Areas of Interest
Intracellular transport * Motor proteins * Structural biology * Single molecule biophysics * Cryo-electron microscopy * Cloud computing
We are a research team that is trying to understand the molecular details that determine how, where, and when motor proteins transport intracellular cargo. The past thirty years of cell biology research have set the stage for us to determine the general principles that underlie the complex process of intracellular transport.
Specifically, we are interested in the mechanisms that dictate how cytoplasmic dynein and kinesin are recruited to—and activated for—cargo transport. For each project, we will be trying to answer the following questions:
- How is specificity determined between motor proteins and cargo?
- How are the activities of multi-motor complexes regulated?
- What are the molecular consequences of neurodegenerative disease-causing mutations?
We will be approaching these questions using state of the art technologies that range from mammalian cell protein expression to cryo-EM to single molecule fluorescence assays. This integrated approach will allow us to relate how changes at the molecular level alter the structure and function of transporting motor-cargo complexes.
Tool development for cryo-electron microscopy
As a fast-growing part of structural biology, cryo-electron microscopy (cryo-EM) is determining new and exciting macromolecular structures on a seemingly daily basis. Despite its power, cryo-EM is a field that needs to undergo rapid maturation to allow for new users to come into the fold to solve structures. Unlike other structural biology tools, cryo-EM necessarily requires access to high-performance computing capabilities. The large computational workload will limit the throughput and spread of cryo-EM due to users 1) waiting for cluster time or 2) being unable to find a cluster amenable for cryo-EM.
To address these problems, we are building cloud computing resources at Amazon Web Services and the San Diego Supercomputer Center to help give users access to cryo-EM so they can focus on understanding biology instead of deal with Linux. In addition to these new software tools, we are also considering new methods that will give un-supervised assessment of single particle electron microscopy data quality, given the large computing resources of the cloud.
High-Throughput Cryo-EM Enabled by User-Free Preprocessing Routines.
Li Y, Cash JN, Tesmer JJG, Cianfrocco MA.
Structure. 2020; 28: 858–69.
Golgi-associated BICD adaptors couple ER membrane penetration and disassembly of a viral cargo.
Spriggs CC, Badieyan S, Verhey KJ, Cianfrocco MA, Tsai B.
J Cell Biol. 2020; 219: e201908099.
What Could Go Wrong? A Practical Guide to Single-Particle Cryo-EM: From Biochemistry to Atomic Models.
Cianfrocco MA, Kellogg EH.
J Chem Inf Model. 2020; 60: 2458–69.
Miro: A molecular switch at the center of mitochondrial regulation.
Eberhardt EL, Ludlam AV, Tan Z, Cianfrocco MA.
Protein Sci. 2020; 29: 1269–84.
Cryo–electron microscopy structure and analysis of the P-Rex1–Gβγ signaling scaffold.
Cash JN, Urata S, Li, S, Ravala SK, Avramova LV, Shost MD, Gutkind JS, Tesmer JJG, Cianfrocco MA.
Sci Adv. 2019; 5: eaax8855.
Cryo-EM structure of the human MLL1 core complex bound to the nucleosome.
Park SH, Ayoub A, Lee YT, Xu J, Kim H, Zheng W, Zhang B, Sha L, An S, Zhang Y, Cianfrocco MA, Su M, Dou Y, Cho US.
Nat Commun. 2019; 10: 5540.
cryoem-cloud-tools: A software platform to deploy and manage cryo-EM jobs in the cloud.
Cianfrocco MA#, Lahiri I, DiMaio F, Leschziner AE.
J Struct Biol. 2018; 203: 230–5.
Lis1 Has Two Opposing Modes of Regulating Cytoplasmic Dynein.
DeSantis ME*, Cianfrocco MA*, Htet ZM*, Tran PT, Reck-Peterson SL#, Leschziner AE#.
Cell. 2017; 170: 1197–1208.
For a list of publications at Google Scholar, click HERE