 function. Using biophysical methods and high-resolution X-ray co-crystal structures of TD139 and Gal-3 proteins, we demonstrate that a single amino acid change corresponding to A146 in human Gal-3 is sufficient for the observed reduction in the binding affinity of TD139 in rodents. Site-directed mutagenesis of A146V (in human Gal-3) and V160A (in mouse Gal-3) was sufficient to interchange the affinities, mainly by affecting the off rates of the inhibitor binding. In addition, molecular dynamics simulations of both wild-type and mutant structures revealed the sustained favorable noncovalent interactions between the fluorophenyl ring and the active site A146 (human Gal-3 and mouse V160A) that corroborate the finding from biophysical studies. Current findings have ramifications in the context of optimization of drug candidates against Gal-3.
Collapse
Affiliation(s)
- Amit Kumar
- Discovery Biology and Translational Medicine, Biocon Bristol-Myers Squibb R&D Center, Bristol-Myers Squibb India Pvt. Ltd, Bangalore 560099, India
| | - Marilyn Paul
- Discovery Biology and Translational Medicine, Biocon Bristol-Myers Squibb R&D Center, Bristol-Myers Squibb India Pvt. Ltd, Bangalore 560099, India
| | - Manoranjan Panda
- Medicinal Chemistry, Biocon Bristol-Myers Squibb R&D Center, Bristol-Myers Squibb India Pvt. Ltd, Bangalore 560099, India
| | - Shruthi Jayaram
- Discovery Biology and Translational Medicine, Biocon Bristol-Myers Squibb R&D Center, Bristol-Myers Squibb India Pvt. Ltd, Bangalore 560099, India
| | - Narasimharaju Kalidindi
- Discovery Biology and Translational Medicine, Biocon Bristol-Myers Squibb R&D Center, Bristol-Myers Squibb India Pvt. Ltd, Bangalore 560099, India
| | - Harinath Sale
- Discovery Biology and Translational Medicine, Biocon Bristol-Myers Squibb R&D Center, Bristol-Myers Squibb India Pvt. Ltd, Bangalore 560099, India
| | - Muthalagu Vetrichelvan
- Department of Discovery Synthesis, Biocon Bristol-Myers Squibb R&D Center, Bristol-Myers Squibb India Pvt. Ltd, Bangalore 560099, India
| | - Anuradha Gupta
- Department of Discovery Synthesis, Biocon Bristol-Myers Squibb R&D Center, Bristol-Myers Squibb India Pvt. Ltd, Bangalore 560099, India
| | - Arvind Mathur
- Bristol-Myers Squibb Research and Development, PO Box 4000, Princeton, NJ 08543, USA
| | - Brett Beno
- Bristol-Myers Squibb Research and Development, PO Box 4000, Princeton, NJ 08543, USA
| | - Alicia Regueiro-Ren
- Bristol-Myers Squibb Research and Development, PO Box 4000, Princeton, NJ 08543, USA
| | - Dong Cheng
- Bristol-Myers Squibb Research and Development, PO Box 4000, Princeton, NJ 08543, USA
| | - Manjunath Ramarao
- Discovery Biology and Translational Medicine, Biocon Bristol-Myers Squibb R&D Center, Bristol-Myers Squibb India Pvt. Ltd, Bangalore 560099, India
| | - Kaushik Ghosh
- Discovery Biology and Translational Medicine, Biocon Bristol-Myers Squibb R&D Center, Bristol-Myers Squibb India Pvt. Ltd, Bangalore 560099, India
| |
Collapse
|
19
|
Banfalvi G. Janus-Faced Molecules against Plant Pathogenic Fungi. Int J Mol Sci 2021; 22:12323. [PMID: 34830204 PMCID: PMC8623416 DOI: 10.3390/ijms222212323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/08/2021] [Accepted: 11/11/2021] [Indexed: 11/16/2022] Open
Abstract
The high cytotoxicity of the secondary metabolites of mycotoxins is capable of killing microbes and tumour cells alike, similarly to the genotoxic effect characteristic of Janus-faced molecules. The "double-edged sword" effect of several cytotoxins is known, and these agents have, therefore, been utilized only reluctantly against fungal infections. In this review, consideration was given to (a) toxins that could be used against plant and human pathogens, (b) animal models that measure the effect of antifungal agents, (c) known antifungal agents that have been described and efficiently prevent the growth of fungal cells, and (d) the chemical interactions that are characteristic of antifungal agents. The utilization of apoptotic effects against tumour growth by agents that, at the same time, induce mutations may raise ethical issues. Nevertheless, it deserves consideration despite the mutagenic impact of Janus-faced molecules for those patients who suffer from plant pathogenic fungal infections and are older than their fertility age, in the same way that the short-term cytotoxicity of cancer treatment is favoured over the long-term mutagenic effect.
Collapse
Affiliation(s)
- Gaspar Banfalvi
- Department of Molecular Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, 1 Egyetem Square, 4010 Debrecen, Hungary
| |
Collapse
|
20
|
Lippold S, Knaupp A, de Ru AH, Tjokrodirijo RTN, van Veelen PA, van Puijenbroek E, de Taeye SW, Reusch D, Vidarsson G, Wuhrer M, Schlothauer T, Falck D. Fc gamma receptor IIIb binding of individual antibody proteoforms resolved by affinity chromatography-mass spectrometry. MAbs 2021; 13:1982847. [PMID: 34674601 PMCID: PMC8726612 DOI: 10.1080/19420862.2021.1982847] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The crystallizable fragment (Fc) of immunoglobulin G (IgG) activates key immunological responses by interacting with Fc gamma receptors (FcɣR). FcɣRIIIb contributes to neutrophil activation and is involved in antibody-dependent cellular cytotoxicity (ADCC) and antibody-dependent cellular phagocytosis (ADCP). These processes present important mechanisms-of-actions of therapeutic antibodies. The very low affinity of IgG toward FcɣRIIIb (KD ~ 10 µM) is a technical challenge for interaction studies. Additionally, the interaction is strongly dependent on IgG glycosylation, a major contributor to proteoform heterogeneity. We developed an affinity chromatography–mass spectrometry (AC-MS) assay for analyzing IgG-FcɣRIIIb interactions in a proteoform-resolved manner. This proved to be well suited to study low-affinity interactions. The applicability and selectivity of the method were demonstrated on a panel of nine different IgG monoclonal antibodies (mAbs), including no-affinity, low-affinity and high-affinity Fc-engineered or glycoengineered mAbs. Thereby, we could reproduce reported affinity rankings of different IgG glycosylation features and IgG subclasses. Additional post-translational modifications (IgG1 Met252 oxidation, IgG3 hinge-region O-glycosylation) showed no effect on FcɣRIIIb binding. Interestingly, we observed indications of an effect of the variable domain sequence on the Fc-binding that deserves further attention. Our new AC-MS method is a powerful tool for expanding knowledge on structure–function relationships of the IgG-FcɣRIIIb interaction. Hence, this assay may substantially improve the efficiency of assessing critical quality attributes of therapeutic mAbs with respect to an important aspect of neutrophil activation.
Collapse
Affiliation(s)
- Steffen Lippold
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Alexander Knaupp
- Pharma Research and Early Development, Roche Innovation Center, Munich, Germany
| | - Arnoud H de Ru
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Rayman T N Tjokrodirijo
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter A van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Steven W de Taeye
- Department of Experimental Immunohematology, Sanquin Research and Landsteiner Laboratory, Amsterdam Umc, University of Amsterdam, Amsterdam, The Netherlands
| | - Dietmar Reusch
- Pharma Technical Development, Roche Innovation Center, Munich, Germany
| | - Gestur Vidarsson
- Department of Experimental Immunohematology, Sanquin Research and Landsteiner Laboratory, Amsterdam Umc, University of Amsterdam, Amsterdam, The Netherlands
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Tilman Schlothauer
- Pharma Research and Early Development, Roche Innovation Center, Munich, Germany.,Biological Technologies, Genentech Inc, South San Francisco, USA
| | - David Falck
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| |
Collapse
|
21
|
Lee JY, Kim JH, La TY, Choi JA. Structure-Function Relationship and Vision-Related Quality of Life in Glaucoma Secondary to Anterior Uveitis: Comparison with Open Angle Glaucoma. J Clin Med 2021; 10:4231. [PMID: 34575341 DOI: 10.3390/jcm10184231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/13/2021] [Accepted: 09/15/2021] [Indexed: 12/13/2022] Open
Abstract
Purpose: The aim of this study is to investigate the structure–function characteristics and vision-related quality of life (VR-QoL) in uveitic glaucoma (UG) compared with open-angle glaucoma (OAG). Method: The study included 69 patients with UG and 138 patients with primary open angle glaucoma, normal-tension glaucoma. A 25-item National Eye Institute Visual Function Questionnaire (VFQ-25) was used to evaluate the patients’ VR-QoL. The retinal nerve fiber layer thickness (RNFLT) was measured using optical coherence tomography, and the integrated visual field (IVF) was determined using the best location method. Results: There were no significant differences in the binocular IVF and mean deviation (MD) of the affected eye between the OAG and UG group, whereas the average RNFLT was significant thinner in the OAG group (p = 0.008). The patients with UG showed a significantly lower composite score and five subscales of the VFQ-25, compared with those with OAG (p < 0.05, for all, general linear model). Multivariate linear regression analyses showed that the composite score showed the strongest associations with the whole IVF (β = 1.240, p < 0.001) in the OAG group, whereas in the UG group, a significant association was seen only with the inferior VF of the affected eye (β = 0.596, p = 0.038). Conclusions: The eyes with UG exhibited distinctive structure–function characteristics and worse VR-QoL that differentiated them from OAG eyes.
Collapse
|
22
|
Sun YQ, Ge Y. Temporal Changes in the Function of Bacterial Assemblages Associated With Decomposing Earthworms. Front Microbiol 2021; 12:682224. [PMID: 34456883 PMCID: PMC8386022 DOI: 10.3389/fmicb.2021.682224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 07/19/2021] [Indexed: 11/29/2022] Open
Abstract
Soil invertebrate corpse decomposition is an ecologically significant, yet poorly understood, process affecting nutrient biogeochemical cycling in terrestrial ecosystems. Here, we attempted to answer how the substrate chemistry and microbial community change during soil invertebrate (earthworm) decomposition and what roles microbes play in this process. Specifically, the dead earthworms (Amynthas corticis) were buried in two soils where the earthworms inhabited, or not, until more than 50% of the earthworm mass was lost. For both soils, earthworms decomposed faster during the early stage (between 0 and 3 days), as reflected by the higher rate of decomposition and increased accumulation of dissolved organic matter (DOM). This decomposition pattern was paralleled by bacterial community dynamics, where bacterial richness and diversity were significantly higher during early decomposition (p < 0.05) with the relative abundances of many genera decreasing as decomposition progressed. The succession of the bacterial community composition was significantly correlated with time-course changes in DOM composition (p < 0.05). Particularly, more functional groups (e.g., microbes associated with carbon, nitrogen, and sulfur cycling) were identified to be linked with the change of a specific DOM type during the early decomposition phase. By exploring the ecologically important process of soil invertebrate decomposition and its associated bacterial communities, this study provides evidence, e.g., a statistically significant positive correlation between bacterial community and DOM compositions, which supports the widely recognized yet less-tested microbial community structure–function relationship hypothesis in invertebrate decomposition.
Collapse
Affiliation(s)
- Yao-Qin Sun
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yuan Ge
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
23
|
Hniopek J, Bocklitz T, Schmitt M, Popp J. Probing Protein Secondary Structure Influence on Active Centers with Hetero Two-Dimensional Correlation (Resonance) Raman Spectroscopy: A Demonstration on Cytochrome C. Appl Spectrosc 2021; 75:1043-1052. [PMID: 34242104 PMCID: PMC8320570 DOI: 10.1177/00037028211028916] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 06/10/2021] [Indexed: 06/13/2023]
Abstract
The functionality of active centers in proteins is governed by the secondary and higher structure of proteins which often lead to structures in the active center that are different from the structures found in protein-free models of the active center. To elucidate this structure-function relationship, it is therefore necessary to investigate both the protein structure and the local structure of the active center. In this work, we investigate the application of hetero (resonance) Raman two-dimensional correlation spectroscopy (2D-COS) to this problem. By employing a combination of near-infrared-Fourier transform-Raman- and vis-resonance Raman spectroscopy, we could show that this combination of techniques is able to directly probe the structure-function relationship of proteins. We were able to correlate the transition of the heme center in cytochrome c from low to high spin with changes in the secondary structure with the above mentioned two spectroscopic in situ techniques and without sample preparation. Thereby, we were able to reveal that the combination of a spectroscopic method to selectively observe the active center with a technique that monitors the whole system offers a promising toolkit to investigate the structure-function relationship of proteins with photoactive centers in general.
Collapse
Affiliation(s)
- Julian Hniopek
- Department of Spectroscopy/Imaging, Leibniz-Institute of Photonic Technologies, Jena, Germany
- Institute of Physical Chemistry & Abbe Center of Photonics, Friedrich Schiller University Jena, Jena, Germany
| | - Thomas Bocklitz
- Department of Spectroscopy/Imaging, Leibniz-Institute of Photonic Technologies, Jena, Germany
- Department of Photonic Data Science, Leibniz-Institute of Photonic Technologies, Jena, Germany
| | - Michael Schmitt
- Institute of Physical Chemistry & Abbe Center of Photonics, Friedrich Schiller University Jena, Jena, Germany
| | - Jürgen Popp
- Department of Spectroscopy/Imaging, Leibniz-Institute of Photonic Technologies, Jena, Germany
- Institute of Physical Chemistry & Abbe Center of Photonics, Friedrich Schiller University Jena, Jena, Germany
| |
Collapse
|
24
|
Buck M. Letting go: Deep computational modeling insights into pH-dependent calcium affinity. J Biol Chem 2021; 297:100974. [PMID: 34280436 PMCID: PMC8350533 DOI: 10.1016/j.jbc.2021.100974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Calcium and other cofactors can feature as key additions to a molecular interface, to the extent that the cofactor is completely buried in the bound state. How can such an interaction be regulated then? The answer: By facilitating a switch through an allosteric network. Although a number of unbinding mechanisms are being characterized, an extensive computational study by Joswig et al. reveals a detailed model for the pattern recognition receptor langerin.
Collapse
Affiliation(s)
- Matthias Buck
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio, USA.
| |
Collapse
|
25
|
Abstract
An antimicrobial supramolecular assembly (ASA) is conspicuous in biomedical applications. Among the alternatives to overcome microbial resistance to antibiotics and drugs, ASAs, including antimicrobial peptides (AMPs) and polymers (APs), provide formulations with optimal antimicrobial activity and acceptable toxicity. AMPs and APs have been delivered by a variety of carriers such as nanoparticles, coatings, multilayers, hydrogels, liposomes, nanodisks, lyotropic lipid phases, nanostructured lipid carriers, etc. They have similar mechanisms of action involving adsorption to the cell wall, penetration across the cell membrane, and microbe lysis. APs, however, offer the advantage of cheap synthetic procedures, chemical stability, and improved adsorption (due to multipoint attachment to microbes), as compared to the expensive synthetic routes, poor yield, and subpar in vivo stability seen in AMPs. We review recent advances in polymer-based antimicrobial assemblies involving AMPs and APs.
Collapse
Affiliation(s)
- Ana Maria Carmona-Ribeiro
- Biocolloids Laboratory, Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Professor Lineu Prestes 748, São Paulo 05508-000, Brazil;
| | | |
Collapse
|
26
|
Abstract
The structural paradigm that the sequence of a protein encodes for a unique three-dimensional native fold does not acknowledge the intrinsic plasticity encapsulated in conformational free energy landscapes. Metamorphic proteins are a recently discovered class of biomolecules that illustrate this plasticity by folding into at least two distinct native state structures of comparable stability in the absence of ligands or cofactors to facilitate fold-switching. The expanding list of metamorphic proteins clearly shows that these proteins are not mere aberrations in protein evolution, but may have actually been a consequence of distinctive patterns in selection pressure such as those found in virus–host co-evolution. In this review, we describe the structure–function relationships observed in well-studied metamorphic protein systems, with specific focus on how functional residues are sequestered or exposed in the two folds of the protein. We also discuss the implications of metamorphosis for protein evolution and the efforts that are underway to predict metamorphic systems from sequence properties alone.
Collapse
Affiliation(s)
- Kulkarni Madhurima
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - Bodhisatwa Nandi
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - Ashok Sekhar
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| |
Collapse
|
27
|
Kalienkova V, Clerico Mosina V, Paulino C. The Groovy TMEM16 Family: Molecular Mechanisms of Lipid Scrambling and Ion Conduction. J Mol Biol 2021; 433:166941. [PMID: 33741412 DOI: 10.1016/j.jmb.2021.166941] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/09/2021] [Accepted: 03/09/2021] [Indexed: 12/28/2022]
Abstract
The TMEM16 family of membrane proteins displays a remarkable functional dichotomy - while some family members function as Ca2+-activated anion channels, the majority of characterized TMEM16 homologs are Ca2+-activated lipid scramblases, which catalyze the exchange of phospholipids between the two membrane leaflets. Furthermore, some TMEM16 scramblases can also function as channels. Due to their involvement in important physiological processes, the family has been actively studied ever since their molecular identity was unraveled. In this review, we will summarize the recent advances in the field and how they influenced our view of TMEM16 family function and evolution. Structural, functional and computational studies reveal how relatively small rearrangements in the permeation pathway are responsible for the observed functional duality: while TMEM16 scramblases can adopt both ion- and lipid conductive conformations, TMEM16 channels can only populate the former. Recent data further provides the molecular details of a stepwise activation mechanism, which is initiated by Ca2+ binding and modulated by various cellular factors, including lipids. TMEM16 function and the surrounding membrane properties are inextricably intertwined, with the protein inducing bilayer deformations associated with scrambling, while the surrounding lipids modulate TMEM16 conformation and activity.
Collapse
|
28
|
Rachadech W, Kato Y, Abou El-Magd RM, Shishido Y, Kim SH, Sogabe H, Maita N, Yorita K, Fukui K. P219L substitution in human D-amino acid oxidase impacts the ligand binding and catalytic efficiency. J Biochem 2021; 168:557-567. [PMID: 32730563 DOI: 10.1093/jb/mvaa083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 06/23/2020] [Indexed: 11/13/2022] Open
Abstract
Human D-amino acid oxidase (DAO) is a flavoenzyme that is implicated in neurodegenerative diseases. We investigated the impact of replacement of proline with leucine at Position 219 (P219L) in the active site lid of human DAO on the structural and enzymatic properties, because porcine DAO contains leucine at the corresponding position. The turnover numbers (kcat) of P219L were unchanged, but its Km values decreased compared with wild-type, leading to an increase in the catalytic efficiency (kcat/Km). Moreover, benzoate inhibits P219L with lower Ki value (0.7-0.9 µM) compared with wild-type (1.2-2.0 µM). Crystal structure of P219L in complex with flavin adenine dinucleotide (FAD) and benzoate at 2.25 Å resolution displayed conformational changes of the active site and lid. The distances between the H-bond-forming atoms of arginine 283 and benzoate and the relative position between the aromatic rings of tyrosine 224 and benzoate were changed in the P219L complex. Taken together, the P219L substitution leads to an increase in the catalytic efficiency and binding affinity for substrates/inhibitors due to these structural changes. Furthermore, an acetic acid was located near the adenine ring of FAD in the P219L complex. This study provides new insights into the structure-function relationship of human DAO.
Collapse
Affiliation(s)
- Wanitcha Rachadech
- Division of Enzyme Pathophysiology, Institute for Enzyme Research, Tokushima University, 3-18-15 Kuramoto, Tokushima 770-8503, Japan.,Division of Chemistry, Faculty of Science, Udon Thani Rajabhat University, 64 Thahan Road, Muang, Udon Thani 41000, Thailand
| | - Yusuke Kato
- Division of Enzyme Pathophysiology, Institute for Enzyme Research, Tokushima University, 3-18-15 Kuramoto, Tokushima 770-8503, Japan
| | - Rabab M Abou El-Magd
- Division of Enzyme Pathophysiology, Institute for Enzyme Research, Tokushima University, 3-18-15 Kuramoto, Tokushima 770-8503, Japan
| | - Yuji Shishido
- Division of Enzyme Pathophysiology, Institute for Enzyme Research, Tokushima University, 3-18-15 Kuramoto, Tokushima 770-8503, Japan
| | - Soo Hyeon Kim
- Division of Enzyme Pathophysiology, Institute for Enzyme Research, Tokushima University, 3-18-15 Kuramoto, Tokushima 770-8503, Japan
| | - Hirofumi Sogabe
- Division of Enzyme Pathophysiology, Institute for Enzyme Research, Tokushima University, 3-18-15 Kuramoto, Tokushima 770-8503, Japan
| | - Nobuo Maita
- Division of Disease Proteomics, Institute for Enzyme Research, Tokushima University, 3-18-15 Kuramoto, Tokushima 770-8503, Japan
| | - Kazuko Yorita
- Division of Enzyme Pathophysiology, Institute for Enzyme Research, Tokushima University, 3-18-15 Kuramoto, Tokushima 770-8503, Japan
| | - Kiyoshi Fukui
- Division of Enzyme Pathophysiology, Institute for Enzyme Research, Tokushima University, 3-18-15 Kuramoto, Tokushima 770-8503, Japan
| |
Collapse
|
29
|
Fuentes-Prior P. Priming of SARS-CoV-2 S protein by several membrane-bound serine proteinases could explain enhanced viral infectivity and systemic COVID-19 infection. J Biol Chem 2020; 296:100135. [PMID: 33268377 PMCID: PMC7834812 DOI: 10.1074/jbc.rev120.015980] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 11/30/2020] [Accepted: 12/02/2020] [Indexed: 12/13/2022] Open
Abstract
The ongoing COVID-19 pandemic has already caused over a million deaths worldwide, and this death toll will be much higher before effective treatments and vaccines are available. The causative agent of the disease, the coronavirus SARS-CoV-2, shows important similarities with the previously emerged SARS-CoV-1, but also striking differences. First, SARS-CoV-2 possesses a significantly higher transmission rate and infectivity than SARS-CoV-1 and has infected in a few months over 60 million people. Moreover, COVID-19 has a systemic character, as in addition to the lungs, it also affects the heart, liver, and kidneys among other organs of the patients and causes frequent thrombotic and neurological complications. In fact, the term "viral sepsis" has been recently coined to describe the clinical observations. Here I review current structure-function information on the viral spike proteins and the membrane fusion process to provide plausible explanations for these observations. I hypothesize that several membrane-associated serine proteinases (MASPs), in synergy with or in place of TMPRSS2, contribute to activate the SARS-CoV-2 spike protein. Relative concentrations of the attachment receptor, ACE2, MASPs, their endogenous inhibitors (the Kunitz-type transmembrane inhibitors, HAI-1/SPINT1 and HAI-2/SPINT2, as well as major circulating serpins) would determine the infection rate of host cells. The exclusive or predominant expression of major MASPs in specific human organs suggests a direct role of these proteinases in e.g., heart infection and myocardial injury, liver dysfunction, kidney damage, as well as neurological complications. Thorough consideration of these factors could have a positive impact on the control of the current COVID-19 pandemic.
Collapse
Affiliation(s)
- Pablo Fuentes-Prior
- Molecular Bases of Disease, Biomedical Research Institute (IIB) Sant Pau, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain.
| |
Collapse
|
30
|
Cheung MY, Ngo JC, Chen Z, Jia Q, Li T, Gou Y, Wang Y, Lam HM. A structure model explaining the binding between a ubiquitous unconventional G-protein (OsYchF1) and a plant-specific C2-domain protein (OsGAP1) from rice. Biochem J 2020; 477:3935-49. [PMID: 32955089 DOI: 10.1042/BCJ20200380] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 09/08/2020] [Accepted: 09/21/2020] [Indexed: 11/17/2022]
Abstract
The unconventional G-protein OsYchF1 plays regulatory roles in plant defense and abiotic stress responses. We have previously resolved the crystal structures of OsYchF1 and its plant-specific regulator, OsGAP1, and determined the residues on OsGAP1 that are essential for its binding to OsYchF1. In this study, we employed site-directed mutagenesis to identify four critical residues on the TGS domain of OsYchF1 that are critical for its binding to OsGAP1. We also generated a docking model of the OsYchF1 : OsGAP1 complex to dissect the molecular basis of their interactions. Our finding not only reveals the roles of the key interacting residues controlling the binding between OsYchF1 and OsGAP1, but also provides a working model on the potential regulatory mechanism mediated by a TGS domain, particularly in the class of GTPase of the OBG family.
Collapse
|
31
|
Sajid N, Parr T, Gajardo-Vidal A, Price CJ, Friston KJ. Paradoxical lesions, plasticity and active inference. Brain Commun 2020; 2:fcaa164. [PMID: 33376985 PMCID: PMC7750943 DOI: 10.1093/braincomms/fcaa164] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/07/2020] [Accepted: 09/09/2020] [Indexed: 12/01/2022] Open
Abstract
Paradoxical lesions are secondary brain lesions that ameliorate functional deficits caused by the initial insult. This effect has been explained in several ways; particularly by the reduction of functional inhibition, or by increases in the excitatory-to-inhibitory synaptic balance within perilesional tissue. In this article, we simulate how and when a modification of the excitatory-inhibitory balance triggers the reversal of a functional deficit caused by a primary lesion. For this, we introduce in-silico lesions to an active inference model of auditory word repetition. The first in-silico lesion simulated damage to the extrinsic (between regions) connectivity causing a functional deficit that did not fully resolve over 100 trials of a word repetition task. The second lesion was implemented in the intrinsic (within region) connectivity, compromising the model's ability to rebalance excitatory-inhibitory connections during learning. We found that when the second lesion was mild, there was an increase in experience-dependent plasticity that enhanced performance relative to a single lesion. This paradoxical lesion effect disappeared when the second lesion was more severe because plasticity-related changes were disproportionately amplified in the intrinsic connectivity, relative to lesioned extrinsic connections. Finally, this framework was used to predict the physiological correlates of paradoxical lesions. This formal approach provides new insights into the computational and neurophysiological mechanisms that allow some patients to recover after large or multiple lesions.
Collapse
Affiliation(s)
- Noor Sajid
- Wellcome Centre for Human Neuroimaging, University College London, London WC1N 3AR, UK
| | - Thomas Parr
- Wellcome Centre for Human Neuroimaging, University College London, London WC1N 3AR, UK
| | - Andrea Gajardo-Vidal
- Wellcome Centre for Human Neuroimaging, University College London, London WC1N 3AR, UK
| | - Cathy J Price
- Wellcome Centre for Human Neuroimaging, University College London, London WC1N 3AR, UK
| | - Karl J Friston
- Wellcome Centre for Human Neuroimaging, University College London, London WC1N 3AR, UK
| |
Collapse
|
32
|
Elimari N, Lafargue G. Network Neuroscience and the Adapted Mind: Rethinking the Role of Network Theories in Evolutionary Psychology. Front Psychol 2020; 11:545632. [PMID: 33101120 PMCID: PMC7545950 DOI: 10.3389/fpsyg.2020.545632] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 09/02/2020] [Indexed: 11/29/2022] Open
Abstract
Evolutionary psychology is the comprehensive study of cognition and behavior in the light of evolutionary theory, a unifying paradigm integrating a huge diversity of findings across different levels of analysis. Since natural selection shaped the brain into a functionally organized system of interconnected neural structures rather than an aggregate of separate neural organs, the network-based account of anatomo-functional architecture is bound to yield the best mechanistic explanation for how the brain mediates the onset of evolved cognition and adaptive behaviors. While this view of a flexible and highly distributed organization of the brain is more than a century old, it was largely ignored up until recently. Technological advances are only now allowing this approach to find its rightful place in the scientific landscape. Historically, early network theories mostly relied on lesion studies and investigations on white matter circuitry, subject areas that still provide great empirical findings to this day. Thanks to new neuroimaging techniques, the traditional localizationist framework, in which any given cognitive process is thought to be carried out by its dedicated brain structure, is slowly being abandoned in favor of a network-based approach. We argue that there is a special place for network neuroscience in the upcoming quest for the biological basis of information-processing systems identified by evolutionary psychologists. By reviewing history of network theories, and by addressing several theoretical and methodological implications of this view for evolutionary psychologists, we describe the current state of knowledge about human neuroanatomy for those who wish to be mindful of both evolutionary and network neuroscience paradigms.
Collapse
Affiliation(s)
| | - Gilles Lafargue
- Department of Psychology, Université de Reims Champagne Ardenne, C2S EA 6291, Reims, France
| |
Collapse
|
33
|
Khan MI, Hariprasad G. Human Secretary Phospholipase A2 Mutations and Their Clinical Implications. J Inflamm Res 2020; 13:551-561. [PMID: 32982370 PMCID: PMC7502393 DOI: 10.2147/jir.s269557] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 08/13/2020] [Indexed: 01/05/2023] Open
Abstract
Phospholipases A2 (PLA2s) belong to a superfamily of enzymes responsible for hydrolysis of the sn-2 fatty acids of membrane phospholipids to release arachidonic acid. PLA2s are the rate limiting enzyme for the downstream synthesis of prostaglandins and leukotrienes that are the main mediators of inflammation. The extracellular forms of this enzyme are also called the secretary phospholipase A2 (sPLA2) and are distributed extensively in most of the tissues in the human body. Their integral role in inflammatory pathways has been the primary reason for the extensive research on this molecule. The catalytic mechanism of sPLA2 is initiated by a histidine/aspartic acid/calcium complex within the active site. Though they are known to have certain housekeeping functions, certain mutations of sPLA2 are known to be implicated in causation of certain pathologies leading to diseases such as atherosclerosis, cardiovascular diseases, benign fleck retina, neurodegeneration, and asthma. We present an overview of human sPLA2 and a comprehensive compilation of the mutations that result in various disease phenotypes. The study not only helps to have a holistic understanding of human sPLA2 mutations and their clinical implications, but is also a useful platform to initiate research pertaining to structure–function relationship of the mutations to develop effective therapies for management of these diseases.
Collapse
Affiliation(s)
- Mohd Imran Khan
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Gururao Hariprasad
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| |
Collapse
|
34
|
Abstract
Glaucoma, a well-defined group of progressive optic neuropathies is one of the leading causes of irreversible blindness worldwide. In order to stop or slow down the progression of glaucomatous vision deterioration, intraocular pressure reduction by medical, laser or surgical treatment is needed. To ensure that treatment is efficient and tailored to the actual needs both cross sectional evaluation of disease severity and measurement of rate of progression are essential. Currently staging and progression are investigated with visual field and retinal thickness measurements. Perimetry, however, is influenced by several biological factors which are not related to glaucoma, and the use of retinal thinning is limited by floor effect. Therefore, clinical application of optical retinal coherence tomography angiography, a new and rapidly developing non-invasive measurement of the capillary perfusion in the various retinal layers, respectively, is now in the focus of clinical glaucoma research. This comprehensive review summarizes the current knowledge on one of the most important research areas in optical coherence tomography angiography in glaucoma, the relationship between retinal capillary perfusion and the spatially corresponding visual field threshold sensitivity.
Collapse
Affiliation(s)
- Gábor Holló
- Department of Ophthalmology, Semmelweis University, Budapest, Hungary
| |
Collapse
|
35
|
Hollenbach R, Völp AR, Höfert L, Rudat J, Ochsenreither K, Willenbacher N, Syldatk C. Interfacial and Foaming Properties of Tailor-Made Glycolipids-Influence of the Hydrophilic Head Group and Functional Groups in the Hydrophobic Tail. Molecules 2020; 25:molecules25173797. [PMID: 32825508 PMCID: PMC7504461 DOI: 10.3390/molecules25173797] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 08/16/2020] [Accepted: 08/19/2020] [Indexed: 11/20/2022] Open
Abstract
Glycolipids are a class of biodegradable surfactants less harmful to the environment than petrochemically derived surfactants. Here we discuss interfacial properties, foam stability, characterized in terms of transient foam height, gas volume fraction and bubble diameter as well as texture of seven enzymatically synthesized surfactants for the first time. Glycolipids consisting of different head groups, namely glucose, sorbitol, glucuronic acid and sorbose, combined with different C10 acyl chains, namely decanoate, dec-9-enoate and 4-methyl-nonanoate are compared. Equilibrium interfacial tension values vary between 24.3 and 29.6 mN/m, critical micelle concentration varies between 0.7 and 3.0 mM. In both cases highest values were found for the surfactants with unsaturated or branched tail groups. Interfacial elasticity and viscosity, however, were significantly reduced in these cases. Head and tail group both affect foam stability. Foams from glycolipids with sorbose and glucuronic acid derived head groups showed higher stability than those from surfactants with glucose head group, sorbitol provided lowest foam stability. We attribute this to different head group hydration also showing up in the time to reach equilibrium interfacial adsorption. Unsaturated tail groups reduced whereas branching enhanced foam stability compared to the systems with linear, saturated tail. Moreover, the tail group strongly influences foam texture. Glycolipids with unsaturated tail groups produced foams quickly collapsing even at smallest shear loads, whereas the branched tail group yielded a higher modulus than the linear tails. Normalized shear moduli for the systems with different head groups varied in a narrow range, with the highest value found for decylglucuronate.
Collapse
Affiliation(s)
- Rebecca Hollenbach
- Technical Biology, Institute of Process Engineering in Life Sciences II, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany; (L.H.); (J.R.); (K.O.); (C.S.)
- Correspondence: ; Tel.:+49-721-60846737
| | - Annika Ricarda Völp
- Applied Mechanics, Institute of Mechanical Process Engineering and Mechanics, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany; (A.R.V.); (N.W.)
| | - Ludwig Höfert
- Technical Biology, Institute of Process Engineering in Life Sciences II, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany; (L.H.); (J.R.); (K.O.); (C.S.)
| | - Jens Rudat
- Technical Biology, Institute of Process Engineering in Life Sciences II, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany; (L.H.); (J.R.); (K.O.); (C.S.)
| | - Katrin Ochsenreither
- Technical Biology, Institute of Process Engineering in Life Sciences II, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany; (L.H.); (J.R.); (K.O.); (C.S.)
| | - Norbert Willenbacher
- Applied Mechanics, Institute of Mechanical Process Engineering and Mechanics, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany; (A.R.V.); (N.W.)
| | - Christoph Syldatk
- Technical Biology, Institute of Process Engineering in Life Sciences II, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany; (L.H.); (J.R.); (K.O.); (C.S.)
| |
Collapse
|
36
|
Ramirez-Ramirez J, Martin-Diaz J, Pastor N, Alcalde M, Ayala M. Exploring the Role of Phenylalanine Residues in Modulating the Flexibility and Topography of the Active Site in the Peroxygenase Variant PaDa-I. Int J Mol Sci 2020; 21:E5734. [PMID: 32785123 DOI: 10.3390/ijms21165734] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 08/07/2020] [Accepted: 08/07/2020] [Indexed: 11/28/2022] Open
Abstract
Unspecific peroxygenases (UPOs) are fungal heme-thiolate enzymes able to catalyze a wide range of oxidation reactions, such as peroxidase-like, catalase-like, haloperoxidase-like, and, most interestingly, cytochrome P450-like. One of the most outstanding properties of these enzymes is the ability to catalyze the oxidation a wide range of organic substrates (both aromatic and aliphatic) through cytochrome P450-like reactions (the so-called peroxygenase activity), which involves the insertion of an oxygen atom from hydrogen peroxide. To catalyze this reaction, the substrate must access a channel connecting the bulk solution to the heme group. The composition, shape, and flexibility of this channel surely modulate the catalytic ability of the enzymes in this family. In order to gain an understanding of the role of the residues comprising the channel, mutants derived from PaDa-I, a laboratory-evolved UPO variant from Agrocybe aegerita, were obtained. The two phenylalanine residues at the surface of the channel, which regulate the traffic towards the heme active site, were mutated by less bulky residues (alanine and leucine). The mutants were experimentally characterized, and computational studies (i.e., molecular dynamics (MD)) were performed. The results suggest that these residues are necessary to reduce the flexibility of the region and maintain the topography of the channel.
Collapse
|
37
|
Kavanagh MA, Karlsson JKG, Colburn JD, Barter LMC, Gould IR. A TDDFT investigation of the Photosystem II reaction center: Insights into the precursors to charge separation. Proc Natl Acad Sci U S A 2020; 117:19705-12. [PMID: 32747579 DOI: 10.1073/pnas.1922158117] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Examining the excited states of the Photosystem II reaction center furthers our understanding of available charge separation pathways that lead to successful photosynthesis. Our results comprise the largest complete model of the Photosystem II reaction center to be described using time-dependent density functional theory reported in the literature to date. We reveal the molecular orbitals contributing to the excited states that are precursors to charge separation. We demonstrate that our model can successfully predict the action of specific mutations, a valuable tool for the agricultural industry. These models may also be beneficial in informing the design of artificial photosynthetic complexes as well as enhanced bioengineered photosystems. Photosystem II (PS II) captures solar energy and directs charge separation (CS) across the thylakoid membrane during photosynthesis. The highly oxidizing, charge-separated state generated within its reaction center (RC) drives water oxidation. Spectroscopic studies on PS II RCs are difficult to interpret due to large spectral congestion, necessitating modeling to elucidate key spectral features. Herein, we present results from time-dependent density functional theory (TDDFT) calculations on the largest PS II RC model reported to date. This model explicitly includes six RC chromophores and both the chlorin phytol chains and the amino acid residues <6 Å from the pigments’ porphyrin ring centers. Comparing our wild-type model results with calculations on mutant D1-His-198-Ala and D2-His-197-Ala RCs, our simulated absorption-difference spectra reproduce experimentally observed shifts in known chlorophyll absorption bands, demonstrating the predictive capabilities of this model. We find that inclusion of both nearby residues and phytol chains is necessary to reproduce this behavior. Our calculations provide a unique opportunity to observe the molecular orbitals that contribute to the excited states that are precursors to CS. Strikingly, we observe two high oscillator strength, low-lying states, in which molecular orbitals are delocalized over ChlD1 and PheD1 as well as one weaker oscillator strength state with molecular orbitals delocalized over the P chlorophylls. Both these configurations are a match for previously identified exciton–charge transfer states (ChlD1+PheD1−)* and (PD2+PD1−)*. Our results demonstrate the power of TDDFT as a tool, for studies of natural photosynthesis, or indeed future studies of artificial photosynthetic complexes.
Collapse
|
38
|
Fedeli D, Del Maschio N, Caprioglio C, Sulpizio S, Abutalebi J. Sulcal Pattern Variability and Dorsal Anterior Cingulate Cortex Functional Connectivity Across Adult Age. Brain Connect 2020; 10:267-278. [PMID: 32567343 DOI: 10.1089/brain.2020.0751] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Background: The dorsal anterior cingulate cortex (dACC) is a key network hub for cognitive control and environmental adaptation. Previous studies have shown that task-based functional activity in this area is constrained by individual differences in sulcal pattern, a morphologic feature of cortex anatomy determined during fetal life and stable throughout development. Methods: By using anatomical magnetic resonance imaging and seed-based resting-state functional connectivity (rsFC), we explored the influence of sulcal pattern variability on the functional architecture of the dACC in a sample of healthy adults aged 20-80 years (n = 173). Results: Overall, rsFC was associated with individual differences in sulcal pattern. Furthermore, rsFC was modulated by the age-sulcal pattern interaction. Conclusion: Our results suggest a relationship between brain structure and function that partly traces back to early stages of brain development. The modulation of rsFC by the age-sulcal pattern interaction indicates that the effects of sulcal pattern variability on the functional architecture of the dACC may change over adulthood, with potential repercussions for brain network efficiency and cognitive function in aging.
Collapse
Affiliation(s)
- Davide Fedeli
- Centre for Neurolinguistics and Psycholinguistics (CNPL), Università Vita-Salute San Raffaele, Milano, Italy
| | - Nicola Del Maschio
- Centre for Neurolinguistics and Psycholinguistics (CNPL), Università Vita-Salute San Raffaele, Milano, Italy
| | - Camilla Caprioglio
- Laboratory of Neuroimaging of Aging (LANVIE), University of Geneva, Geneva, Switzerland
| | - Simone Sulpizio
- Centre for Neurolinguistics and Psycholinguistics (CNPL), Università Vita-Salute San Raffaele, Milano, Italy.,Department of Psychology, University of Milano-Bicocca, Milano, Italy
| | - Jubin Abutalebi
- Centre for Neurolinguistics and Psycholinguistics (CNPL), Università Vita-Salute San Raffaele, Milano, Italy.,The Arctic University of Norway, Tromsø, Norway.,Centre for Cognition and Decision Making, National Research University Higher School of Economics, Moscow, Russia
| |
Collapse
|
39
|
Bhatt HB, Singh SP. Cloning, Expression, and Structural Elucidation of a Biotechnologically Potential Alkaline Serine Protease From a Newly Isolated Haloalkaliphilic Bacillus lehensis JO-26. Front Microbiol 2020; 11:941. [PMID: 32582046 PMCID: PMC7283590 DOI: 10.3389/fmicb.2020.00941] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 04/20/2020] [Indexed: 12/14/2022] Open
Abstract
An alkaline protease gene of Bacillus lehensis JO-26 from saline desert, Little Rann of Kutch, was cloned and expressed in Escherichia coli BL21 (DE3). A 1,014-bp ORF encoded 337 amino acids. The recombinant protease (APrBL) with Asp 97, His 127, and Ser 280 forming catalytic triad belongs to the subtilase S8 protease family. The gene was optimally expressed in soluble fraction with 0.2 mM isopropyl β-D-thiogalactopyranoside (IPTG), 2% (w/v) NaCl at 28°C. APrBL, a monomer with a molecular mass of 34.6 kDa was active over pH 8–11 and 30°C−70°C, optimally at pH 10 and 50°C. The enzyme was highly thermostable and retained 73% of the residual activity at 80°C up to 3 h. It was significantly stimulated by sodium dodecyl sulfate (SDS), Ca2+, chloroform, toluene, n-butanol, and benzene while completely inhibited by phenylmethylsulfonyl fluoride (PMSF) and Hg2+. The serine nature of the protease was confirmed by its strong inhibition by PMSF. The APrBL gene was phylogenetically close to alkaline elastase YaB (P20724) and was distinct from the well-known commercial proteases subtilisin Carlsberg (CAB56500) and subtilisin BPN′ (P00782). The structural elucidation revealed 31.75% α-helices, 22.55% β-strands, and 45.70% coils. Although high glycine and fewer proline residues are a characteristic feature of the cold-adapted enzymes, the similar observation in thermally active APrBL suggests that this feature cannot be solely responsible for thermo/cold adaptation. The APrBL protease was highly effective as a detergent additive and in whey protein hydrolysis.
Collapse
Affiliation(s)
- Hitarth B Bhatt
- UGC-CAS Department of Biosciences, Saurashtra University, Rajkot, India
| | - Satya P Singh
- UGC-CAS Department of Biosciences, Saurashtra University, Rajkot, India
| |
Collapse
|
40
|
Moulisová V, Jiřík M, Schindler C, Červenková L, Pálek R, Rosendorf J, Arlt J, Bolek L, Šůsová S, Nietzsche S, Liška V, Dahmen U. Novel morphological multi-scale evaluation system for quality assessment of decellularized liver scaffolds. J Tissue Eng 2020; 11:2041731420921121. [PMID: 32523667 PMCID: PMC7257850 DOI: 10.1177/2041731420921121] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 04/02/2020] [Indexed: 12/19/2022] Open
Abstract
Decellularized scaffolds can serve as an excellent three-dimensional environment for cell repopulation. They maintain tissue-specific microarchitecture of extracellular matrix proteins with important spatial cues for cell adhesion, migration, growth, and differentiation. However, criteria for quality assessment of the three-dimensional structure of decellularized scaffolds are rather fragmented, usually study-specific, and mostly semi-quantitative. Thus, we aimed to develop a robust structural assessment system for decellularized porcine liver scaffolds. Five scaffolds of different quality were used to establish the new evaluation system. We combined conventional semi-quantitative scoring criteria with a quantitative scaffold evaluation based on automated image analysis. For the quantitation, we developed a specific open source software tool (ScaffAn) applying algorithms designed for texture analysis, segmentation, and skeletonization. ScaffAn calculates selected parameters characterizing structural features of porcine liver scaffolds such as the sinusoidal network. After evaluating individual scaffolds, the total scores predicted scaffold interaction with cells in terms of cell adhesion. Higher scores corresponded to higher numbers of cells attached to the scaffolds. Moreover, our analysis revealed that the conventional system could not identify fine differences between good quality scaffolds while the additional use of ScaffAn allowed discrimination. This led us to the conclusion that only using the combined score resulted in the best discrimination between different quality scaffolds. Overall, our newly defined evaluation system has the potential to select the liver scaffolds most suitable for recellularization, and can represent a step toward better success in liver tissue engineering.
Collapse
Affiliation(s)
- Vladimíra Moulisová
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University in Prague, Pilsen, Czech Republic
| | - Miroslav Jiřík
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University in Prague, Pilsen, Czech Republic.,Department of Cybernetics, University of West Bohemia, Pilsen, Czech Republic
| | - Claudia Schindler
- Experimental Transplantation Surgery, Department of General, Visceral and Vascular Surgery, University Hospital Jena, Jena, Germany
| | - Lenka Červenková
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University in Prague, Pilsen, Czech Republic.,Department of Pathology, Third Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Richard Pálek
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University in Prague, Pilsen, Czech Republic.,Department of Surgery, Faculty of Medicine in Pilsen, Charles University in Prague, Pilsen, Czech Republic
| | - Jáchym Rosendorf
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University in Prague, Pilsen, Czech Republic.,Department of Surgery, Faculty of Medicine in Pilsen, Charles University in Prague, Pilsen, Czech Republic
| | - Janine Arlt
- Experimental Transplantation Surgery, Department of General, Visceral and Vascular Surgery, University Hospital Jena, Jena, Germany
| | - Lukáš Bolek
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University in Prague, Pilsen, Czech Republic.,Department of Biophysics, Faculty of Medicine in Pilsen, Charles University in Prague, Pilsen, Czech Republic
| | - Simona Šůsová
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University in Prague, Pilsen, Czech Republic.,Department of Toxicogenomics, National Institute of Public Health, Prague, Czech Republic
| | - Sandor Nietzsche
- Centre for Electron Microscopy, University Hospital Jena, Jena, Germany
| | - Václav Liška
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University in Prague, Pilsen, Czech Republic.,Department of Surgery, Faculty of Medicine in Pilsen, Charles University in Prague, Pilsen, Czech Republic
| | - Uta Dahmen
- Experimental Transplantation Surgery, Department of General, Visceral and Vascular Surgery, University Hospital Jena, Jena, Germany
| |
Collapse
|
41
|
Azouz RAM, Hegazy UM, Said MM, Bassuiny RI, Salem AM, Fahmy AS. Improving the catalytic efficiency of thermostable Geobacillus stearothermophilus xylanase XT6 by single-amino acid substitution. J Biochem 2020; 167:203-215. [PMID: 31617574 DOI: 10.1093/jb/mvz086] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 10/02/2019] [Indexed: 01/09/2023] Open
Abstract
Directed evolution using error-prone polymerase chain reaction was employed in the current study to enhance the catalytic efficiency of a thermostable Geobacillus stearothermophilus xylanase XT6 parent. High-throughput screening identified two variants with enhanced activity. Sequencing analysis revealed the presence of a single-amino acid substitution (P209L or V161L) in each variant. The maximum activity of mutant V161L and P209L was at 85°C and 70°C, respectively. Both mutants exhibited maximum activity at pH 7. The thermal and alkaline tolerance of mutant V161L only were markedly improved. The two mutants were more resistant to ethanol inhibition than the parent. Substrate specificity of the two mutants was shifted from beechwood xylan to birchwood xylan. The potential of the two mutants to hydrolyze rice straw and sugarcane bagasse increased. Both turnover number (kcat) and catalytic efficiency (kcat/kM) increased 12.2- and 5.7-folds for variant P209L and 13- and 6.5-folds for variant V161L, respectively, towards birchwood xylan. Based on the previously published crystal structure of extracellular G. stearothermophilus xylanase XT6, V161L and P209L mutation locate on βα-loops. Conformational changes of the respective loops could potentiate the loop swinging, product release and consequently result in enhancement of the catalytic performance.
Collapse
Affiliation(s)
- Rasha A M Azouz
- Genetic Engineering and Biotechnology Research Division, Molecular Biology Department, National Research Centre, El-Behouth Street, Dokki, 12622 Giza, Egypt
| | - Usama M Hegazy
- Genetic Engineering and Biotechnology Research Division, Molecular Biology Department, National Research Centre, El-Behouth Street, Dokki, 12622 Giza, Egypt
| | - Mahmoud M Said
- Faculty of Science, Department of Biochemistry, Ain Shams University, El-Khalyfa El-Mamoun Street, Abbasya, 11566 Cairo, Egypt
| | - Roqaya I Bassuiny
- Genetic Engineering and Biotechnology Research Division, Molecular Biology Department, National Research Centre, El-Behouth Street, Dokki, 12622 Giza, Egypt
| | - Ahmed M Salem
- Faculty of Science, Department of Biochemistry, Ain Shams University, El-Khalyfa El-Mamoun Street, Abbasya, 11566 Cairo, Egypt
| | - Afaf S Fahmy
- Genetic Engineering and Biotechnology Research Division, Molecular Biology Department, National Research Centre, El-Behouth Street, Dokki, 12622 Giza, Egypt
| |
Collapse
|
42
|
Tararina MA, Allen KN. Bioinformatic Analysis of the Flavin-Dependent Amine Oxidase Superfamily: Adaptations for Substrate Specificity and Catalytic Diversity. J Mol Biol 2020; 432:3269-3288. [PMID: 32198115 DOI: 10.1016/j.jmb.2020.03.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 02/24/2020] [Accepted: 03/06/2020] [Indexed: 12/29/2022]
Abstract
The flavin-dependent amine oxidase (FAO) superfamily consists of over 9000 nonredundant sequences represented in all domains of life. Of the thousands of members identified, only 214 have been functionally annotated to date, and 40 unique structures are represented in the Protein Data Bank. The few functionally characterized members share a catalytic mechanism involving the oxidation of an amine substrate through transfer of a hydride to the FAD cofactor, with differences observed in substrate specificities. Previous studies have focused on comparing a subset of superfamily members. Here, we present a comprehensive analysis of the FAO superfamily based on reaction mechanism and substrate recognition. Using a dataset of 9192 sequences, a sequence similarity network, and subsequently, a genome neighborhood network were constructed, organizing the superfamily into eight subgroups that accord with substrate type. Likewise, through phylogenetic analysis, the evolutionary relationship of subgroups was determined, delineating the divergence between enzymes based on organism, substrate, and mechanism. In addition, using sequences and atomic coordinates of 22 structures from the Protein Data Bank to perform sequence and structural alignments, active-site elements were identified, showing divergence from the canonical aromatic-cage residues to accommodate large substrates. These specificity determinants are held in a structural framework comprising a core domain catalyzing the oxidation of amines with an auxiliary domain for substrate recognition. Overall, analysis of the FAO superfamily reveals a modular fold with cofactor and substrate-binding domains allowing for diversity of recognition via insertion/deletions. This flexibility allows facile evolution of new activities, as shown by reinvention of function between subfamilies.
Collapse
Affiliation(s)
- Margarita A Tararina
- Program in Biomolecular Pharmacology, Boston University School of Medicine, 72 East Concord Street, Boston, MA 02118, USA
| | - Karen N Allen
- Program in Biomolecular Pharmacology, Boston University School of Medicine, 72 East Concord Street, Boston, MA 02118, USA; Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, MA 02215, USA.
| |
Collapse
|
43
|
Kim J, Ko J, Hong C, So I. Structure-Function Relationship and Physiological Roles of Transient Receptor Potential Canonical (TRPC) 4 and 5 Channels. Cells 2019; 9:E73. [PMID: 31892199 DOI: 10.3390/cells9010073] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 12/24/2019] [Accepted: 12/24/2019] [Indexed: 12/11/2022] Open
Abstract
The study of the structure–function relationship of ion channels has been one of the most challenging goals in contemporary physiology. Revelation of the three-dimensional (3D) structure of ion channels has facilitated our understanding of many of the submolecular mechanisms inside ion channels, such as selective permeability, voltage dependency, agonist binding, and inter-subunit multimerization. Identifying the structure–function relationship of the ion channels is clinically important as well since only such knowledge can imbue potential therapeutics with practical possibilities. In a sense, recent advances in the understanding of the structure–relationship of transient receptor potential canonical (TRPC) channels look promising since human TRPC channels are calcium-permeable, non-selective cation channels expressed in many tissues such as the gastrointestinal (GI) tract, kidney, heart, vasculature, and brain. TRPC channels are known to regulate GI contractility and motility, pulmonary hypertension, right ventricular hypertrophy, podocyte injury, seizure, fear, anxiety-like behavior, and many others. In this article, we tried to elaborate recent findings of Cryo-EM (cryogenic-electron microscopy) based structural information of TRPC 4 and 5 channels and domain-specific functions of the channel, such as G-protein mediated activation mechanism, extracellular modification of the channel, homo/hetero-tetramerization, and pharmacological gating mechanisms.
Collapse
|
44
|
Ford RC, Marshall-Sabey D, Schuetz J. Linker Domains: Why ABC Transporters 'Live in Fragments no Longer'. Trends Biochem Sci 2020; 45:137-48. [PMID: 31839525 DOI: 10.1016/j.tibs.2019.11.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/30/2019] [Accepted: 11/13/2019] [Indexed: 11/20/2022]
Abstract
ATP-binding cassette (ABC) transporters are membrane proteins present in all kingdoms of life. We have considered the disordered region that connects the N- and C-terminal halves in many eukaryotic ABC transporters, allowing all four consensus functional domains to be linked. The recent availability of structures of ABC transporters containing linker regions has allowed us to identify the start and end points of the connectors as well as hinting at their localisation. We address questions such as: Where did the linker regions come from? Why do some ABC transporters have connectors and others not? What are the rules and roles of the linker regions? What are the consequences of mutations in these connector regions for disease in humans?
Collapse
|
45
|
Ryskamp DA, Zhemkov V, Bezprozvanny I. Mutational Analysis of Sigma-1 Receptor's Role in Synaptic Stability. Front Neurosci 2019; 13:1012. [PMID: 31607852 PMCID: PMC6761230 DOI: 10.3389/fnins.2019.01012] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Accepted: 09/05/2019] [Indexed: 01/01/2023] Open
Abstract
Sigma-1 receptor (S1R) is an endoplasmic reticulum (ER) resident transmembrane protein. In our previous experiments, we demonstrated neuroprotective effects of pridopidine, an agonist of S1R, in cellular and animal models of Huntington’s disease (HD) and Alzheimer’s disease (AD). Consistent with previous observations, deletion of endogenous S1R with CRISPR/Cas9 in cultured hippocampal neurons resulted in fewer mushroom-shaped dendritic spines. Overexpression of human S1R restored mushroom spine density to control levels. In contrast, overexpression of S1R with the Δ31–50 deletion (linked to distal hereditary motor neuropathy) or the E102Q mutation (linked to amyotrophic lateral sclerosis) destabilized mushroom spines. Recently a crystal structure of S1R was determined in lipidic cubic phase. In the present study, we took an advantage of this structural information and performed docking studies with pridopidine and the S1R structural model. We generated a series of S1R point mutations based on residues predicted to be involved in direct association with pridopidine. We discovered that all ligand binding-site mutants were able to compensate for loss of endogenous S1R. However, most of these mutants were not able to support pridopidine-induced rescue of mushroom spines in presenilin-1-mutant cultures. Our mutational analysis was in agreement with in silico docking based on the published S1R crystal structure, with an exception of R119 residue. Our data also suggest that basal S1R activity is required for mature spine stability, whereas agonist-mediated S1R activity is required for stabilization of mushroom spines in the context of disease-causing mutations.
Collapse
Affiliation(s)
- Daniel A Ryskamp
- Department of Physiology, UT Southwestern Medical Center, Dallas, TX, United States
| | - Vladimir Zhemkov
- Department of Physiology, UT Southwestern Medical Center, Dallas, TX, United States
| | - Ilya Bezprozvanny
- Department of Physiology, UT Southwestern Medical Center, Dallas, TX, United States.,Laboratory of Molecular Neurodegeneration, Peter the Great Saint Petersburg State Polytechnic University, Saint Petersburg, Russia
| |
Collapse
|
46
|
Lang DE, Morris JS, Rowley M, Torres MA, Maksimovich VA, Facchini PJ, Ng KKS. Structure-function studies of tetrahydroprotoberberine N-methyltransferase reveal the molecular basis of stereoselective substrate recognition. J Biol Chem 2019; 294:14482-14498. [PMID: 31395658 DOI: 10.1074/jbc.ra119.009214] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 08/01/2019] [Indexed: 12/18/2022] Open
Abstract
Benzylisoquinoline alkaloids (BIAs) are a structurally diverse class of plant-specialized metabolites that have been particularly well-studied in the order Ranunculales. The N-methyltransferases (NMTs) in BIA biosynthesis can be divided into three groups according to substrate specificity and amino acid sequence. Here, we report the first crystal structures of enzyme complexes from the tetrahydroprotoberberine NMT (TNMT) subclass, specifically for GfTNMT from the yellow horned poppy (Glaucium flavum). GfTNMT was co-crystallized with the cofactor S-adenosyl-l-methionine (d min = 1.6 Å), the product S-adenosyl-l-homocysteine (d min = 1.8 Å), or in complex with S-adenosyl-l-homocysteine and (S)-cis-N-methylstylopine (d min = 1.8 Å). These structures reveal for the first time how a mostly hydrophobic L-shaped substrate recognition pocket selects for the (S)-cis configuration of the two central six-membered rings in protoberberine BIA compounds. Mutagenesis studies confirm and functionally define the roles of several highly-conserved residues within and near the GfTNMT-active site. The substrate specificity of TNMT enzymes appears to arise from the arrangement of subgroup-specific stereospecific recognition elements relative to catalytic elements that are more widely-conserved among all BIA NMTs. The binding mode of protoberberine compounds to GfTNMT appears to be similar to coclaurine NMT, with the isoquinoline rings buried deepest in the binding pocket. This binding mode differs from that of pavine NMT, in which the benzyl ring is bound more deeply than the isoquinoline rings. The insights into substrate recognition and catalysis provided here form a sound basis for the rational engineering of NMT enzymes for chemoenzymatic synthesis and metabolic engineering.
Collapse
Affiliation(s)
- Dean E Lang
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Jeremy S Morris
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Michael Rowley
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Miguel A Torres
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada.,Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305
| | - Vook A Maksimovich
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Peter J Facchini
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Kenneth K S Ng
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| |
Collapse
|
47
|
Qian X, Zhao J, Yeung PY, Zhang QC, Kwok CK. Revealing lncRNA Structures and Interactions by Sequencing-Based Approaches. Trends Biochem Sci 2018; 44:33-52. [PMID: 30459069 DOI: 10.1016/j.tibs.2018.09.012] [Citation(s) in RCA: 283] [Impact Index Per Article: 47.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 09/11/2018] [Accepted: 09/19/2018] [Indexed: 11/28/2022]
Abstract
Long noncoding RNAs (lncRNAs) have emerged as significant players in almost every level of gene function and regulation. Thus, characterizing the structures and interactions of lncRNAs is essential for understanding their mechanistic roles in cells. Through a combination of (bio)chemical approaches and automated capillary and high-throughput sequencing (HTS), the complexity and diversity of RNA structures and interactions has been revealed in the transcriptomes of multiple species. These methods have uncovered important biological insights into the mechanistic and functional roles of lncRNA in gene expression and RNA metabolism, as well as in development and disease. In this review, we summarize the latest sequencing strategies to reveal RNA structure, RNA-RNA, RNA-DNA, and RNA-protein interactions, and highlight the recent applications of these approaches to map functional lncRNAs. We discuss the advantages and limitations of these strategies, and provide recommendations to further advance methodologies capable of mapping RNA structure and interactions in order to discover new biology of lncRNAs and decipher their molecular mechanisms and implication in diseases.
Collapse
Affiliation(s)
- Xingyang Qian
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China; These authors contributed equally to this work
| | - Jieyu Zhao
- Department of Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China; These authors contributed equally to this work
| | - Pui Yan Yeung
- Department of Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China; These authors contributed equally to this work
| | - Qiangfeng Cliff Zhang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.
| | - Chun Kit Kwok
- Department of Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China.
| |
Collapse
|
48
|
Abstract
Fungal toxins are secondary metabolites, in which many of them were mycotoxins, affecting eukaryotic cells with a broad range of structural and functional variety contributing to the multitude of their classification. This refers to the harmful genotoxic (mutagenic, teratogenic, and carcinogenic) effects of mycotoxins on the one hand, and their cytocidic and antineoplastic properties on the other hand. This "double edged sword" effect could be utilized against the spread of tumors in older patients when the survival is much more important than the mutagenic side effects. To decide which fungal toxins could be used as combined cytotoxic and antimetastatic agents, mycotoxins were divided into three categories: (a) highly genotoxic (mutagenic, teratogenic, and carcinogenic), (b) adversely toxic, and (c) antitumorigenic agents. Highly cytotoxic mycotoxins with tolerable side effects, combined with an antineoplastic character, could be potential candidates against metastasis. From the structure-function relationship of antimetastatic mycotoxins, only general conclusions have been drawn. The presence of ring structures containing heteroatoms, functional groups, and the cumulative presence of oxygen atoms contributed to the oxidative stress and cytotoxicity of mycotoxins. The preselection of mycotoxins excluded category (a), and only the categories (b) and
Collapse
Affiliation(s)
- István Pócsi
- 1 Department of Biotechnology and Microbiology, University of Debrecen, Debrecen, Hungary
| | - Gábor Király
- 1 Department of Biotechnology and Microbiology, University of Debrecen, Debrecen, Hungary
| | - Gáspár Bánfalvi
- 1 Department of Biotechnology and Microbiology, University of Debrecen, Debrecen, Hungary
| |
Collapse
|
49
|
Abeyasinghe PM, de Paula DR, Khajehabdollahi S, Valluri SR, Owen AM, Soddu A. Role of Dimensionality in Predicting the Spontaneous Behavior of the Brain Using the Classical Ising Model and the Ising Model Implemented on a Structural Connectome. Brain Connect 2018; 8:444-455. [PMID: 29936876 PMCID: PMC6152861 DOI: 10.1089/brain.2017.0516] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
There is accumulating evidence that spontaneous fluctuations of the brain are sustained by a structural architecture of axonal fiber bundles. Various models have been used to investigate this structure–function relationship. In this work, we implemented the Ising model using the number of fibers between each pair of brain regions as input. The output of the Ising model simulations on a structural connectome was then compared with empirical functional connectivity data. A simpler two-dimensional classical Ising model was used as the baseline model for comparison purpose. Thermodynamic properties, such as the magnetic susceptibility and the specific heat, illustrated a phase transition from an ordered phase to a disordered phase at the critical temperature. Despite the differences between the two models, the lattice Ising model and the Ising model implemented on a structural connectome (the generalized Ising model) exhibited similar patterns of global properties. To study the behavior of the generalized Ising model around criticality, calculation of the dimensionality and critical exponents was performed for the first time, by introducing a new concept of distance based on structural connectivity. Same value inside the fitting error was found for the dimensionality in both models suggesting similar behavior of the models around criticality.
Collapse
Affiliation(s)
- Pubuditha M Abeyasinghe
- Department of Physics and Astronomy, Western University, London, Ontario, Canada.,The Brain and Mind Institute, Western University, London, Ontario, Canada
| | - Demetrius Ribeiro de Paula
- Department of Physics and Astronomy, Western University, London, Ontario, Canada.,The Brain and Mind Institute, Western University, London, Ontario, Canada
| | - Sina Khajehabdollahi
- Department of Physics and Astronomy, Western University, London, Ontario, Canada.,The Brain and Mind Institute, Western University, London, Ontario, Canada
| | - Sree Ram Valluri
- Department of Physics and Astronomy, Western University, London, Ontario, Canada
| | - Adrian M Owen
- The Brain and Mind Institute, Western University, London, Ontario, Canada.,Department of Psychology, Western University, London, Ontario, Canada
| | - Andrea Soddu
- Department of Physics and Astronomy, Western University, London, Ontario, Canada.,The Brain and Mind Institute, Western University, London, Ontario, Canada
| |
Collapse
|
50
|
Batista-García-Ramó K, Fernández-Verdecia CI. What We Know About the Brain Structure-Function Relationship. Behav Sci (Basel) 2018; 8:E39. [PMID: 29670045 DOI: 10.3390/bs8040039] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 04/11/2018] [Accepted: 04/16/2018] [Indexed: 11/21/2022] Open
Abstract
How the human brain works is still a question, as is its implication with brain architecture: the non-trivial structure–function relationship. The main hypothesis is that the anatomic architecture conditions, but does not determine, the neural network dynamic. The functional connectivity cannot be explained only considering the anatomical substrate. This involves complex and controversial aspects of the neuroscience field and that the methods and methodologies to obtain structural and functional connectivity are not always rigorously applied. The goal of the present article is to discuss about the progress made to elucidate the structure–function relationship of the Central Nervous System, particularly at the brain level, based on results from human and animal studies. The current novel systems and neuroimaging techniques with high resolutive physio-structural capacity have brought about the development of an integral framework of different structural and morphometric tools such as image processing, computational modeling and graph theory. Different laboratories have contributed with in vivo, in vitro and computational/mathematical models to study the intrinsic neural activity patterns based on anatomical connections. We conclude that multi-modal techniques of neuroimaging are required such as an improvement on methodologies for obtaining structural and functional connectivity. Even though simulations of the intrinsic neural activity based on anatomical connectivity can reproduce much of the observed patterns of empirical functional connectivity, future models should be multifactorial to elucidate multi-scale relationships and to infer disorder mechanisms.
Collapse
|