1
|
Dokuyucu Hİ, Özmen NG. Achievements and future directions in self‐reconfigurable modular robotic systems. J FIELD ROBOT 2022. [DOI: 10.1002/rob.22139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Halil İ. Dokuyucu
- Department of Mechanical Engineering Karadeniz Technical University Trabzon Turkey
| | - Nurhan Gürsel Özmen
- Department of Mechanical Engineering Karadeniz Technical University Trabzon Turkey
| |
Collapse
|
2
|
Physical, Modular and Articulated Interface for Interactive Molecular Manipulation. SENSORS 2020; 20:s20185415. [PMID: 32967319 PMCID: PMC7570834 DOI: 10.3390/s20185415] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/14/2020] [Accepted: 09/17/2020] [Indexed: 11/25/2022]
Abstract
Rational drug design is an approach based on detailed knowledge of molecular interactions and dynamic of bio-molecules. This approach involves designing new digital and interactive tools including classical desktop interaction devices as well as advanced ones such as haptic arms or virtual reality devices. These approaches however struggle to deal with flexibility of bio-molecules by simultaneously steering the numerous degrees of freedom. We propose a new method that follows a direct interaction approach by implementing an innovative methodology benefiting from a physical, modular and articulated molecular interface augmented by wireless embedded sensors. The goal is to create, design and steer its in silico twin virtual model and better interact with dynamic molecular models.
Collapse
|
3
|
Wang Y, Morsali R, Dai Z, Minary-Jolandan M, Qian D. Computational Nanomechanics of Noncollagenous Interfibrillar Interface in Bone. ACS APPLIED MATERIALS & INTERFACES 2020; 12:25363-25373. [PMID: 32407068 DOI: 10.1021/acsami.0c01613] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The noncollagenous interfibrillar interface in bone provides the critical function of transferring loads among collagen fibrils and their bundles, with adhesive mechanisms at this site thus significantly contributing to the mechanical properties of bone. Motivated by the experimental observations and hypotheses, a computational study is presented to elucidate the critical roles of two major proteins at the nanoscale interfibrillar interface, that is, osteopontin (OPN) and osteocalcin (OC) in bone. This study reveals the extremely high interfacial toughness of the OPN/OC composite. The previously proposed hypothesis of sacrificial bonds in the extracellular organic matrix is tested, and the remarkable mechanical properties of the nanoscale bone interface are attributed to the collaborative interactions between the OPN and OC proteins.
Collapse
Affiliation(s)
- Yang Wang
- Department of Mechanical Engineering, The University of Texas at Dallas, 800 West Campbell Road, Richardson, Texas 75080, United States
| | - Reza Morsali
- Department of Mechanical Engineering, The University of Texas at Dallas, 800 West Campbell Road, Richardson, Texas 75080, United States
| | - Zhengwei Dai
- College of Material and Textile Engineering, Jiaxing University, Jiaxing 314001, People's Republic of China
| | - Majid Minary-Jolandan
- Department of Mechanical Engineering, The University of Texas at Dallas, 800 West Campbell Road, Richardson, Texas 75080, United States
| | - Dong Qian
- Department of Mechanical Engineering, The University of Texas at Dallas, 800 West Campbell Road, Richardson, Texas 75080, United States
| |
Collapse
|
4
|
Kerwin SM. Flexible and modular 3D-printed peptide models. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2019; 47:432-437. [PMID: 31026113 DOI: 10.1002/bmb.21250] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 03/16/2019] [Accepted: 04/07/2019] [Indexed: 06/09/2023]
Abstract
A flexible and modular peptide modeling set was designed using freely available software tools. The set consists of space-filling models of all 20 naturally occurring amino acid side chains and a modular kit for constructing peptides employing C-alpha carbons and amide bond groups. Connectors that allow free rotation about phi and psi angles on the peptide, together with explicit representation of peptide backbone hydrogen bond donor and acceptors allows for the construction of a wide range of protein secondary structure motifs. The space-filling side chain models highlight the steric, acid-base, and polarity of these groups. These models were printed using relatively affordable commercially available fused filament fabrication printers with minimal postprinting processing. Use of these models in student group activities focused on amino acids and protein secondary structural features is described. © 2019 International Union of Biochemistry and Molecular Biology, 47(4):432-437, 2019.
Collapse
Affiliation(s)
- Sean M Kerwin
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas
| |
Collapse
|
5
|
Hu R, Huang B, Xue Z, Li Q, Xia T, Zhang W, Lu C, Xu H. Synthesis of photocurable cellulose acetate butyrate resin for continuous liquid interface production of three-dimensional objects with excellent mechanical and chemical-resistant properties. Carbohydr Polym 2019; 207:609-618. [PMID: 30600046 DOI: 10.1016/j.carbpol.2018.12.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 11/09/2018] [Accepted: 12/10/2018] [Indexed: 12/31/2022]
Abstract
Three-dimensional (3D) printing parts with excellent resolution and high performance are of great significance for scientific and engineering applications. In this study, a novel photocurable cellulose acetate butyrate (PC-CAB) resin was synthesized for continuous liquid interface production (CLIP) to construct 3D objects with high resolution, tailored mechanical properties, excellent chemical resistance and thermal stability. Particularly, the tensile and flexural strength of the CLIP 3D printed specimen could reach 44.67 and 64.53 MPa, respectively. Their solvent resistance against various organic solvents and strong acidic/basic solutions was evaluated. As expected, the 3D prints could well maintain their structural integrity and exhibited very low swelling ratios owing to the photo-induced chemical crosslinking structure. Notably, even after immersion in methylene chloride or 1.0 M acid/alkali for 3 h, the 3D prints still showed excellent mechanical and thermal properties. Further study demonstrated that when PC-CAB in the CLIP ink was optimized to 20 wt% while the photoinitiator (PI) was 0.5 wt%, complex-structured 3D printed objects with high surface quality could be obtained under specific printing parameters.
Collapse
Affiliation(s)
- Rui Hu
- State Key Laboratory of Polymer Materials Engineering, Polymer Research Institute at Sichuan University, Chengdu 610065, China
| | - Bingxue Huang
- State Key Laboratory of Polymer Materials Engineering, Polymer Research Institute at Sichuan University, Chengdu 610065, China
| | - Zhouhang Xue
- State Key Laboratory of Polymer Materials Engineering, Polymer Research Institute at Sichuan University, Chengdu 610065, China
| | - Qingye Li
- State Key Laboratory of Polymer Materials Engineering, Polymer Research Institute at Sichuan University, Chengdu 610065, China
| | - Tian Xia
- State Key Laboratory of Polymer Materials Engineering, Polymer Research Institute at Sichuan University, Chengdu 610065, China
| | - Wei Zhang
- State Key Laboratory of Polymer Materials Engineering, Polymer Research Institute at Sichuan University, Chengdu 610065, China; Advanced Polymer Materials Research Center of Sichuan University, Shishi 362700, China.
| | - Canhui Lu
- State Key Laboratory of Polymer Materials Engineering, Polymer Research Institute at Sichuan University, Chengdu 610065, China; Advanced Polymer Materials Research Center of Sichuan University, Shishi 362700, China.
| | - Huagang Xu
- Quanzhou Yunshang 3D Science & Technology Co. Ltd., Shishi 362700, China
| |
Collapse
|
6
|
Olson AJ. Perspectives on Structural Molecular Biology Visualization: From Past to Present. J Mol Biol 2018; 430:3997-4012. [PMID: 30009769 PMCID: PMC6186497 DOI: 10.1016/j.jmb.2018.07.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Revised: 07/03/2018] [Accepted: 07/06/2018] [Indexed: 12/15/2022]
Abstract
Visualization has been a key technology in the progress of structural molecular biology for as long as the field has existed. This perspective describes the nature of the visualization process in structural studies, how it has evolved over the years, and its relationship to the changes in technology that have supported and driven it. It focuses on how technical advances have changed the way we look at and interact with molecular structure, and how structural biology has fostered and challenged that technology.
Collapse
Affiliation(s)
- Arthur J Olson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
| |
Collapse
|
7
|
Assemble-And-Match: A Novel Hybrid Tool for Enhancing Education and Research in Rational Structure Based Drug Design. Sci Rep 2018; 8:849. [PMID: 29339792 PMCID: PMC5770410 DOI: 10.1038/s41598-017-18151-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 12/05/2017] [Indexed: 11/08/2022] Open
Abstract
Rational drug design is the process of finding new medication that can activate or inhibit the biofunction of a target molecule by binding to it and forming a molecular complex. Here, shape and charge complementarities between drug and target are key. To help find effective drug molecules out of a huge pool of possibilities, physical and computer aided tools have been developed. Former offers a tangible experience of the molecular interactions yet lacks measurement and evaluation capabilities. Latter enables accurate and fast evaluations, but does not deliver the interactive tangible experience of physical models. We introduce a novel hybrid model called "Assemble-And-Match" where, we enhance and combine the unique features of the two categories. Assemble-And-Match works based on fabrication of customized molecular fragments using our developed software and a 3D printer. Fragments are hinged to each other in different combinations and form flexible peptide chains, conformable to tertiary structures, to fit in the binding pocket of a (3D printed) target molecule. Through embedded measurement marks, the molecular model is reconstructed in silico and its properties are evaluated. We expect Assemble-And-Match tool can enable combination of visuospatial perception with in silico computational power to aid research and education in drug design.
Collapse
|
8
|
Cooper AK, Oliver-Hoyo MT. Creating 3D physical models to probe student understanding of macromolecular structure. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2017; 45:491-500. [PMID: 28681994 DOI: 10.1002/bmb.21076] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 04/30/2017] [Accepted: 06/12/2017] [Indexed: 06/07/2023]
Abstract
The high degree of complexity of macromolecular structure is extremely difficult for students to process. Students struggle to translate the simplified two-dimensional representations commonly used in biochemistry instruction to three-dimensional aspects crucial in understanding structure-property relationships. We designed four different physical models to address student understanding of electrostatics and noncovalent interactions and their relationship to macromolecular structure. In this study, we have tested these models in classroom settings to determine if these models are effective in engaging students at an appropriate level of difficulty and focusing student attention on the principles of electrostatic attractions. This article describes how to create these unique models for four targeted areas related to macromolecular structure: protein secondary structure, protein tertiary structure, membrane protein solubility, and DNA structure. We also provide evidence that merits their use in classroom settings based on the analysis of assembled models and a behavioral assessment of students enrolled in an introductory biochemistry course. By providing students with three-dimensional models that can be physically manipulated, barriers to understanding representations of these complex structures can be lowered and the focus shifted to addressing the foundational concepts behind these properties. © 2017 by The International Union of Biochemistry and Molecular Biology, 45(6):491-500, 2017.
Collapse
Affiliation(s)
- A Kat Cooper
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina, 27607
| | - M T Oliver-Hoyo
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina, 27607
| |
Collapse
|
9
|
Davenport J, Pique M, Getzoff E, Huntoon J, Gardner A, Olson A. A Self-Assisting Protein Folding Model for Teaching Structural Molecular Biology. Structure 2017; 25:671-678. [PMID: 28380340 DOI: 10.1016/j.str.2017.03.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 01/20/2017] [Accepted: 03/09/2017] [Indexed: 11/19/2022]
Abstract
Structural molecular biology is now becoming part of high school science curriculum thus posing a challenge for teachers who need to convey three-dimensional (3D) structures with conventional text and pictures. In many cases even interactive computer graphics does not go far enough to address these challenges. We have developed a flexible model of the polypeptide backbone using 3D printing technology. With this model we have produced a polypeptide assembly kit to create an idealized model of the Triosephosphate isomerase mutase enzyme (TIM), which forms a structure known as TIM barrel. This kit has been used in a laboratory practical where students perform a step-by-step investigation into the nature of protein folding, starting with the handedness of amino acids to the formation of secondary and tertiary structure. Based on the classroom evidence we collected, we conclude that these models are valuable and inexpensive resource for teaching structural molecular biology.
Collapse
Affiliation(s)
- Jodi Davenport
- Science, Technology, Engineering & Mathematics Program, WestEd, 730 Harrison Street, San Francisco, CA 94107, USA
| | - Michael Pique
- The Scripps Research Institute, Department of Integrative Structural and Computational Biology, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Elizabeth Getzoff
- The Scripps Research Institute, Department of Integrative Structural and Computational Biology, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Jon Huntoon
- The Scripps Research Institute, Department of Integrative Structural and Computational Biology, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Adam Gardner
- The Scripps Research Institute, Department of Integrative Structural and Computational Biology, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Arthur Olson
- The Scripps Research Institute, Department of Integrative Structural and Computational Biology, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
| |
Collapse
|
10
|
Da Veiga Beltrame E, Tyrwhitt-Drake J, Roy I, Shalaby R, Suckale J, Pomeranz Krummel D. 3D Printing of Biomolecular Models for Research and Pedagogy. J Vis Exp 2017. [PMID: 28362403 PMCID: PMC5408980 DOI: 10.3791/55427] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The construction of physical three-dimensional (3D) models of biomolecules can uniquely contribute to the study of the structure-function relationship. 3D structures are most often perceived using the two-dimensional and exclusively visual medium of the computer screen. Converting digital 3D molecular data into real objects enables information to be perceived through an expanded range of human senses, including direct stereoscopic vision, touch, and interaction. Such tangible models facilitate new insights, enable hypothesis testing, and serve as psychological or sensory anchors for conceptual information about the functions of biomolecules. Recent advances in consumer 3D printing technology enable, for the first time, the cost-effective fabrication of high-quality and scientifically accurate models of biomolecules in a variety of molecular representations. However, the optimization of the virtual model and its printing parameters is difficult and time consuming without detailed guidance. Here, we provide a guide on the digital design and physical fabrication of biomolecule models for research and pedagogy using open source or low-cost software and low-cost 3D printers that use fused filament fabrication technology.
Collapse
Affiliation(s)
| | - James Tyrwhitt-Drake
- Bioinformatics and Computational Biosciences Branch (BCBB), NIH/NIAID/OD/OSMO/OCICB
| | - Ian Roy
- Library/LTS/MakerLab, Brandeis University
| | - Raed Shalaby
- Interfaculty Institute of Biochemistry (IFIB), University of Tübingen
| | - Jakob Suckale
- Interfaculty Institute of Biochemistry (IFIB), University of Tübingen;
| | | |
Collapse
|
11
|
MOCHIZUKI Y, NAKAMURA S, YAMANAKA M, YAMADA Y, KUDO M, TOKIWA H, KAWAKAMI M, KITAMOTO S. Practical Usages Of 3D-printer for Scientific Education of Chemistry and Biology. JOURNAL OF COMPUTER CHEMISTRY-JAPAN 2016. [DOI: 10.2477/jccj.2016-0034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
12
|
Tumbleston JR, Shirvanyants D, Ermoshkin N, Janusziewicz R, Johnson AR, Kelly D, Chen K, Pinschmidt R, Rolland JP, Ermoshkin A, Samulski ET, DeSimone JM. Continuous liquid interface production of 3D objects. Science 2015; 347:1349-52. [DOI: 10.1126/science.aaa2397] [Citation(s) in RCA: 1253] [Impact Index Per Article: 139.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
13
|
Gross BC, Erkal JL, Lockwood SY, Chen C, Spence DM. Evaluation of 3D printing and its potential impact on biotechnology and the chemical sciences. Anal Chem 2014; 86:3240-53. [PMID: 24432804 DOI: 10.1021/ac403397r] [Citation(s) in RCA: 739] [Impact Index Per Article: 73.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Nearing 30 years since its introduction, 3D printing technology is set to revolutionize research and teaching laboratories. This feature encompasses the history of 3D printing, reviews various printing methods, and presents current applications. The authors offer an appraisal of the future direction and impact this technology will have on laboratory settings as 3D printers become more accessible.
Collapse
Affiliation(s)
- Bethany C Gross
- Department of Chemistry, Michigan State University , 578 South Shaw Lane, East Lansing, Michigan 48824, United States
| | | | | | | | | |
Collapse
|