About

Pernilla Wittung-Stafshede is a Professor of Chemistry and BioSciences at Rice University, holding the Charles W. Duncan Jr.-Welch Chair in Chemistry and serving as a CPRIT Scholar in Cancer Research. Her research group employs biophysical and biochemical tools to investigate the (dys)functionality of proteins and biological pathways at the molecular level, with a focus on understanding the role of metal ions, particularly copper, in health and disease. Her work explores how human cells regulate copper, how imbalances contribute to diseases such as cancer and neurodegenerative disorders, and the mechanisms by which proteins, including amyloids, interact with metals and catalyze reactions. Her pioneering discoveries include insights into the role of metals in protein folding, macromolecular crowding effects, and mechanisms of copper-transport proteins. Wittung-Stafshede's research integrates biophysics, biochemistry, and bioinorganic chemistry, often in collaboration with other groups, to advance fundamental knowledge aimed at improving human health. She has made significant contributions to understanding the molecular mechanisms underlying diseases like Alzheimer's, Parkinson's, and cancer, and her work includes exploring the emerging roles of amyloids in these conditions. Her academic career spans positions at Tulane University, Umeå University, Chalmers University of Technology, and Rice University, with notable achievements including election to the Royal Swedish Academy of Sciences, the Royal Swedish Academy of Engineering Sciences, and recognition as a Fellow of the Royal Society of Chemistry. She has served on the Nobel Committee in Chemistry and contributed extensively to scientific leadership and outreach, including training numerous students and postdoctoral researchers and leading initiatives to promote research excellence and diversity.

Selected publications

• ATP Hydrolysis by α‐Synuclein Amyloids is Mediated by Enclosing β‐Strand

  Advanced Science · 2025-10-16

  articleOpen accessSenior authorCorresponding

  Pathological amyloids, like those formed by α-synuclein in Parkinson's disease, are recently found to catalyze the hydrolysis of model substrates in vitro. Here it is reported that the universal energy molecule ATP is another substrate for α-synuclein amyloid chemical catalysis. To reveal the underlying mechanism, the high-resolution cryo-EM structure of the amyloids in the presence of ATP is solved. The structure reveals a type 1A amyloid fold with an additional β-strand involving residues 16-22 that wraps around the ATP, creating an enclosed cavity at the interface of the protofilaments. Mutations of putative ATP-interacting residues in the cavity and the additional β-strand showed that replacing any one of Lys21, Lys23, Lys43, Lys45, and Lys60 with Ala reduced amyloid-mediated ATPase activity. High-resolution structural analysis of Lys21Ala α-synuclein amyloids in the presence of ATP reveals the same fold as wild-type α-synuclein amyloids but without the extra β-strand and with ATP oriented differently. It is concluded that positively-charged side chains, along with ordering of the N-terminal part into a β-strand, enclosing the cavity, are essential parameters governing ATP hydrolysis by α-synuclein amyloids. Amyloid-catalyzed ATP hydrolysis may hamper ATP-dependent rescue systems near amyloid deposits in vivo.

  PublisherOA PDFDOI

• In silico identification of substrate-binding sites in type-1A α-synuclein amyloids

  Biophysical Journal · 2025-06-18 · 5 citations

  articleOpen accessSenior author

  Pathological amyloids associated with Parkinson and Alzheimer diseases have been shown to catalyze chemical reactions in vitro. To elucidate how small-molecule substrates interact with cross-β amyloid structures, we here employ computational approaches to investigate α-synuclein amyloid fibrils of the type-1A fold. Our initial binding pocket prediction analysis identified three distinct substrate-binding sites per protofilament, yielding a total of six sites in the dimeric type-1A amyloid structure. Molecular docking of the model phosphoester substrate para-nitrophenyl phosphate (pNPP), previously shown to be dephosphorylated by α-synuclein amyloids in vitro, was performed on the three identified sites. Docking was validated by molecular dynamics simulations for a period of 100 ns. The results revealed a pronounced preference for a single binding site (termed Site 2), as pNPP migrated to this region when primarily placed at the other two sites. Site 2 is located near the interface between the two protofilaments in a cavity enriched with lysine residues and histidine-50. Binding site analysis suggests stable, yet dynamic, interactions between pNPP and these residues in the α-synuclein amyloid fibril. Our work provides molecular-mechanistic details of the interaction between a small-molecule substrate and one α-synuclein amyloid polymorph. This framework may be extended to other reactive substrates and amyloid polymorphs.

  PublisherDOI

• <scp>CAPIM</scp> : Catalytic activity and site prediction and analysis tool in multimer proteins

  Protein Science · 2025-10-18

  articleOpen accessSenior authorCorresponding

  Enzymes play a fundamental role in living organisms by catalyzing vital chemical reactions. While much is known about enzyme function, a substantial portion of the proteome remains uncharacterized. Computational tools have become indispensable in this field, yet most focus exclusively on either enzymatic activity prediction or active site detection, creating a gap between residue-level annotation and functional characterization. To bridge this gap, we present Catalytic Activity and Site Prediction and Analysis Tool In Multimer Proteins (CAPIM) -an integrative computational pipeline that combines binding pocket identification and catalytic site annotation with enzymatic activities, along with functional validation via enzyme-substrate docking. CAPIM unifies the capabilities of three established tools: P2Rank, GASS, and AutoDock Vina. P2Rank uses a machine learning-based approach to predict binding pockets, while genetic active site search (GASS) identifies catalytically active residues and annotates them with Enzyme Commission numbers. These outputs are merged to generate residue-level activity profiles within predicted pockets. Functional validation is then performed using AutoDock Vina, enabling substrate docking simulations for user-defined ligands. CAPIM supports any number of peptide chains in the protein complex-which may be crucial for enzymatic functions dependent on quaternary and/or polymeric (e.g., amyloid) structures. The utility of CAPIM is demonstrated through case studies involving both well-characterized enzymes and unannotated multi-chain targets. By delivering residue-level predictions and docking analyses in a unified framework, CAPIM offers a powerful resource with broad applications in drug discovery and protein engineering. CAPIM is available both as a standalone application at https://git.chalmers.se/ozsari/capim-app and as a hosted web service at https://capim-app.serve.scilifelab.se.

  PublisherOA PDFDOI

• Biological Amyloids Chemically Damage DNA

  ACS Chemical Neuroscience · 2025-01-09 · 8 citations

  articleOpen accessSenior authorCorresponding

  Amyloid fibrils are protein polymers noncovalently assembled through β-strands arranged in a cross-β structure. Biological amyloids were considered chemically inert until we and others recently demonstrated their ability to catalyze chemical reactions in vitro. To further explore the functional repertoire of amyloids, we here probe if fibrils of α-synuclein (αS) display chemical reactivity toward DNA. We demonstrate that αS amyloids bind DNA at micromolar concentrations in vitro. Using the activity of DNA repair enzymes as proxy for damage, we unravel that DNA-amyloid interactions promote chemical modifications, such as single-strand nicks, to the DNA. Double-strand breaks are also evident based on nanochannel analysis of individual long DNA molecules. The amyloid fold is essential for the activity as no DNA chemical modification is detected with αS monomers. In a yeast cell model, there is increased DNA damage when αS is overexpressed. Chemical perturbation of DNA adds another chemical reaction to the set of activities emerging for biological amyloids. Since αS amyloids are also found in the nuclei of neuronal cells of Parkinson's disease (PD) patients, and increased DNA damage is a hallmark of PD, we propose that αS amyloids contribute to PD by direct chemical perturbation of DNA.

  PublisherDOI

• Metal ions control amyloid catalysis

  Journal of Inorganic Biochemistry · 2025-10-15

  articleSenior authorCorresponding
  PublisherDOI

• Yoga as a Complementary Therapy for Cancer Patients: From Clinical Observations to Biochemical Mechanisms

  Complementary Medicine Research · 2024-07-18 · 8 citations

  reviewOpen accessSenior author

  BACKGROUND: Integrative oncology combines conventional and complementary, or integrative, therapies for a holistic treatment of cancer patients. Yoga is increasingly used as a complementary therapy for cancer patients, but there is no direct evidence for its effect on cancer pathophysiology like tumor response, or patient outcome like overall survival. SUMMARY: In this narrative review, we present in detail published studies from randomized clinical trials on complementary yoga therapy for cancer patients, including details about the biochemical mechanisms involved. Medicinal hatha yoga with breathing, postures, meditation, and relaxation enhances the quality of life of cancer patients by providing both psychological and physiological health benefits, highlighting the interconnectedness of mind and body. Yoga therapy reduces stress levels improving heart rate variability, leading to changes in hormonal regulation (e.g., cortisol), reduced oxidative stress, and improved immune function with reduced inflammation. Still, the biochemical effects of yoga on the cancer disease itself are unrevealed. KEY MESSAGES: More clinical and basic research is needed for further establishment of yoga as complementary therapy in oncology.

  PublisherDOI

• Copper ion incorporation in α‐synuclein amyloids

  Protein Science · 2024-03-21 · 19 citations

  articleOpen accessSenior authorCorresponding

  Copper ion dys-homeostasis is linked to neurodegenerative diseases involving amyloid formation. Even if many amyloidogenic proteins can bind copper ions as monomers, little is known about copper interactions with the resulting amyloid fibers. Here, we investigate copper interactions with α-synuclein, the amyloid-forming protein in Parkinson's disease. Copper (Cu(II)) binds tightly to monomeric α-synuclein in vitro involving the N-terminal amine and the side chain of His50. Using purified protein and biophysical methods in vitro, we reveal that copper ions are readily incorporated into the formed amyloid fibers when present at the start of aggregation reactions, and the metal ions also bind if added to pre-formed amyloids. Efficient incorporation is observed for α-synuclein variants with perturbation of either one of the high-affinity monomer copper-binding residues (i.e., N-terminus or His50) whereas a variant with both N-terminal acetylation and His50 substituted with Ala does not incorporate any copper into the amyloids. Both the morphology of the resulting α-synuclein amyloids (amyloid fiber pitch, secondary structure, proteinase sensitivity) and the copper chemical properties (redox activity, chemical potential) are altered when copper is incorporated into amyloids. We speculate that copper chelation by α-synuclein amyloids contributes to the observed copper dys-homeostasis (e.g., reduced bioavailable levels) in Parkinson's disease patients. At the same time, amyloid-copper interactions may be protective to neuronal cells as they will shield aberrantly free copper ions from promotion of toxic reactive oxygen species.

  PublisherOA PDFDOI

• Comparing lipid remodeling of brown adipose tissue, white adipose tissue, and liver after one‐week high fat diet intervention with quantitative Raman microscopy

  Journal of Cellular Biochemistry · 2023-01-30 · 7 citations

  articleOpen access

  Brown adipose tissue (BAT) consists of highly metabolically active adipocytes that catabolize nutrients to produce heat. Playing an active role in triacylglycerol (TAG) clearance, research has shown that dietary fatty acids can modulate the TAG chemistry deposition in BAT after weeks-long dietary intervention, similar to what has been shown in white adipose tissue (WAT). Our objective was to compare the influence of sustained, nonchronic dietary intervention (a 1-week interval) on WAT and interscapular BAT lipid metabolism and deposition in situ. We use quantitative, label-free chemical microscopy to show that 1 week of high fat diet (HFD) intervention results in dramatically larger lipid droplet (LD) growth in BAT (and liver) compared to LD growth in inguinal WAT (IWAT). Moreover, BAT showed lipid remodeling as increased unsaturated TAGs in LDs, resembling the dietary lipid composition, while WAT (and liver) did not show lipid remodeling on this time scale. Concurrently, expression of genes involved in lipid metabolism, particularly desaturases, was reduced in BAT and liver from HFD-fed mice after 1 week. Our data show that BAT lipid chemistry remodels exceptionally fast to dietary lipid intervention compared WAT, which further points towards a role in TAG clearance.

  PublisherOA PDFDOI

• Chemical catalysis by biological amyloids

  Biochemical Society Transactions · 2023-09-25 · 18 citations

  articleOpen access1st authorCorresponding

  Toxic aggregation of proteins and peptides into amyloid fibers is the basis of several human diseases. In each disease, a particular peptide noncovalently assembles into long thin structures with an overall cross-β fold. Amyloids are not only related to disease: functional amyloids are found in many biological systems and artificial peptide amyloids are developed into novel nanomaterials. Amyloid fibers can act as template for the generation of more amyloids but are considered nonreactive in chemical catalysis. The perception of amyloids as chemically inert species was recently challenged by in vitro work on three human amyloid systems. With the use of model substrates, amyloid-β, α-synuclein and glucagon amyloids were found to catalyze biologically relevant chemical reactions. The detected catalytic activity was much less than that of 'real' enzymes, but like that of designed (synthetic) catalytic amyloids. I here describe the current knowledge around this new activity of natural amyloids and the putative connection to metabolic changes in amyloid diseases. These pioneering studies imply that catalytic activity is an unexplored gain-of-function activity of disease amyloids. In fact, all biological amyloids may harbor intrinsic catalytic activity, tuned by each amyloid's particular fold, that await discovery.

  PublisherOA PDFDOI

• Amyloids of α-Synuclein Promote Chemical Transformations of Neuronal Cell Metabolites

  International Journal of Molecular Sciences · 2023-08-16 · 18 citations

  articleOpen accessSenior authorCorresponding

  The assembly of α-synuclein into cross-β structured amyloid fibers results in Lewy body deposits and neuronal degeneration in Parkinson's disease patients. As the cell environment is highly crowded, interactions between the formed amyloid fibers and a range of biomolecules can occur in cells. Although amyloid fibers are considered chemically inert species, recent in vitro work using model substrates has shown α-synuclein amyloids, but not monomers, to catalyze the hydrolysis of ester and phosphoester bonds. To search for putative catalytic activity of α-synuclein amyloids on biologically relevant metabolites, we here incubated α-synuclein amyloids with neuronal SH-SY5Y cell lysates devoid of proteins. LC-MS-based metabolomic (principal component and univariate) analysis unraveled distinct changes in several metabolite levels upon amyloid (but not monomer) incubation. Of 63 metabolites identified, the amounts of four increased (3-hydroxycapric acid, 2-pyrocatechuic acid, adenosine, and NAD), and the amounts of seventeen decreased (including aromatic and apolar amino acids, metabolites in the TCA cycle, keto acids) in the presence of α-synuclein amyloids. Many of these metabolite changes match what has been reported previously in Parkinson's disease patients and animal-model metabolomics studies. Chemical reactivity of α-synuclein amyloids may be a new gain-of-function that alters the metabolite composition in cells and, thereby, modulates disease progression.

  PublisherOA PDFDOI

Awards & honors

• Royal Swedish Academy of Sciences (2016)
• Royal Swedish Academy of Engineering Sciences (2020)
• Honorary Fellow of the Royal Society of Chemistry (2024)
• European Academy of Sciences (2024)
• Finnish Society of Sciences and Letters (2024)