• Center for Macromolecular Interactions
  • CMI Laboratory

    Welcome to the CMI

    An HMS core for the characterization of macromolecules and their interactions.

  • CMI SEC-MALS system

    CMI SEC-MALS system

    Multi-Angle Light Scattering and Dynamic Light Scattering are used to measure the molar mass and hydrodynamic radius.

  • CMI Jasco J815 CD instrument

    CMI Spectropolarimeter

    Circular Dichroism is used to examine protein secondary structure in solution.

  • CMI MST and ITC instruments

    CMI MST and ITC Instruments

    Isothermal Titration Calorimetry and Microscale Thermophoresis measuring binding in solution.

  • CMI SPR and BLI instruments

    CMI SPR and BLI Instruments

    Surface Plasmon Resonance and Biolayer Interferometry are used to measure binding kinetics.

Coronavirus Update

The CMI is in Phase 2 Re-Entry, as of Monday,  June 15.  The CMI COVID-19 Plan summarizes the changes implemented at CMI to maintain social distancing, enhance safety and accomodate as many users as possible.

All existing CMI Users  must submit a CMI COVID-19 Re-entry Form to regain instrument access. Trained academic CMI users from local institutions who have submitted this form will be able to book instruments at that time.

New Users should request an account at the CMI, but note that all training is being deferred at this time.


Center for Macromolecular Interactions

Welcome to the Center for Macromolecular Interactions (CMI) in the department of Biological Chemistry and Molecular Pharmacology at Harvard Medical School.  Our mission is to enhance basic research in the HMS community by providing scientific consultation, training and access to shared biophysical instruments for the characterization and analysis of macromolecules and their complexes.

The facility currently includes instruments for Isothermal Titration Calorimetry (ITC)Surface Plasmon Resonance (SPR)Biolayer Interferometry (BLI)Differential Scanning Fluorimetry (DSF)Circular Dichroism (CD)Light Scattering: size-exclusion chromatography with multi-angle light scattering (SEC-MALS) and Dynamic Light Scattering (DLS), and MicroScale Thermophoresis (MST)

Recent User Publications

Lowey B, Whiteley AT, Keszei AFA, Morehouse BR, Mathews IT, Antine SP, Cabrera VJ, Kashin D, Niemann P, Jain M, Schwede F, Mekalanos JJ, Shao S, Lee ASY, Kranzusch PJ. CBASS Immunity Uses CARF-Related Effectors to Sense 3'-5'- and 2'-5'-Linked Cyclic Oligonucleotide Signals and Protect Bacteria from Phage Infection. Cell 2020;Abstract
cGAS/DncV-like nucleotidyltransferase (CD-NTase) enzymes are immune sensors that synthesize nucleotide second messengers and initiate antiviral responses in bacterial and animal cells. Here, we discover Enterobacter cloacae CD-NTase-associated protein 4 (Cap4) as a founding member of a diverse family of >2,000 bacterial receptors that respond to CD-NTase signals. Structures of Cap4 reveal a promiscuous DNA endonuclease domain activated through ligand-induced oligomerization. Oligonucleotide recognition occurs through an appended SAVED domain that is an unexpected fusion of two CRISPR-associated Rossman fold (CARF) subunits co-opted from type III CRISPR immunity. Like a lock and key, SAVED effectors exquisitely discriminate 2'-5'- and 3'-5'-linked bacterial cyclic oligonucleotide signals and enable specific recognition of at least 180 potential nucleotide second messenger species. Our results reveal SAVED CARF family proteins as major nucleotide second messenger receptors in CBASS and CRISPR immune defense and extend the importance of linkage specificity beyond mammalian cGAS-STING signaling.
Patsoukis N, Duke-Cohan JS, Chaudhri A, Aksoylar H-I, Wang Q, Council A, Berg A, Freeman GJ, Boussiotis VA. Interaction of SHP-2 SH2 domains with PD-1 ITSM induces PD-1 dimerization and SHP-2 activation. Commun Biol 2020;3(1):128.Abstract
Programmed cell death-1 (PD-1) inhibits T cell responses. This function relies on interaction with SHP-2. PD-1 has one immunoreceptor tyrosine-based inhibitory motif (ITIM) at Y223 and one immunoreceptor tyrosine-based switch motif (ITSM) at Y248. Only ITSM-Y248 is indispensable for PD-1-mediated inhibitory function but how SHP-2 enzymatic activation is mechanistically regulated by one PD-1 phosphotyrosine remains a puzzle. We found that after PD-1 phosphorylation, SHP-2 can bridge phosphorylated ITSM-Y248 residues on two PD-1 molecules via its amino terminal (N)-SH2 and carboxyterminal (C)-SH2 domains forming a PD-1: PD-1 dimer in live cells. The biophysical ability of SHP-2 to interact with two ITSM-pY248 residues was documented by isothermal titration calorimetry. SHP-2 interaction with two ITSM-pY248 phosphopeptides induced robust enzymatic activation. Our results unravel a mechanism of PD-1: SHP-2 interaction that depends only on ITSM-Y248 and explain how a single docking site within the PD-1 cytoplasmic tail can activate SHP-2 and PD-1-mediated inhibitory function.
Gorgulla C, Boeszoermenyi A, Wang Z-F, Fischer PD, Coote P, Padmanabha Das KM, Malets YS, Radchenko DS, Moroz YS, Scott DA, Fackeldey K, Hoffmann M, Iavniuk I, Wagner G, Arthanari H. An open-source drug discovery platform enables ultra-large virtual screens. Nature 2020;Abstract
On average, an approved drug today costs $2-3 billion and takes over ten years to develop. In part, this is due to expensive and time-consuming wet-lab experiments, poor initial hit compounds, and the high attrition rates in the (pre-)clinical phases. Structure-based virtual screening (SBVS) has the potential to mitigate these problems. With SBVS, the quality of the hits improves with the number of compounds screened. However, despite the fact that large compound databases exist, the ability to carry out large-scale SBVSs on computer clusters in an accessible, efficient, and flexible manner has remained elusive. Here we designed VirtualFlow, a highly automated and versatile open-source platform with perfect scaling behaviour that is able to prepare and efficiently screen ultra-large ligand libraries of compounds. VirtualFlow is able to use a variety of the most powerful docking programs. Using VirtualFlow, we have prepared the largest and freely available ready-to-dock ligand library available, with over 1.4 billion commercially available molecules. To demonstrate the power of VirtualFlow, we screened over 1 billion compounds and discovered a small molecule inhibitor (iKeap1) that engages KEAP1 with nanomolar affinity (K = 114 nM) and disrupts the interaction between KEAP1 and the transcription factor NRF2. We also identified a set of structurally diverse molecules that bind to KEAP1 with submicromolar affinity. This illustrates the potential of VirtualFlow to access vast regions of the chemical space and identify binders with high affinity for target proteins.

CMI News

CMI Getting Started Guides updated

May 22, 2020
Instrument getting started guides have all been updated with new content and a new look. Get the latest version in instrument pages in Technologies.  Please let us know if you find any problems.

The CMI welcomes Ahmad Almawi

March 30, 2020
Ahmad Almawi, PhD, has joined the team at the CMI as a protein scientist.  Ahmad trained as a structural biologist and has expertise in protein production and purification. He will be spearheading the nanobody production effort.

HMS Shutdown

March 19, 2020

In response to the COVID-19 pandemic, the CMI is closing for general access.  See the latest guidelines from Harvard Medical School (https://hms.harvard.edu/coronavirus) for more information.  If you are doing COVID-19 research and require access to CMI instrumentation, contact Kelly Arnett at cmi@hms.harvard.edu.