Biochemistry

Our cells engage in protein production, and many of those proteins are enzymes responsible for the chemistry of life.
— Randy Schekman

Fundamental techniques

• Protein quantification

  • SDS-PAGE(In-gel)
  • Western blot
  • ELISA

• Protein purification

  • Purifying Challenging Proteins, Principles and Methods [PDF]

• Protein interaction

  • co-IP
  • Proximity labeling

• Protein identification

  • Protein sequencing:
  • IP-MS:

• Organelle isolation

  • mitochondria: Mito-IP []
  • Lysosome: LysoIP []
  • ER:
  • Golgi: Golgi-IP []
  • Synaptosome:

• Cell culture basis

  • ATCC® ANIMAL CELL CULTURE GUIDE(tips and techniques for continuous cell lines) [PDF]
  • Guideline of Cell biology experiment, Part I (In Chinese, 细胞实验指南(上)) [PDF]
  • Guideline of Cell biology experiment, Part II (In Chinese, 细胞实验指南(下)) [PDF]
  • Gibco Cell Culture Basics Handbook(In Chinese) [PDF]

Vendor companies

1. Cell Signaling Technology
2. Abcam
3. ThermoFisher
4. R&D Systems
5. BioRad
6. ATCC: ATCC has the world’s largest and most extensive product catalog of human and animal cell lines for research purposes.
7. Gibco
8. Corning
9. HyClone
10. Sigma

Ref. Labs

Signaling pathways

1. Zhijian-James Chen lab, UTSW

• Discovery of cGAS-cGAMP pathway and its role in immune defense
  • Sun, Lijun, et al. “Cyclic GMP-AMP synthase is a cytosolic DNA sensor that activates the type I interferon pathway.” Science 339.6121 (2013): 786-791. [PDF | PMID: 23258413 | DOI Link]
  • Wu, Jiaxi, et al. “Cyclic GMP-AMP is an endogenous second messenger in innate immune signaling by cytosolic DNA.” Science 339.6121 (2013): 826-830. [PDF | DOI Link]

2. David M. Sabatini lab, WIBR, MIT

• The discovery of mTOR
  • Sabatini et al. “RAFT1: a mammalian protein that binds to FKBP12 in a rapamycin-dependent fashion and is homologous to yeast TORs.” Cell 78.1 (1994): 35-43. [PDF | DOI Link]
  • iBiology Talk [PartI: Introduction to mTOR and the regulation of growth]
• Systematic characterization of basic mechanisms that regulate growth including nutrient sensing pathways [CASTOR | Sestrin2 | SAMTOR]
  • iBiology Talks [PartII: Regulation of mTORC1 by nutrients | PartIII: Ribophagy and nucleotide recycling]

3. Xiaodong Wang lab, UTSW, NIBS

• The discovery of mitochondria CytoC mediated apoptosis pathway
  • Zou, Hua, et al. “Apaf-1, a human protein homologous to C. elegans CED-4, participates in cytochrome c–dependent activation of caspase-3.” Cell 90.3 (1997): 405-413. [PDF | PMID: 9267021 | DOI Link]

4. Ronald David Vale Lab, University of California, San Francisco/HHMI

• The discovery of Kinesin [iBiology Talk]
  • Vale, Ronald D., et al. “Direct observation of single kinesin molecules moving along microtubules.” Nature 380.6573 (1996): 451-453. [PDF | PMID: 8602245 | DOI Link]
• The Characterization of Molecular Motor Proteins [iBiology Talk 1 | iBiology Talk 2 | iBiology Talk 3]
  • Sablin, Elena P., et al. “Crystal structure of the motor domain of the kinesin-related motor ncd.” Nature 380.6574 (1996): 555-559. [PDF | PMID: 8606780 | DOI Link]

5. Judy Lieberman, HMS

• The first to show that RNAi could be the basis for therapy in an animal model

• Identification of novel mechanisms of mitochondrial and DNA damage activated by granzyme A

6. Feng Shao lab, NIBS

• The discovery and characterization of GSDMD mediated pyroptosis pathway [Online Talk]
  • Shi, Jianjin, et al. “Cleavage of GSDMD by inflammatory caspases determines pyroptotic cell death.” Nature 526.7575 (2015): 660-665. [PDF | DOI Link]

Transcriptional regulation and epigenetics

1. Robert Tjian, University of California, Berkeley/HHMI

• The discovery of the SV40 large T antigen
  • Tjian, Robert. “The binding site on SV40 DNA for a T antigen-related protein.” Cell 13.1 (1978): 165-179. [PMID: 202398 | DOI Link]

2. Yi Zhang lab, University of North Carolina at Chapel Hill/HMS/HHMI

3. Yang Shi lab, HMS/HHMI/University of Oxford

• The discovery of first histone demethylase, LSD1
  • Shi, Yujiang, et al. “Histone demethylation mediated by the nuclear amine oxidase homolog LSD1.” Cell 119.7 (2004): 941-953. [PDF | DOI Link]

4. Chuan He lab, University of Chicago/HHMI

• The discovery of first RNA demethylase that oxidatively reverses N6-methyladenosine (m6A) methylation in mammalian messenger RNA
  • Jia, Guifang, et al. “N6-methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO.” Nature chemical biology 7.12 (2011): 885-887. [PDF | DOI Link]

Structural Biology

1. Yigong Shi lab, Princeton University/Tsinghua University/Westlake University

• Structural basis of pre-mRNA splicing
• Structural basis of Apoptosis (Programmed Cell Death)
• Alzheimer’s Disease (AD) and Regulated Intramembrane Proteolysis (RIP)

2. Hao Wu lab, Harvard Medical School

• The discoverer of signalosomes, which are large macromolecular complexes involved in cell death and in innate and adaptive immune pathways.
  • Wu, Hao. “Higher-order assemblies in a new paradigm of signal transduction.” Cell 153.2 (2013): 287-292. [PDF | DOI Link]

3. Nieng Yan lab, Tsinghua University/Princeton University

• Structural basis of Membrane transport
• Structural and mechanistic investigation of sterol homeostasis

Ref. softwares

1. PyMOL: PyMOL is a user-sponsored molecular visualization system on an open-source foundation, maintained and distributed by Schrödinger.
2. UCSF ChimeraX: UCSF ChimeraX (or simply ChimeraX) is the next-generation molecular visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera.
3. HMMER: HMMER is a software package that provides tools for making probabilistic models of protein and DNA sequence domain families – called profile hidden Markov models, profile HMMs, or just profiles – and for using these profiles to annotate new sequences, to search sequence databases for additional homologs, and to make deep multiple sequence alignments.
   • HMMER underlies several comprehensive collections of alignments and profiles of known protein and DNA sequence domain families, including the Pfam database. [User’s Guide]
4. Pfam 35.0
   • The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs).
   • Pfam 35.0 contains a total of 19,632 families and clans.

Tool development

1. Alice Ting lab, Stanford

• PROXIMITY LABELING

  • APEX
  • TurbID

• Stanford Neuro-omics Initiative, 2020 Virtual Workshop

  • “Proteomics and proximity labeling in neuroscience”, by Alice Ting [Slides]
  • “Design and execution of proximity labeling experiments”, by Tess Branon [Slides]
  • “Analysis of proximity labeling data”, by Shuo Han [Slides]

Ref. Protocols

1. Bio-protocol
2. Protocol Exchange

Nobel laureates

• Carolyn Bertozzi, Stanford University, Stanford, CA, USA; Howard Hughes Medical Institute, USA [lab link]
  The Nobel Prize in Chemistry 2022
  The Bioorthogonal Chemistry Journey, from Laboratory to Life [Nobel Lecture video | Lecture Slides | Read the Lecture | Source]

  • iBiology Talk[PartII: Imaging the glycome]

• Sir Peter J. Ratcliffe, University of Oxford, Oxford, United Kingdom; Francis Crick Institute, London, United Kingdom The Nobel Prize in Physiology or Medicine 2019
  Elucidation of Oxygen Sensing Mechanisms in Human and Animal Cells [Nobel Lecture video | Lecture Slides | Read the Lecture | Source]

• William G. Kaelin Jr, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA; Dana-Farber Cancer Institute, Boston, MA, USA; Brigham and Women’s Hospital, Boston, MA, USA The Nobel Prize in Physiology or Medicine 2019
  The von Hippel-Lindau Tumor Suppressor Gene: Insights into Oxygen Sensing and Cancer [Nobel Lecture video | Lecture Slides | Read the Lecture | Source]

• Gregg L. Semenza, Johns Hopkins University, Baltimore, MD, USA The Nobel Prize in Physiology or Medicine 2019
  Hypoxia-Inducible Factors in Physiology and Medicine [Nobel Lecture video | Lecture Slides | Read the Lecture | Source]

• Yoshinori Ohsumi, Tokyo Institute of Technology, Tokyo, Japan
  The Nobel Prize in Physiology or Medicine 2016
  Molecular Mechanisms of Autophagy in Yeast [Nobel Lecture video | Lecture Slides | Read the Lecture | Source]

• Randy Schekman, University of California, Berkeley
  The Nobel Prize in Physiology or Medicine 2013
  Genes and Proteins That Control the Secretory Pathway [Nobel Lecture video | Lecture Slides | Read the Lecture | Source]

• Thomas C. Südhof, Stanford University
  The Nobel Prize in Physiology or Medicine 2013
  The Molecular Machine of Neurotransmitter Release [Nobel Lecture video | Lecture Slides | Read the Lecture | Source]

• Thomas A. Steitz, Yale University, New Haven, CT, USA/HHMI
  The Nobel Prize in Chemistry 2009
  From the Structure and Function of the Ribosome to New Antibiotics [[Nobel Lecture video | Lecture Slides | Read the Lecture | Source]

• Roger D. Kornberg(1947-), Stanford University, Stanford, CA, USA
  The Nobel Prize in Chemistry 2006
  The Molecular Basis of Eukaryotic Transcription [[Nobel Lecture video | Lecture Slides | Read the Lecture | Source]

• Aaron Ciechanover(1947-), Technion - Israel Institute of Technology, Haifa, Israel
  The Nobel Prize in Chemistry 2004
  Intracellular Protein Degradation: From a Vague Idea thru the Lysosome and the Ubiquitin-Proteasome System and onto Human Diseases and Drug Targeting [[Nobel Lecture video | Lecture Slides | Read the Lecture | Source]

• Avram Hershko(1937-), Technion - Israel Institute of Technology, Haifa, Israel
  The Nobel Prize in Chemistry 2004
  The Ubiquitin System for Protein Degradation and some of its Roles in the Control of the Cell Division Cycle [[Nobel Lecture video | Lecture Slides | Read the Lecture | Source]

• Irwin Rose(1926-2015), University of California, Irvine, CA, USA
  The Nobel Prize in Chemistry 2004
  Ubiquitin at Fox Chase [[Nobel Lecture video | Lecture Slides | Read the Lecture | Source]

• H. Robert Horvitz, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
  The Nobel Prize in Physiology or Medicine 2002
  Worms, Life and Death [[Nobel Lecture video | Read the Lecture | Source]

• John E. Sulston, The Wellcome Trust Sanger Institute, Cambridge, United Kingdom
  The Nobel Prize in Physiology or Medicine 2002
  C. elegans: The Cell Lineage and Beyond [[Nobel Lecture video | Read the Lecture | Source]

• Tim Hunt, Imperial Cancer Research Fund, London, United Kingdom
  The Nobel Prize in Physiology or Medicine 2001
  Protein Synthesis, Proteolysis, and Cell Cycle Transitions [Nobel Lecture video | Read the Lecture | Source | Careers interview]

• Paul Greengard(1925-2019), Rockefeller University, New York, NY, USA
  The Nobel Prize in Physiology or Medicine 2000
  The Neurobiology of Dopamine Signaling [[Nobel Lecture video | Read the Lecture | Source]

• Günter Blobel(1936-2018), Rockefeller University, New York, NY, USA/HHMI
  The Nobel Prize in Physiology or Medicine 1999
  Protein Targeting [Nobel Lecture video | Read the Lecture | Source]

• Jens C. Skou(1918-2018), Aarhus University, Aarhus, Denmark
  The Nobel Prize in Chemistry 1997
  The Identification of the Sodium-Potassium Pump [Read the Lecture | Source]

• Michael S. Brown, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, USA
  The Nobel Prize in Physiology or Medicine 1985
  A Receptor-Mediated Pathway for Cholesterol Homeostasis [Nobel Lecture video | Read the Lecture | Source]

• Joseph L. Goldstein, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, USA
  The Nobel Prize in Physiology or Medicine 1985
  A Receptor-Mediated Pathway for Cholesterol Homeostasis [Nobel Lecture video | Read the Lecture | Source]

• David Baltimore, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
  The Nobel Prize in Physiology or Medicine 1975
  Viruses, Polymerases and Cancer [Read the Lecture | Source]

• Christian de Duve(1917-2013), Rockefeller University, New York, NY, USA, Université Catholique de Louvain, Louvain, Belgium
  The Nobel Prize in Physiology or Medicine 1974
  Exploring Cells with a Centrifuge [Read the Lecture | Source]

• Hans Adolf Krebs(1900-1981), Sheffield University, Sheffield, United Kingdom
  The Nobel Prize in Physiology or Medicine 1953
  The Citric Acid Cycle [Read the Lecture | Source]

• Fritz Albert Lipmann(1899-1986), Harvard Medical School, Boston, MA, USA, Massachusetts General Hospital, Boston, MA, USA
  The Nobel Prize in Physiology or Medicine 1953
  Development of the Acetylation Problem: A Personal Account [Read the Lecture | Source]

• Otto Heinrich Warburg(1883-1970), Kaiser-Wilhelm-Institut (now Max-Planck-Institut) für Biologie, Berlin-Dahlem, Germany
  The Nobel Prize in Physiology or Medicine 1931
  The Oxygen-Transferring Ferment of Respiration [Read the Lecture | Source]