A CHALLENGE OF OUR TIME
Post-translational modifications (PTMs): Chemical or proteinaceous modifications that occur on proteins after their translation inside living cells, and essential for several life processes including cell division, signaling, epigenetic regulation, and more.
An Exponential Problem
Since the discovery of protein phosphorylation in the early 1950s, our ability to detect PTMs has increased exponentially. Over 300 different types of PTM are now known to exist - phosphorylation being the most common. We know now that most (if not all) proteins become modified and regulated at some point during the life of a cell. This rapid expansion of knowledge presents a challenge for the biologists of our time who seek to understand how cells work.
Our "State" of Knowledge
In 2017, well over 600,000 experimentally verified unique PTMs have been publicly curated (equivalent to the combined area of the red states). In comparison, only ~10,000 (~2%) have been experimentally verified as biologically functional (equivalent to the size of Vermont)!
Thus, the rate at which we can experimentally detect PTMs now far surpasses the rate at which we can understand their biological significance through purely empirical means.
We believe that finding solutions to these challenges will fundamentally impact our understanding of cell biology and provide new avenues and opportunities for improving and protecting human health.
What We Do
Our research spans three major areas of focus
Systematic Analysis of PTM Hotspots (SAPH-ire)
A computational solution to finding functional PTMs
We develop computational tools for the identification of PTMs that are likely to impact protein function. SAPH-ire is our premier tool, which utilizes machine learning to recommend PTMs for experimental analysis.
PTMs as Regulators of
G Protein Signaling
From computation to experimentation
We study how PTMs regulate G protein signaling - a process responsible for the transduction of hormones, neurotransmitters, and even photons of light. G protein signaling systems are the most prominent targets for the pharmaceutical treatment of disease.
Mass Spectrometry & Proteomics
Deciphering PTM codes
We utilize state-of-the-art mass spectrometers to study PTMs on proteins extracted from cells, protein-protein interactions, and protein-small-molecule interactions.
We are always seeking extraordinary new members to contribute. Here is our current group.
Matt Torres, PhD
Matt is a former Tar Heel from UNC Chapel Hill. His training is in mass spectrometry-based proteomics and G protein signaling. He has been investigating PTMs since 2001. He is also a co-director of the Systems Mass Spectrometry Core (SYMS-C) facility at Georgia Tech.
Wei Li, PhD
Wei is working on proteomics of the extra-cellular matrix and also on developing methods for identifying phosphorylation-mediated protein transitions from states of disorder to order.
Maneesha Aluru, PhD
Visiting Research Assist. Prof.
Maneesha has been leading the systems biology branch of the lab and is studying molecular mechanisms of aging linked to G protein and other MAPK signaling pathways.
PhD Candidate - Chemistry and Biochemistry
Hyojung is studying proteome dynamics in response to cellular stress and heme homeostasis.
PhD Candidate - Quantitative Biosciences
Nolan is establishing a new, state-of-the-art PTM database that he will combine with existing datasets to explore computational models for human disease.
PhD Graduate Student - Biological Sciences
Xinya is conducting kinome-wide screens to identify kinases involved in the regulation of G protein gamma subunits and G protein signaling.
MS Graduate Student - Bioinformatics
Hubert is making large strides in expanding the accessibility of PTM data from large-scale mass spectrometry data.
Former Team Members
These are folks that have come and gone. We thank them for the contributions they've made!
Shilpa Choudhury, PhD
Torres Lab Graduate - Biological Sciences
Shilpa is credited with several discoveries in the lab centering on the phosphoregulation of G protein signaling. She is also our first PhD graduate and is now gifting her talents as a post-doctoral fellow at Genentech!
Rushika Pandya, MS
MS Graduate in Bioinformatics
Rushika investigated the PTM topologies of RGS protein domain families and in curating data for a new PTM database. She was very successful, with 2 publications in 1.5 years and a third one on the way! She is now at the UCSF Bioinformatics core facility!
Ramya Madupuri, MS
MS Graduate in Bioinformatics
Ramya is an incredible bioinformatician who significantly advanced our understanding of PTMs based on protein structural studies. She is now applying creative bioinformatics techniques to study cancer at Memorial Sloan Kettering Cancer Center!
Niveda Sundararaman, MS
MS Graduate in Bioinformatics
Niveda was instrumental in establishing alternative uses for the SAPH-ire algorithm. She now is working at Cedar-Sinai Medical Center as a proteomics bioinformatician!
Paris was an undergraduate student who helped Shilpa to create yeast strains that harbor PTM site mutations. She's now in medical school training to heal people!
Henry Dewhurst, MS
MS Graduate in Bioinformatics
Henry was instrumental in the early development stages of SAPH-ire.
Tori McKinney, BS
Tori started with us as an undergraduate and made significant contributions to studies in yeast aging under the mentorship of Maneesha Aluru. She later became our lab manager and kept us all in line!
Nagender Panyala, PhD
Nagender established preliminary studies in protein cross linking and top-down proteomics in our lab.
Anne-Kathryn (A.K.) Love-Venerro, BS
AK started as an undergraduate in our lab and quickly excelled to lab manager. She helped to create several yeast strains that we use to this day! She is now at the CDC saving us from who knows what!
Krishna Vukoti, PhD
Research Scientist II
Krish was instrumental in helping the lab get off the ground. His focus was on using mass spectrometry to study proteolytic cleavage by membrane aspartyl proteases. You may know his son who is a world champion speller!
Charlie Winter, BS
Charlie was our first lab manager and did an amazing job helping to build the lab from nothing to something!
Jiani Long, MS
MS Graduate in Bioinformatics
Jiani made amazing strides in domain family SAPH-ire analysis for our lab, which we are incorporating into the traditional familial analysis workflow now. She is currently in Boston working as a bioinformatics consultant.
Ragy Haddad, MS
MS Graduate in Bioinformatics
Ragy is the first to develop a user friendly and web-accessible tool for SAPH-ire, which we will release very soon! He is now a computational biologist at DeepBiome at Harvard Life Labs.
Kuntal Mukherjee, PhD
Research Scientist II
Kuntal used yeast to test the function of phosphorylation hotspots predicted by SAPH-ire. He discovered that phosphorylation of linker histones plays a very important role in DNA maintenance. He is now studying the incorporation of RNA into DNA in Francesca Storici's lab.
Alex Jonke, PhD
Research Scientist II
Alex is a GT-trained analytical chemist who contributed to several proteomics projects including the development of a novel ion source for improved MS detection of proteins (in collaboration with the Fedorov Lab at GT).
Manasa Vagesna, MS
MS Graduate in Bioinformatics
Manasa was an MS-BINF student working on PTM feature extraction from MS data files for automated data curation. She is now expanding her influence as a bioinformatician with Niveda Sundararaman at Cedars-Sinai Hospital in LA California.
Zahra Nassiri Toosi, PhD
PhD Graduate in Biological Sciences
Zahra made significant contributions to our understanding of G protein gamma subunits as targets of combinatorial phosphorylation-based regulation. She is doing a postdoc at MD Anderson Cancer Center in Houston, Texas and from there....onward and upward!
Selected work from the Torres Lab at Georgia Tech (*corresponding author).
For a complete list of publications click here.
Combinatorial phosphorylation modulates the structure and function of the G protein gamma subunit in yeast
The Gγ subunit is the smallest member of the heterotrimeric G protein, and it may have more functional roles beyond its important role in anchoring the Gβγ dimer to the plasma membrane. Nassiri Toosi et al. showed that the N-terminal region of the yeast Gγ subunit Ste18 contains two serine residues within an intrinsically disordered region that were phosphorylated by different kinases in response to distinct stimuli. These combinatorial phosphorylation events likely altered the structure of Gγ and modulated the activation of a downstream effector. Together, these results suggest that distinct phosphorylation events in the Gγ intrinsically disordered region determine functional outcomes.
Systematic Analysis of Linker Histone PTM Hotspots Reveals Phosphorylation Sites that Modulate Homologous Recombination and DSB Repair
Mukherjee, English, Meers, Kim, Jonke, Storici, Torres*; DNA Repair (2019)
In this study, potentially functional phosphorylation hotspots in the linker histone protein family were identified using SAPH-ire - our machine-learning tool for functional PTM prioritization. Five hotspots ranging from low to high SAPH-ire probability score were investigated using the yeast linker histone, Hho1, as a model. Each phosphosite was mutated to nullify (S/T-A) or mimic (S/T-E) phosphorylation in vivo and then tested in parallel to quantify effects of each on DNA double strand break (DSB) repair. These results identified a strong dependence of DSB repair on site-specific phosphorylation of the linker histone protein.
Genetic heterogeneity within collective invasion packs drives leader and follower cell phenotypes
Zoeller, Pedro, Konen, Dwivedi, Rupji, Sundararaman, Wang, Horton, Zhong, Barwick, Cheng, Martinez, Torres, Kowalski, Marcus, Vertino*; Jour. Cell Sci. (2019)
Mutations enriched in metastatic leader versus follower cells from H1299 non-small cell lung cancer cells were investigated individually to understand their essentiality for such invasive phenotypes. As part of this analysis, we utilized SAPH-ire to understand PTMs in Arp3 - one of the primary candidates found mutated in these studies.
Different Grp94 components interact transiently with the myocilin olfactomedin domain in vitro to enhance or retard its amyloid aggregation
Huard, Jonke, Torres & Lieberman*; Sci. Rep. (2019)
Here we worked with the Lieberman lab to map transient structural interactions between myocilin and the heat shock protein Grp94 using cross linking mass spectrometry. Interaction between these two proteins serves as an important drug target for the treatment of glaucoma.
Citrullination of fibronectin alters integrin clustering and focal adhesion stability promoting stromal cell invasion.
Stefanelli, Choudhury, Hu, Liu, Schwenzer, Yeh, Chambers, Pesson, Li W, Segura, Midwood, Torres, Barker*; Matrix Biology (2019)
Here we used mass spectrometry to discover citrullination sites on fibronectin, the role of this PTM on cell motility and in the immune response of patients with rheumatoid arthritis.
Genetic Analysis of Rare Human Variants of Regulators of G Protein Signaling Proteins and Their Role in Human Physiology and Disease
Squires, Montañez-Miranda, Pandya, Torres, Hepler*; Pharmacol. Rev. (2018).
In this study, we summarize physiologic roles for RGS proteins and links to human diseases/traits and report rare variants found within each human RGS protein exome sequence derived from global population studies. Each RGS sequence is analyzed using recently described bioinformatics and proteomic tools for measures of missense tolerance ratio paired with combined annotation-dependent depletion scores, and protein post-translational modification (PTM) alignment cluster analysis. We highlight selected variants within the well-studied RGS domain that likely disrupt RGS protein functions and provide comprehensive variant and PTM data for each RGS protein for future study.
The dynamic and stress-adaptive signaling hub of 14-3-3: Emerging mechanisms of regulation and context-dependent protein-protein interactions
Pennington, Chan, Torres, Anderson*; Oncogene (2018)
This review covers a wide range of 14-3-3 regulatory mechanisms including PTM. We used SAPH-ire to thoroughly predict the function potential of experimental PTMs observed on 14-3-3 proteins across eukaryotes - only some of which have been studied previously. Among the more interesting discoveries was that the family harbors 4 distinct clusters of PTM - two of which were unrealized previously.
Negative Feedback Phosphorylation
of G gamma Subunit Ste18 and the Ste5 Scaffold Synergistically Regulates MAPK Activation in Yeast
Choudhury, Baradaran-Mashinchi, Torres*; Cell Reports (2018)
This work demonstrates for the first time that G gamma (Gg) subunits, besides acting as anchors for their obligate G beta (Gb) subunits, have more complex roles in regulating G protein signaling. Furthermore, they show that this tuning of G protein signaling by the phosphorylated Gg N-terminal tail is achieved by altering the interaction between Gbg and downstream effectors in a PTM-dependent manner.
Mitogen-activated protein kinases, Fus3 and Kss1, regulate chronological lifespan in yeast.
Aluru, McKinney, Venero, Choudhury, Torres*; Aging (2017)
Dr. Maneesha Aluru and team discovered that specific MAPKs thought to have very restricted roles in the process of yeast mating are in fact important regulators of cellular longevity.
Predicted functional implications of phosphorylation of RGS proteins in plants
Tunc-Ozdemir, Li, Jaiswal, Urano, Jones*, Torres*; Frontiers in Plant Science (2017)
In this project, we utilized several elements of SAPH-ire to explore the relationships and functional implications of plant and mammalian PTMs found on Regulator of G protein Signaling (RGS) proteins.
Acylation of SOD1 at K122 governs SOD1-mediated inhibition of mitochondrial respiration
Banks,Rodriquez, Gashler, Pandya, Mortenson, Whited, Soderblom, Thompson, Moseley, Reddi, Tessem, Torres, Anderson*; Mol. Cell Biol. (2017)
Using SAPH-ire, we identified PTMs with elevated function potential in superoxide dismutase proteins. One of these ranking in the top 10 (K122 acylation) was tested and found to have an important function in regulating mitochondrial respiration.
Systematic analysis of PTM features for function potential prediction
Dewhurst and Torres*; PLOS ONE (2017)
Here we describe the impact of PTM features on function potential prediction by SAPH-ire.
Proteome-wide structural analysis of PTM hotspots reveals regulatory elements predicted to impact biological function and disease
Torres*, Dewhurst, Sundararaman; Molecular and Cellular Proteomics (2016)
Here we demonstrate a neural network machine learning approach for prediction of functional PTMs.
Heterotrimeric G protein ubiquitination as a regulator of G-protein signaling
Torres*; in Progress in Molecular Biology and Translational Science (2016)
A review of heterotrimeric G protein regulation by ubiquitination including a comparison of ubiquitin site topologies between large and small G proteins.
Catalytic properties of intramembrane aspartyl protease substrate hydrolysis evaluated using a FRET peptide cleavage assay
Naing, Vukoti, Drury, Johnson, Kalyoncu, Hill, Torres, Lieberman*; ACS Chemical Biology (2015)
Here we characterized the proteolytic cleavage site preference of an intramembrane aspartyl protease by mass spectrometry.
Structural Analysis of PTM Hotspots (SAPH-ire): A quantitative informatics method enabling the discovery of novel regulatory elements in protein families
Dewhurst, Choudhury, Torres*; Molecular and Cellular Proteomics (2015)
The inaugural proof-of-principle test for SAPH-ire, showing that integration of PTM features serves to improve prediction of functional PTMs. Using the approach, we discovered novel PTM regulatory elements in heterotrimeric G protein systems.
Deciphering post-translational modification codes
Lothrop, Torres*, Fuchs*; Febs Letters (2013)
This manuscript highlights several examples of combinatorial PTMs in proteins, and describes recent technological developments, which are driving our ability to understand how PTM patterns may "code" for biological outcomes.
In The News....
We thank those who have taken notice and decided to say something about it!
Uncovering a Hidden Protein “Tail” that Puts the Brakes on Cell Signaling
By John Toon (2018)
Using an informatics tool that identifies “hotspots” of post-translational modification (PTM) activity on proteins, researchers have found a previously-unknown mechanism that puts the brakes on an important cell signaling process involving the G proteins found in most living organisms. (Click Here for More Info)
SAPH-ire Helps Scientists Prioritize Protein Modification ResearchTitle Text
By John Toon (2015)
Researchers have developed a new informatics technology that analyzes existing data repositories of protein modifications and 3D protein structures to help scientists identify and target research on “hotspots” most likely to be important for biological function.
SAPH-ire: Structural analysis of PTM hotspots!
By Ben Orsburn (2015)
Continuing theme alert! What do we do with all of this proteomics PTM data? Maybe we run it through this awesome new program from Henry Dewhurst et al., that they call SAPH-ire.....
Some Fun Had By All
....and random things to celebrate.
Quantitative BioSciences Student Appreciation Lunch
Appreciating all that Nolan does for our lab....and eating pizza!
Masters Rushika and Rumya Graduate!!!
Can't believe they are on their way! We are so happy to have worked with them and proud of their contributions to our science. CONGRATULATIONS!!!
Graduation thumbs up from the PhD students and Postdocs!
Painted Pin Bowling 2017!!
...minus a few folks who had to bowl and dash!
A motley crew of bowlers! Painted Pin party 2017!!!
This was a send off party for Tori on her last day at Tech! We'll miss you Tori!
Tori (and Tim) stand onlooking and hesitant to approach the bowling lane! Sadegh (Zahra's husband) looks on with suspicion.
Hyojung and Shilpa pause from their discussion about whether there is a penalty for throwing the bowling ball backwards....
Paris was on fire this night. She had Zahra and Sadegh in stitches - or at least she was in stitches.
Rushika and Ramya - shortly after throwing the bowling ball backwards....
Torres and Tori head to head for the last time!
The Torres lab and families got together for food, ping pong, and tie dye!!!
The inaugural tie-dye event.
Outreach Content - Middle School
Here are a few useful links and images for outreach in protein biochemistry!
Protein Gel Electrophoresis Time-Lapse
This is what our protein gels would look like if you could speed up time!
This is an outstanding video from Sheila Marsh at Stanford University
Amylase - An Enzyme that Breaks Down Starch!
Here is an experiment that shows the ability of amylase to breakdown starch in a test tube!
This is the enzyme alpha-Amylase, which is found in your saliva!
The blue are amino acids in the enzyme. The yellow is starch bound at the active site of the enzyme.
Zooming into the enzyme Amylase!
This is one long chain of amino acids! The active site is where the yellow starch molecules are seen here. The white and red balls and sticks on the right correspond to amino acid side chains that help to catalyze the breakdown of the starch.
What is the most powerful enzyme we know of?
OMP Decarboxylase is VERY good at doing a tough job.
Molecular Evolution - All Life on Earth Shares a Common Ancestor!
We share the same code!
Do Proteins Evolve? - Molecular Evolution
Sequences of myoglobin from five different animals are compared to create a phylogenetic tree. Each molecule is colored to show differences from the human protein. Amino acids that are identical are pink, amino acids that are different but similar are lighter pink, and amino acids that are completely different are in white. The heme is shown in bright red. The tree was calculated with the online server at phylogeny.fr. PDB entries 3rgk, 1ymb, 1mbo, 1lhs, 2nrl. Re-posted from our brilliant friends at the PDB! https://pdb101.rcsb.org/motm/206
Amylase from Henderson Middle Students!
We visit Ms. Shaw's and Ms. Clarke's science classes and asked for volunteer students to provide saliva samples that we could analyze by gel electrophoresis. We were able to detect the enzyme Amylase in each student's saliva sample! Some other bigger and smaller proteins were also visible. We compared this to a protein sample from a cell (where we expected to see thousands of proteins)....and we see many more bands.
Outreach Content - Elementary School
Here are a few useful links and images for outreach at the Elementary School level
The Scientific Method
Here is a great video for young students to help them learn the scientific method.
The Scientific Method is Simple!
First Grader Scientists at Ridgepoint Elementary School!
I visit Mrs. Torres' first grade elementary school class at Ridgepoint Elementary School in Sacramento California to teach them the scientific method. The kids were AWESOME!!!!
We started by OBSERVING each others arms (students only).
Next - we asked the QUESTION: "Which student has the longest wingspan?"
Then we all sat down and formulated a HYPOTHESIS, where each student PREDICTED who they thought had the longest arms/wingspan.
Then we did an EXPERIMENT where we measured everyone's wingspan to test our individual hypotheses.
We ANALYZED THE DATA (pictured above) by putting all of the results into a bar graph.
Lastly, we drew a CONCLUSION about who had the longest wingspan based on the data. Students could then see if their hypothesis was supported by the data or not!
A First Grader's Thank You...
Mrs. Torres' class was such a pleasure! They even sent me thank you notes, some of which I show here. Thank you little scientists!