About

Shabnam Akhtari is a professor at the Department of Mathematics in the Eberly College of Science at Pennsylvania State University. Her research interests include Number Theory, Geometry of Numbers, and Diophantine Analysis. Her work involves exploring fundamental questions in these areas, contributing to the understanding of mathematical structures and their properties.

Research topics

• Biology
• Biochemistry
• Chemistry
• Medicine
• Microbiology
• Materials science
• Cell biology
• Nanotechnology
• Biomedical engineering
• Biophysics
• Internal medicine

Selected publications

• Phosphorylation modulates secondary structure of intrinsically disorder regions in RNA polymerase II

  Journal of Biological Chemistry · 2025-04-22 · 2 citations

  articleOpen accessSenior author

  The intrinsically disordered C-terminal domain (CTD) of RNA polymerase II contains tandem repeats with the consensus sequence YSPTSPS and coordinates transcription and cotranscriptional events through dynamic phosphorylation patterns. While it has been long hypothesized that phosphorylation induces structural changes in the CTD, a direct comparison of how different phosphorylation patterns modulate the CTD conformation has been limited. Here, we generated two distinct phosphorylation patterns in an essential <i>Drosophila</i> CTD region with the kinase Dyrk1a: one where Ser2 residues are primarily phosphorylated, mimicking the state near transcription termination, and a hyperphosphorylation state where most Ser2, Ser5, and Thr residues are phosphorylated, expanding on our work on Ser5 phosphorylation, which mimics early transcription elongation. Using ¹³C Direct-Detect NMR, we show that the CTD tends to form transient beta strands and beta turns, which are altered differently by Ser2 and Ser5 phosphorylation. Small-angle X-ray scattering revealed no significant changes in the CTD global dimensions even at high phosphorylation levels, contradicting the common assumption of phosphorylation-induced chain expansion. Our findings support a transient beta model in which unphosphorylated CTD adopts transient beta strands at Ser2 during transcription preinitiation. These transient structures are disrupted by Ser5 phosphorylation in early elongation, and later restored by Ser2 phosphorylation near termination for recruiting beta turn-recognizing termination factors.

  PublisherDOI

• Residue-level mapping of crowding effects on protein phase separation

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-10-04

  preprintOpen accessSenior authorCorresponding

  ABSTRACT Proteins can undergo liquid-liquid phase separation to form condensates within the crowded cellular environment. In vitro , polymer-based crowding agents are widely used to mimic this effect, but how their chemical environments influence phase separation compared to native cytosol remains unclear. Here, we use NMR to probe the chemical influences on the intrinsically disordered region of RNA polymerase II under different crowding conditions, including polymer-based crowders, protein-based crowders, and reconstituted E. coli cytosol. We find a general trend of enhanced protein self-interactions across all conditions, but also distinct chemical environments that depend on crowder identity, reflecting changes in preferential interactions. Given the widespread use of polymer crowders in phase separation studies, our results establish a strategy to dissect the microscopic role of crowders and lay the foundation for designing more physiologically relevant in vitro crowding models of protein phase separation. More broadly, this framework enables systematic probing of residue-level environmental influences in complex settings including within the cellular milieu.

  PublisherOA PDFDOI

• BPS2025 - Insights into non-specific RNA binding by a small intrinsically disordered protein

  Biophysical Journal · 2025-02-01

  article
  PublisherDOI

• BPS2025 - Effects of phosphorylation on conformational dynamics of RNA polymerase II CTD in variant sequences

  Biophysical Journal · 2025-02-01

  article
  PublisherDOI

• Phosphorylation patterns modulate the transient secondary structure of RNA polymerase II CTD without altering its global conformation

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-01-13 · 1 citations

  preprintOpen accessSenior authorCorresponding

  Abstract The intrinsically disordered C-terminal domain (CTD) of RNA polymerase II coordinates transcription and co-transcriptional events through dynamic phosphorylation patterns. While it has been long hypothesized that phosphorylation induces structural changes in the CTD, a direct comparison of how different phosphorylation patterns modulate the CTD conformation has been limited. Here, we generated two distinct phosphorylation patterns in an essential Drosophila CTD region with the kinase Dyrk1a: one where Ser2 are primarily phosphorylated, mimicking the state near transcription termination, and a hyperphosphorylation state where most Ser2, Ser5, and Thr4 residues are phosphorylated, expanding on our work on Ser5 phosphorylation, which mimics early transcription elongation. Using 13 C Direct-Detect NMR, we show that the CTD has a tendency to form transient beta strands and beta turns, which is altered differently by Ser2 and Ser5 phosphorylation. Small angle x-ray scattering (SAXS) revealed no significant changes in the CTD global dimensions even at high levels of phosphorylation, contradicting the common assumption of phosphorylation-induced chain expansion. Our findings support a transient beta model in which unphosphorylated CTD adopts transient beta strands at Ser2 during transcription pre-initiation. These transient structures are disrupted by Ser5 phosphorylation in early elongation, and later restored by Ser2 phosphorylation near termination for recruiting beta turn-recognizing termination factors.

  PublisherDOI

• Probing Enzymatic Acetylation Events in Real Time With NMR Spectroscopy: Insights Into Acyl‐Cofactor Dependent p300 Modification of Histone <scp>H4</scp>

  Proteins Structure Function and Bioinformatics · 2025-06-01 · 1 citations

  articleOpen accessSenior authorCorresponding

  ABSTRACT Lysine acylation is a rapidly expanding class of post‐translational modifications with largely unexplored functional roles; the study of acylations beyond acetylation is especially impeded by limited methods for their preparation, detection, and characterization in vitro. We previously reported a nuclear magnetic resonance (NMR)‐based approach to monitor Nε‐lysine acetylation following Ada2/Gcn5‐catalyzed installation of a 13 C‐acetyl probe on the histone H3 tail. Building on this foundation, here we expand those techniques by demonstrating the installation and 1 H, 13 C‐HSQC based NMR detection of both 13 C‐acetyl and 13 C‐propionyl probes on the histone H4 tail using a mutant p300 lysine acetyltransferase (KAT) enzyme with enhanced activity. Additionally, we introduce a continuous evaluation method for acyltransferase reaction data, enabling the extraction of relative rate constants—a technique inspired by our laboratory's recent work on NMR methyltransferase kinetics. This study demonstrates that our NMR‐based approach to assay enzymatic 13 C‐acylation is adaptable, providing a versatile platform for investigating a range of acylations, KAT enzymes, and protein substrates. Notably, in the process of developing these methods, we observed that p300 KAT may display distinct modification site preferences and regulatory mechanisms depending on the acyl cofactor utilized, underscoring the method's potential to advance the emerging field of lysine acylation biochemistry.

  PublisherOA PDFDOI

• RNA polymerase II CTD Ser5 phosphorylation induces competing effects of expansion and compaction

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-09-11

  preprintOpen access

  Abstract The carboxy-terminal domain (CTD) of RNA Polymerase II, composed of tandem heptad repeats with the consensus sequence YSPTSPS, orchestrates the transcription cycle through a dynamic series of post-translational modifications. Among these, the phosphorylation of Ser5 is critical for initiator/promoter clearance and the recruitment of capping enzymes. However, the exact conformational consequences of these modifications are still not fully understood. This study investigates how Ser5 phosphorylation affects the local and global conformation of the CTD, its influence on proline isomerization, and how variations in the repeat sequence modulate these effects. We employed Gaussian accelerated Molecular Dynamics (GaMD) simulations on 3-heptad models of both the consensus CTD sequence and an Asn7 variant. We found that Ser5 phosphorylation promotes expansion of the peptide due to the repulsion between the negatively-charged phosphate groups, but also increases the population of cis -Pro6, which leads to compaction. We used a clustering algorithm to identify commonly populated conformations, with a focus on those conformations that change in population with Ser5 phosphorylation. Our simulations reveal that the expansion of the CTD due to Ser5 phosphorylation is accompanied by a change in local, intra-heptad interactions in both variants. Notably, phosphorylation significantly increases the population of cis -Pro6 due to steric repulsion between the Asn7 side chain and the large side chain of the phosSer5, but has a smaller increase in the consensus variant. These results clarify the underlying mechanisms by which phosphorylation can modulate the CTD’s structural landscape to regulate the transcription cycle. Significance The RNA Polymerase II CTD is a critical part of the machinery that regulates transcription, and therefore, understanding how it functions in this process is essential. However, the conformational effects of known modifications to the CTD, such phosphorylation and proline isomerization, are not fully understood. This paper uses all-atom molecular dynamics simulations to identify the specific conformational changes to the disordered CTD with phosphorylation, and with changing heptad sequence. We also identify the interactions that are responsible for these changes. Our results emphasize that two chemical properties of phosphate groups, their negative charge and their large size, can affect protein conformation. For the CTD, these properties have competing effects on the overall compaction of the disordered sequence.

  PublisherOA PDFDOI

• BPS2025 - Insights into non-specific RNA binding by a small, intrinsically disordered protein

  Biophysical Journal · 2025-02-01

  article
  PublisherDOI

• BPS2025 - Transient non-local interactions dominate the dynamics of the intrinsically disordered C-terminal of phosphatase Fcp1

  Biophysical Journal · 2025-02-01

  article
  PublisherDOI

• Charge-driven dynamical heterogeneity in the intrinsically disordered C-terminal of phosphatase Fcp1

  Biophysical Journal · 2024-02-01

  articleOpen access
  PublisherOA PDFDOI

Recent grants

• Specificity of miRNA Processing Provided by Double-Stranded RNA Binding Domains

  NIH · $1.5M · 2011–2018

• Structure and Mechanism of Transcription Factors in Pancreatic Beta Cells

  NIH · $1.2M · 2019–2024

• NIH Grant F32CA117702

  NIH · $137k · 2008

• Carbon-Detected NMR Studies of Intrinsically Disordered Protein Post-Translational Modification

  NSF · $959k · 2019–2025

• Quantitative Studies of Intrinsically Disordered Protein Structure and Function

  NSF · $982k · 2015–2019

Frequent coauthors

• Rafael Brüschweiler

  The Ohio State University

  37 shared

• Loïc Salmon

  Université Claude Bernard Lyon 1

  26 shared

• Guillaume Bouvignies

  École Normale Supérieure - PSL

  21 shared

• Martin Blackledge

  CEA Grenoble

  21 shared

• Phineus R. L. Markwick

  University of California, San Diego

  21 shared

• Eric Johnson

  Mount St. Joseph University

  16 shared

• Emery T. Usher

  Washington University in St. Louis

  15 shared

• Dawei Li

  The Ohio State University

  12 shared

Labs

• Showalter Research GroupPI

Awards & honors

• Milton S. Eisenhower Award for Distinguished Teaching (2024)
• Fellow of the American Association for the Advancement of Sc…
• Eberly College of Science Distinguished Faculty Mentoring Aw…
• Eastern Analytical Symposium New Faculty Award in NMR Spectr…
• NSF Career Award (2010)