About

Rutilio Fratti is a professor in the Department of Biochemistry at the Illinois College of Liberal Arts & Sciences, specializing in biomolecular structure and dynamics with a focus on membrane biology, protein dynamics, and receptor biochemistry. His research investigates how the chemical and physical properties of membrane bilayers control protein function, emphasizing the importance of protein-lipid interactions in cellular processes such as membrane fusion, signaling, and organelle function. His lab uses yeast vacuoles and synthetic vesicles to study how lipid modifications regulate proteins involved in membrane fusion, with particular attention to regulatory lipids like phosphatidic acid, diacylglycerol, phosphoinositides, cholesterol, and sphingolipids, and their roles in health and disease.

Research topics

• Biology
• Biochemistry
• Cell biology
• Chemistry

Selected publications

• Data Sheet 1_Differential effects of lysophospholipid headgroups, acyl chain length and saturation on vacuole acidification, Ca2+ transport, membrane fluidity, and fusion.pdf

  Figshare · 2026-04-29

  datasetSenior author

  SNARE-mediated membrane fusion is regulated by the lipid composition of the engaged bilayers. Lipids impact fusion through direct protein-lipid interactions or through modulating the physical properties of membranes to affect protein function. Lysophospholipids (LPLs) can affect membrane curvature, fluidity and energy of deformation. Their effects are due to their head group, and the length and saturation of their single acyl chains. Here we examined how the properties of LPLs affect yeast vacuole fusion, membrane fluidity and ion transport. We found that lysophosphatidylcholine (LPC) with 14–18 carbon acyl chains inhibited fusion with IC₅₀ values of ≅ 40–120 µM. While acyl chain length moderately affected fusion, the head group played a major role. Unlike LPCs, Lysophosphatidic acid (LPA 18:1) failed to fully inhibit fusion, while lysophosphatidylethanolamine (LPE 18:1) had no effect. Unlike fusion, fluidity was sensitive to head group type. Fluidity was significantly decreased by LPA 18:1 but not LPCs. Separately we found that changes in acyl chain length and saturation differentially affected Ca²⁺ transport and vacuole acidification. Together these data show that the effects of LPLs on membrane fusion, fluidity, and ion transport were due to a combination of head group type and acyl chain length and saturation.

  DOI

• Differential effects of lysophospholipid headgroups, acyl chain length and saturation on vacuole acidification, Ca2+ transport, membrane fluidity, and fusion

  Frontiers in Cell and Developmental Biology · 2026-04-29

  articleOpen accessSenior author

  SNARE-mediated membrane fusion is regulated by the lipid composition of the engaged bilayers. Lipids impact fusion through direct protein-lipid interactions or through modulating the physical properties of membranes to affect protein function. Lysophospholipids (LPLs) can affect membrane curvature, fluidity and energy of deformation. Their effects are due to their head group, and the length and saturation of their single acyl chains. Here we examined how the properties of LPLs affect yeast vacuole fusion, membrane fluidity and ion transport. We found that lysophosphatidylcholine (LPC) with 14–18 carbon acyl chains inhibited fusion with IC 50 values of ≅ 40–120 µM. While acyl chain length moderately affected fusion, the head group played a major role. Unlike LPCs, Lysophosphatidic acid (LPA 18:1) failed to fully inhibit fusion, while lysophosphatidylethanolamine (LPE 18:1) had no effect. Unlike fusion, fluidity was sensitive to head group type. Fluidity was significantly decreased by LPA 18:1 but not LPCs. Separately we found that changes in acyl chain length and saturation differentially affected Ca 2+ transport and vacuole acidification. Together these data show that the effects of LPLs on membrane fusion, fluidity, and ion transport were due to a combination of head group type and acyl chain length and saturation.

  PublisherDOI

• Use of Bio-Layer Interferometry (BLI) to Measure Binding Affinities of SNAREs and Phosphoinositides

  Methods in molecular biology · 2025-01-01 · 5 citations

  articleOpen accessSenior author
  PublisherOA PDFDOI

• Broad-Spectrum Activity and Mechanisms of Action of SQ109 on a Variety of Fungi

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-02-03

  preprintOpen access

  ABSTRACT We investigated the activity of the tuberculosis drug SQ109 against sixteen fungal pathogens: Candida albicans , C. auris , C. glabrata , C. guilliermondi , C. kefyr , C. krusei , C. lusitaniae , Candida parapsilosis , C. tropicalis, Cryptococcus neoformans , Rhizopus spp., Mucor spp., Fusarium spp., Coccidioides spp., Histoplasma capsulatum and Aspergillus fumigatus . MIC values varied widely (125 ng/mL to >64 µg/mL) but in many cases we found promising (MIC∼4 µg/mL) activity as well as MFC/MIC ratios of ∼2. SQ109 metabolites were inactive. The activity of 12 analogs of SQ109 against Saccharomyces cerevisiae correlated with protonophore uncoupling activity, suggesting mitochondrial targeting, consistent with the observation that growth inhibition was rescued by agents which inhibit ROS species accumulation. SQ109 disrupted H + /Ca 2+ homeostasis in S. cerevisiae vacuoles, and there was synergy (FICI∼0.31) with pitavastatin, indicating involvement of isoprenoid biosynthesis pathway inhibition. SQ109 is, therefore, a potential antifungal agent with multi-target activity.

  PublisherOA PDFDOI

• Broad-Spectrum Activity and Mechanisms of Action of SQ109 on a Variety of Fungi

  ACS Infectious Diseases · 2025-05-14 · 3 citations

  article

  We investigated the activity of the tuberculosis drug SQ109 against 16 fungal pathogens: Candida albicans, C. auris, C. glabrata, C. guilliermondi, C. kefyr, C. krusei, C. lusitaniae, C. parapsilosis, C. tropicalis, Cryptococcus neoformans, Rhizopus spp., Mucor spp., Fusarium spp., Coccidioides spp., Histoplasma capsulatum and Aspergillus fumigatus. MIC values varied widely (125 ng/mL to >64 μg/mL) but in many cases we found promising (MIC ∼ 4 μg/mL) activity as well as MFC/MIC ratios of ∼ 2. SQ109 metabolites were inactive. The activity of 12 analogs of SQ109 against Saccharomyces cerevisiae correlated with protonophore uncoupling activity, suggesting mitochondrial targeting, consistent with the observation that growth inhibition was rescued by agents which inhibit ROS species accumulation. SQ109 disrupted H+/Ca2+ homeostasis in S. cerevisiae vacuoles, and there was synergy (FICI ∼ 0.26) with pitavastatin, indicating involvement of isoprenoid biosynthesis pathway inhibition. SQ109 is, therefore, a potential antifungal agent with multitarget activity.

  PublisherDOI

• Vacuolar Phosphatidylinositol 3,4,5-trisphosphate controls fusion through binding Vam7, and membrane microdomain assembly

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-08-02

  preprintOpen accessSenior authorCorresponding

  Abstract Membrane trafficking is regulated by phosphoinositides (PI) and their modification. The endolysosomal pathway is controlled by PI3P, PI(4,5)P 2 and PI(3,5)P 2 , whereas a role for PI(3,4,5)P 3 is less clear. We report that yeast vacuoles produce PI(3,4,5)P 3 through Vps34 activity. In vitro assays showed that dioctanoyl (C8) PI(3,4,5)P 3 or the PI(3,4,5)P 3 -binding domain Grp1-PH blocked fusion. Furthermore, modifying endogenous PI(3,4,5)P 3 with the phosphatase PTEN abolished fusion. Fluorescence microscopy showed that PI(3,4,5)P 3 was present at the plasma membrane and the vertex microdomains of vacuoles. PI(3,4,5)P 3 staining was blocked by PTEN, C8-PI(3,4,5)P 3 , the Vps34 inhibitor SAR405 and a VPS34 temperature sensitive mutation. Importantly, blocking or eliminating PI(3,4,5)P 3 prevented the vertex enrichment of Ypt7 and the HOPS subunit Vps33. Finally, we show that the SNARE Vam7 binds PI(3,4,5)P 3 and that both Grp1-PH and PTEN displaced it from membranes to block trans-SNARE pairing. Our results demonstrate that vacuolar PI(3,4,5)P 3 coordinates vertex assembly and SNARE function.

  PublisherOA PDFDOI

• Spectroscopic Methods for Detecting Conformational Changes During Sec18-Lipid Interactions

  Methods in molecular biology · 2025-01-01

  article1st authorCorresponding
  PublisherDOI

• Sphingolipids containing very long-chain fatty acids regulate Ypt7 function during the tethering stage of vacuole fusion

  Journal of Biological Chemistry · 2024-09-20 · 9 citations

  articleOpen accessSenior author

  Sphingolipids are essential in membrane trafficking and cellular homeostasis. Here, we show that sphingolipids containing very long-chain fatty acids (VLCFAs) promote homotypic vacuolar fusion in Saccharomyces cerevisiae. The elongase Elo3 adds the last two carbons to VLCFAs that are incorporated into sphingolipids. Cells lacking Elo3 have fragmented vacuoles, which is also seen when WT cells are treated with the sphingolipid synthesis inhibitor Aureobasidin-A. Isolated elo3Δ vacuoles show acidification defects and increased membrane fluidity, and this correlates with deficient fusion. Fusion arrest occurs at the tethering stage as elo3Δ vacuoles fail to cluster efficiently in vitro. Unlike HOPS and fusogenic lipids, GFP-Ypt7 does not enrich at elo3Δ vertex microdomains, a hallmark of vacuole docking prior to fusion. Pulldown assays using bacterially expressed GST-Ypt7 showed that HOPS from elo3Δ vacuole extracts failed to bind GST-Ypt7 while HOPS from WT extracts interacted strongly with GST-Ypt7. Treatment of WT vacuoles with the fluidizing anesthetic dibucaine recapitulates the elo3Δ phenotype and shows increased membrane fluidity, mislocalized GFP-Ypt7, inhibited fusion, and attenuated acidification. Together these data suggest that sphingolipids contribute to Rab-mediated tethering and docking required for vacuole fusion.

  PublisherOA PDFDOI

• Erratum to “High throughput analysis of vacuolar acidification” [Anal. Biochem. 658C (2022) 114927]

  Analytical Biochemistry · 2022-11-18

  erratumSenior author
  PublisherDOI

• Use of Microscale Thermophoresis to Measure Protein-Lipid Interactions

  Journal of Visualized Experiments · 2022-02-10 · 8 citations

  articleSenior author

  The ability to determine the binding affinity of lipids to proteins is an essential part of understanding protein-lipid interactions in membrane trafficking, signal transduction and cytoskeletal remodeling. Classic tools for measuring such interactions include surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC). While powerful tools, these approaches have setbacks. ITC requires large amounts of purified protein as well as lipids, which can be costly and difficult to produce. Furthermore, ITC as well as SPR are very time consuming, which could add significantly to the cost of performing these experiments. One way to bypass these restrictions is to use the relatively new technique of microscale thermophoresis (MST). MST is fast and cost effective using small amounts of sample to obtain a saturation curve for a given binding event. There currently are two types of MST systems available. One type of MST requires labeling with a fluorophore in the blue or red spectrum. The second system relies on the intrinsic fluorescence of aromatic amino acids in the UV range. Both systems detect the movement of molecules in response to localized induction of heat from an infrared laser. Each approach has its advantages and disadvantages. Label-free MST can use untagged native proteins; however, many analytes, including pharmaceuticals, fluoresce in the UV range, which can interfere with determination of accurate KD values. In comparison, labeled MST allows for a greater diversity of measurable pairwise interactions utilizing fluorescently labeled probes attached to ligands with measurable absorbances in the visible range as opposed to UV, limiting the potential for interfering signals from analytes.

  PublisherDOI

Recent grants

• NIH Grant R01GM101132

  NIH · $1.4M · 2018

• Regulation of the AAA+ protein Sec18 through membrane lipid modification

  NSF · $900k · 2018–2024

Frequent coauthors

• Vojo Deretić

  University of New Mexico

  18 shared

• Gregory E. Miner

  University of North Carolina at Chapel Hill

  17 shared

• Matthew L. Starr

  University of Illinois Urbana-Champaign

  16 shared

• Robert P. Sparks

  University of South Florida

  15 shared

• Chi Zhang

  Purdue University West Lafayette

  14 shared

• William Wickner

  Dartmouth College

  13 shared

• Logan R. Hurst

  University of Illinois Urbana-Champaign

  13 shared

• Jennifer Chua

  United States Army Medical Research Institute of Infectious Diseases

  12 shared

Labs

• Center for Biophysics and Quantitative BiologyPI

Awards & honors

• NIH Pre-Doctoral Fellow, 1999-2001
• Helen Hay Whitney Postdoctoral Fellowship, 2003-2005
• University of Illinois Research Board Arnold O Beckman Award…