課程資訊
課程名稱
分子辨識
Molecular Recognition 
開課學期
109-1 
授課對象
生命科學院  基因體與系統生物學學位學程  
授課教師
徐駿森 
課號
AC5066 
課程識別碼
623 U4340 
班次
 
學分
2.0 
全/半年
半年 
必/選修
選修 
上課時間
星期三8,9(15:30~17:20) 
上課地點
農化一第五 
備註
總人數上限:20人 
Ceiba 課程網頁
http://ceiba.ntu.edu.tw/1091AC5066_MR 
課程簡介影片
 
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課程概述

分子辨識課程是應用結構生物、化學生物與分子生物學來探討生命科學的一門課。無論在動物、植物或是微生物的系統,生命現象從微觀的角度來看就是細胞內生物分子經由交互作用而造成訊息傳遞與命令執行之功能。此外,醫學或農業上的病毒或病菌感染、也是藉由特定分子的辨識為起始,進而入侵宿主。瞭解這些生物分子之分子辨識作用,除了能說明其作用機制,並在應用上可發展策略用於抑制或促進其辨識作用及生物活性。  

課程目標
此課程以深入淺出的方式,一開始說明分子辨識的化學原理,接著介紹各項研究分子交互作用之結構與生物物理工具。並以數個具有啟發性的生物交互作用系統為範例。最後由文獻討論來讓參與課程者能將分子結構觀念帶入本身正在研究或有興趣的領域。  
課程要求
歡迎大三以上與研究所不同背景學生,但若未修過生物化學,請先與老師溝通。 
預期每週課後學習時數
 
Office Hours
每週三 13:00~15:00 
參考書目
Arthur M. Lesk, (2004). Introduction of Protein Science. Oxford University Press.
Gordon C.K. Roberts, (2000). NMR of Macromolecules-A practical approach, Oxford University Press.
Gale Rhodes, (2000). Crystallography Made Crystal Clear, Academic Press
 
指定閱讀
 
評量方式
(僅供參考)
 
No.
項目
百分比
說明
1. 
報告 
30% 
 
2. 
作業 
20% 
 
3. 
期末考 
30% 
 
4. 
期中考 
20% 
 
 
課程進度
週次
日期
單元主題
第1週
9/16  Introduction 
第2週
9/23  Structural and Chemical Properties of Biological Macromolecules 
第3週
9/30  Protein Crystallography 
第4週
10/7  Electron Microscopy 
第5週
10/14  Principle of Nuclear Magnetic Resonance Spectroscopy:
(I)Biomolecular NMR technique 
第6週
10/21  Principle of Nuclear Magnetic Resonance Spectroscopy:
(II)Multi-dimesional NMR for protein determination 
第7週
10/28  Structural Bioinformatics 
第8週
11/4  Structural Bioinformatics 
第9週
11/11  Mid-term (同步輻射中心用戶會議) 
第10週
11/18  Biophysical Methods to Probe Non-covalent Molecular Interaction (I):Circular Dichroism, UV and Fluorescence Spectroscopy  
第11週
11/25  Biophysical Methods to Probe Non-covalent Molecular Interaction (II):Surface Plasmon Resonance, ITC and Analytical Ultracentrifugation 
第12週
12/2  Structural Basis of Signal Transduction and Post-translation Modification 
第13週
12/9  Molecular Enzymology 
第14週
12/16  Protein/peptide interaction with membrane 
第15週
12/23  Structural Features of Receptors and ligands 
第16週
12/30  Structural View of Protein-DNA Recognition in Gene Regulation 
第17週
1/6  Molecular Docking and Bioinformatics Approach:Strategies for Drug Discovery, Rational Drug Design versus Drug screen 
第18週
1/13  (1) 12/02
黃詒敏
1. Shin D, Mukherjee R, Grewe D, Bojkova D, Baek K, Bhattacharya A, Schulz L, Widera M, Mehdipour AR, Tascher G, Geurink PP, Wilhelm A, van der Heden van Noort GJ, Ovaa H, Müller S, Knobeloch KP, Rajalingam K, Schulman BA, Cinatl J, Hummer G, Ciesek S, Dikic I. Papain-like protease regulates SARS-CoV-2 viral spread and innate immunity. Nature. 2020 Jul 29. doi: 10.1038/s41586-020-2601-5. Epub ahead of print. PMID: 32726803.

李冠緯
2. Zhang L, Lin D, Sun X, Curth U, Drosten C, Sauerhering L, Becker S, Rox K, Hilgenfeld R. Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors. Science. 2020 Apr 24;368(6489):409-412. doi: 10.1126/science.abb3405. Epub 2020 Mar 20. PMID: 32198291; PMCID: PMC7164518.

(2) 12/09
李政祐
3. Structures of a dimodular nonribosomal peptide synthetase reveal conformational flexibility. Reimer JM, Eivaskhani M, Harb I, Guarné A, Weigt M, Schmeing TM.
Science. 2019 Nov 8;366(6466):eaaw4388. doi: 10.1126/science.aaw4388.

林竺諼
4. Structures of two distinct conformations of holo-non-ribosomal peptide synthetases. Drake EJ, Miller BR, Shi C, Tarrasch JT, Sundlov JA, Allen CL, Skiniotis G, Aldrich CC, Gulick AM. Nature. 2016 Jan 14;529(7585):235-8. doi: 10.1038/nature16163.


(3) 12/16
何宗彥
5. Characterization of a dual function macrocyclase enables design and use of efficient macrocyclization substrates. Czekster, C.M., Ludewig, H., McMahon, S.A., Naismith, J.H. (2017) Nat Commun 8: 1045-1045

呂彥儒
6. Trapping conformational states of a flavin-dependent N -monooxygenase in crystallo reveals protein and flavin dynamics. Campbell, A.C., Stiers, K.M., Martin Del Campo, J.S., Mehra-Chaudhary, R., Sobrado, P., Tanner, J.J. (2020) J Biol Chem 295: 13239-13249

黃尉嘉

7. Structural basis for precursor protein-directed ribosomal peptide macrocyclization. Li, K., Condurso, H.L., Li, G., Ding, Y., Bruner, S.D. (2016) Nat Chem Biol 12: 973-979

(4)12/23
鄭光淳
Feline coronavirus drug inhibits the main protease of SARS-CoV-2 and blocks virus replication. Vuong W, Khan MB, Fischer C, Arutyunova E, Lamer T, Shields J, Saffran HA, McKay RT, van Belkum MJ, Joyce MA, Young HS, Tyrrell DL, Vederas JC, Lemieux MJ. Nat Commun. 2020 Aug 27;11(1):4282. doi: 10.1038/s41467-020-18096-2.

范宏綦

Hydrophobic and charged residues in the C-terminal arm of hepatitis C virus RNA-dependent RNA polymerase regulate initiation and elongation. Cherry AL, Dennis CA, Baron A, Eisele LE, Thommes PA, Jaeger J. J Virol. 2015 Feb;89(4):2052-63. doi: 10.1128/JVI.01106-14. Epub 2014 Nov 26.

劉佳容

Inhibition of SARS-CoV-2 (previously 2019-nCoV) infection by a highly potent pan-coronavirus fusion inhibitor targeting its spike protein that harbors a high capacity to mediate membrane fusion. Xia S, Liu M, Wang C, Xu W, Lan Q, Feng S, Qi F, Bao L, Du L, Liu S, Qin C, Sun F, Shi Z, Zhu Y, Jiang S, Lu L. Cell Res. 2020 Apr;30(4):343-355. doi: 10.1038/s41422-020-0305-x. Epub 2020 Mar 30.

(5) 12/30
陳奕伯
A β-Mannanase with a Lysozyme-like Fold and a Novel Molecular Catalytic Mechanism. Jin Y, Petricevic M, John A, Raich L, Jenkins H, Portela De Souza L, Cuskin F, Gilbert HJ, Rovira C, Goddard-Borger ED, Williams SJ, Davies GJ.
ACS Cent Sci. 2016 Dec 28;2(12):896-903. doi: 10.1021/acscentsci.6b00232. Epub 2016 Nov 8.

蘇筱晴

HPF1 completes the PARP active site for DNA damage-induced ADP-ribosylation.

Suskiewicz, M.J., Zobel, F., Ogden, T.E.H., Fontana, P., Ariza, A., Yang, J.C., Zhu, K., Bracken, L., Hawthorne, W.J., Ahel, D., Neuhaus, D., Ahel, I.
(2020) Nature 579: 598-602

廖小惟

Identification of a Class of Protein Adp-Ribosylating Sirtuins in Microbial Pathogens. Rack, J.G., Morra, R., Barkauskaite, E., Kraehenbuehl, R., Ariza, A., Qu, Y., Ortmayer, M., Leidecker, O., Cameron, D.R., Matic, I., Peleg, A.Y., Leys, D., Traven, A., Ahel, I.
(2015) Mol Cell 59: 309