• 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

In response to the COVID-19 pandemic, the CMI is closed for general access as of March 19, 2020.  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.  Remote consultations can be requested through PPMS or by contacting cmi@hms.harvard.edu.    Stay safe!

HMS Phase 2 Re-Entry

Harvard Medical School is actively planning a phased re-opening of the campus and research laboratories, under social distancing restrictions. The school has not released a timeline for re-entry.  Likewise, CMI plans for re-opening are being refined and could change.  Our current plan is to begin opening up to the HMS community in stages, when (or shortly after) HMS transitions to phase 2. The first priority will be to support instrument access by previously-trained HMS-affiliated CMI users.  At least for the first several weeks of the ramp-up we will not be training new users at the CMI. We need to figure out how to do that safely and, initially, will focus on accommodating the needs of current users with ongoing projects. 

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

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.
Patnaik D, Pao P-C, Zhao W-N, Silva CM, Hylton NK, Chindavong PS, Pan L, Tsai L-H, Haggarty SJ. Exifone is a Potent HDAC1 Activator with Neuroprotective Activity in Human Neuronal Models of Neurodegeneration. bioRxiv 2020;27(2):2020.03.02.973636.Abstract
Genomic instability caused by a deficiency in the DNA damage response and repair has been linked to age-related cognitive decline and neurodegenerative disease. Preventing this loss of genomic integrity that ultimately leads to neuronal death may provide a broadly effective strategy to protect against multiple potential genotoxic stressors. Recently, the zinc-dependent, class I histone deacetylase HDAC1 has been identified as a critical protein for protecting neurons from deleterious effects mainly caused by double-strand DNA breaks in Alzheimer’s disease (AD), amyotrophic lateral sclerosis (ALS), and frontotemporal dementia (FTD). Translating these observations to a novel neuroprotective therapy for AD, ALS or FTD will benefit from the identification of small molecules capable of selectively increasing the deacetylase activity of HDAC1 over other structurally similar class I HDACs. Here, we demonstrate that exifone, a drug previously shown to be effective in treating cognitive decline associated with AD and Parkinson’s disease, the molecular mechanism of which has remained poorly understood, potently activates the deacetylase activity of HDAC1 and provides protection against genotoxic stress. We show that exifone acts as a mixed, non-essential activator of HDAC1 that is capable of binding to both free and substrate-bound enzyme resulting in an increased relative maximal rate of HDAC1-catalyzed deacetylation. Selectivity profiling and estimation of kinetic parameters using biolayer interferometry suggest HDAC1 is a preferential target compared to other class I HDACs and CDK5. Treatment of human induced pluripotent stem cell (iPSC)-derived neuronal cells resulted in a decrease of histone acetylation, consistent with an intracellular mechanism of deacetylase activation. Moreover, using tauopathy patient-derived iPSC neuronal models subject to oxidative stress through mitochondrial inhibition exifone treatment was neuroprotective. Taken together, these findings reveal exifone as a potent activator of HDAC1-mediated deacetylation, thereby offering a lead for novel therapeutic development aiming to protect genomic integrity in the context of neurodegeneration and aging.

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.