The Drexel Biospectroscopy Research Group

More about our Group

  1. •Principal Investigator

  2. •Graduate Students

  3. •Undergraduate Students

  4. •Research

  5. •List of Publications


Drexel University

Department of Chemistry

32nd and Chestnut Street

Philadelphia, PA 19104

 
 

Spotlight on recent publications:


 
Recent GROUP NEWS September 2018: A paper entitled “Photoreduction of ferricytochrome c in the presence of potassium ferrocyanide”coauthored by Dmitry and Reinhard has been accepted for publication in Photochemical and Photobiological Sciences August 2018: Raghed Kurbaj, a Maryanoff summer fellow, decided to continue his research activities in our group. July 2018: Reinhard gave a seminar entitled “Exploring the Diverse Structures and Functions of Cytochrome c Bound to Anionic Membranes” at the Johann Wolfgang Goethe University in Frankfurt, Germany July 2018: Reinhard is the CoPI on a just awarded NSF-grant over $554,614 that will finance the ongoing research on unfolded peptides. The PI on the grant is Brigita Urbanc from DU’s Department of Physics. The project is aimed at developing an experiment based force field for MD simulations. April 2018: A paper entitled: “ Is a cross-β -sheet structure of low molecular weight peptides necessary for the formation of fibrils and peptide hydrogels” coauthored by Niranjan Ilawe, Bryan Wong (both UC Riverside), David and Reinhard has been accepted for publication in Phys.Chem.Chem.Phys. as perspective article. The work has been supported by an NSF grant to Reinhard March 2018: Reinhard’s monster review article entitled “Relating the Multi-functionality of Cytochrome c to Membrane Binding and Structural Conversion” has been accepted for publication in Biophysical Reviews . February 2018: A major fraction of the Biospectroscopy Group (Bridget, Gabrielle, David, Dmitry and Reinhard) presented posters at the Annual Meeting of the American Biophysical Society in San Francisco. All poster attracted a lot of interest. January 2018: A paper entitled: “Anti-cooperative Nearest Neighbor Interactions between Residues Determine in Unfolded Peptides and Proteins” coauthored by Reinhard and Siobhan Toal (former group member) has been accepted for publication in the Biophysical Journal December 2017: Reinhard gave a seminar about the ‘Demise of the random coil model’ at the Institute for Physical Chemistry of the University of Bonn in Germany August 2017: Reinhard receives a 3 year NSF grant of $390,000 to support the group’s work on hydrogels. Profs. Alvarez (Chem. Engineering) and Urbanc (Physics) are CoPIs on the grant. August 2017: A paper entitled “Probing the Replacement of Water by Dimethyl Sulfoxide in the Hydration Shell of N-Methylacetamide by FTIR Spectroscopy” coauthored by Reinhard, Heather (former undergraduate student from the UK) and David has beeb accepted fur publication in Vibrational Spectroscopy. June 2017: Reinhard gave a seminar about low molecular weight peptide aggregation and gelation for the research group of Prof Ehud Gazit at the Department of Microbiology and Biotechnology of Tel Aviv University May 2017: Reinhard gave an invited talk about cytochrome c binding to liposomes at CanBic 2017 in Parry Sound, Ca. Bridget and Dmitry presented posters May 2017: A paper entitled “ the Conformation-Dependent Preferential Binding of Ethanol to Cationic Glycyl-alanylglycine in Water/Ethanol by Vibrational and NMR Spectroscopy” coauthored by David, Bridget, Gabrielle, Stefanie (alumni) as well as our collaborators Nina Kubertova and Harald Schwalbe has been accepted for publication in J. Phys. Chem. B. April 2017: Dmitry receives the ACS Scholastic Achievement Award for the highest GPA in our BS-program April 2017: A communication entitled: pH Dependence of Ferricytochrome c Conformational Transitions During Binding to Cardiolipin Membranes: Evidence for Histidine as the Distal Ligand at Neutral pH" coauthored by Bridget, Dmitry and Reinhard has been accepted for publication in the The J. Phys. Chem. Lett. November 2016: A paper entitled: “Ferrocyanide-mediated Photoreduction of Ferricytochrome c Utilized to Selectively Probe Non-native Conformations Induced by Binding to Cardiolipin Containing Liposomes” coauthored by Dmitry and Reinhard has been accepted for publication in Chem. Eur. J. September 2016: A paper entitled ”Investigating the Formation of a Repulsive Hydrogel of a Cationic 16mer Peptide at Low Ionic Strength in Water by Vibrational Spectroscopy and Rheology”co-authored by David, Jodi (undergraduate alumna), Siobhan (graduate alumna) and Nicolas Alvarez from Chemical Engineering has been accepted for publication in the Journal of Physical Chemistry B. August 2016: David presented a talk in a session of the Colloid Division of the American Chemical Society at the ACS meeting in Philadelphia. Dmitry and Bridget presented at the poster session of the Physical Chemistry Division. The group and alumni convened afterwards for dinner August 2016: A paper entitled “ The Construction and Comparison of the Statistical Coil states of Unfolded and Intrinsically Disordered Proteins from nearest-Neighbor Corrected Conformational Propensities of Short Peptides” co-authored by Siobhan (graduate alumna) and Reinhard has been accepted for publication in MolBioSyst. June 2016: A paper entitled: “The Interplay of Aggregation, Fibrillization and Gelation of an Unexpected Low Molecular Weight Gelator: Glycylalanylglycine in Ethanol/Water” co-authored by Stefanie, David, Reinhard and Nicolas Alvarez in Chem. Engineering has been accepted for publication in Soft Matter. Dmitry won the departmental Maryanoff Research Prize for juniors. Stefanie won the Hutchins research prize. They will both present at the department seminar on Thursday, May 26. David’s abstract for the ACS Meeting in Philadelphia (August 2016) has been selected for an oral presentation by the Division of Colloid and Surface Chemistry Bridget and Dmitry presented poster at the Annual Meeting of the American Biophysical Society in Los Angeles (March 7-11, 2016). As usual, undergraduates from our group present at regular poster sessions. They are supported by a Wiggins award. December 2015: The group had its traditional Christmas dinner with alumni at Pietro’s. We learnt that Leah got a job at Jasco. November 2015: Valeryia Pratasave, Gabrielle Lewis and Heather Carson joined the group as undergraduate researchers November 2015: David received the department’s Rosenbaum teaching award for his TA activities. He is the first group member who received this award. He defied expectations of his advisors who thought this to be impossible based on natural laws. September 2015: A paper entitled: “Water-Centered Interpretation of Intrinsic pPII Propensities of Amino Acid Residues: In Vitro-Driven Molecular Dynamics Study.” co-authored by Reinhard and Siobhan has been accepted for publication in JPC B. It is the result of a collaboration with the Urbanc group in Drexel’s Department of Physics. September 2015: Bridget’s and Stefanie’s paper entitled : ”Demixing of Water and Ethanol Causes Conformational Redistribution and Gelation of the Cationic GAG Tripeptide” has been accepted for publication in ChemComm. The paper is co-authored by Siobhan and Reinhard September 2015: Leah’s monster paper entitled: "Coexistence of Native-Like and Non-Native Cytochrome c on Anionic Liposomes With Different Cardiolipin Content" has been accepted for publication in JPC B. The paper is co-authored by Reinhard August 2015: A paper entitled: “Assessing Backbone Solvation Effects in the Conformational Propensities of Amino Acid Residues in Unfolded Peptides” produced in collaboration with Bryan Wong and Niranjan Ilawe from the University of Southern California, Riverside, which is coauthored by Reinhard and Siobhan, has been accepted for publication in PhysCheChemPhys. July 2105: Leah successfully defended her thesis and is on her way to obtain her PhD degree. May 2015: Leah won the departmental price for graduate research 2015, Lee won the Hutchins research prize and Bridget the Maryanoff research prize. All three delivered talks about their research at an departmental student research symposium. May 2015: Reinhard presented an invited talked entitled “Exploring Different Binding Sites of Cytochrome c to Cardiolipin Containing Anionic Liposomes Explorted by Fluorescence, Circular Dichroism and Resonance Raman Spectroscopy” at the Vth Georgian Bay International Conference on Bioinorganic Chemistry” March 2015: Leah presented a very well received invited talk about “Conformational Diversity of Cytochrome c on Cardiolipin Containing Liposomes Probed by Fluorescence and Circular Dichroism Spectroscopy” at the spring meeting of American Chemical Society in Denver. February 2015: Leah, David, Stefanie, Jodi, Bridget, Dmitry and Reinhard participate in the annual meeting of the American Biophysical Society in Baltimore. Leah, Jodi, Bridget, Stefanie and Dmitry present posters, Reinhard gives a talk at an IDP session. The group meets Siobhan who presents a poster covering her last project at Drexel. December 2014: Siobhan’s monster paper entitled: ”Randomizing the Unfolded State of Peptides (and Proteins) by Nearest Neighbor Interactions between Unlike Residues.” has been accepted for publication in Chemistry-A European Journal. The paper was produced in collaboration with Prof. Schwalbe’s group at the Johann Wolfgang Goethe University in Frankfurt/Germany December 2014: Leah’s paper entitled: “Coexistence of Native-Like and Non-Native Partially Unfolded Ferricytochrome c on the Surface of Cardiolipin Containing Liposomes” has just been accepted for publication in the Journal of Physical Chemistry B. October 2014: Dmitry’s paper entitled: “Cardiolipin containing liposomes are fully ionized at physiological pH.  An FT-IR study of phosphate group ionization” has been accepted for publication in Vibrational Spectroscopy. Dmitry is a former Maryanoff summer student. September 2014: A theoretical paper entitled: “Entropy Reduction in Unfolded Peptides (and Proteins) due to Conformational Preferences of Amino Acid Residues” written by Reinhard and Siobhan has been accepted for publication in Physical ChemistryChemicalPhysics August 2014: Siobhan receives and accepts an offer to join the group of Elizabeth Rhoades at Yale as postdoc after her defense. July 2014: David DiGuiseppe joins the group as new graduate student June 2014: Siobhan’s invited monster review entitled: “Local Order in the Unfolded State: Conformational Biases, Nearest Neighbor Interactions, and the Thermodynamics Behind Solvent Mediation” has been accepted for a special issue of Biomoleucles June 2014: Jonathan’s paper on “Near-Exact Enthalpy-Entropy Compensation Governs the Thermal Unfolding of Protonation States of Oxidized Cytochrome c." has been accepted for publication in the Journal of Biological Inorganic Chemistry. June 2014: An invited review article written by Reinhard for the New Journal of Science is accepted. May 2014: Siobhan receives a “Highly Commended” reward from the Graduate Studies Office for her recent paper in JPC B. May 2014: Jodi Kraus wins the departmental Maryanoff Research Prize for Chemistry Juniors. The prize was awarded on the CoAS honors day on May 22 April 2014: Pradyuman Kodavatiganti joins the group for undergraduate research. He will be Maryanoff student in the summer April 2014: Siobhan wins the Chemistry Graduate Program research prize. She will present her work at the Chemistry Seminar on May 15, 4.30 p.m. A reception follows the award ceremony and talk. April 2014: Jodi wins the second prize in the category Physical Chemistry for her talk at the 78th Annual Intercollegiate Student Chemists Convention at Albright College April 2014: Bridget Malory has joint the group as Coop student. She will conduct research on solvent-peptide interactions. February 2014: Siobhan and Leah present at the Annual Meeting of the American Biophysical Society in San Francisco (2.15-1.19) January 2013; Siobhan’s paper on: “The role of the Enthalpy-Entropy Compensation Interactions in Determining the Conformational Propensities of Amino Acid Residues in Unfolded Peptides” has been accepted for publication in J. Phys. Chem. B. December 2013: Leah’s paper on “Salt as a Catalyst in the Mitochondria: Returning Cytochrome c to its Native State after it Misfolds on the Surface of Cardiolipin Containing Membranes” has been accepted for publication in Chem.Comm. September 2013: Jonathan defended his PhD thesis on: The partially folded, misfolded and unfolded states of cytochrome c probed by optical spectroscopy. September 2013: Jodi Kraus, Lee Serpas and Stefanie Farrel joined the group as undergraduate researchers July, 2013. Reinhard gave an invited talk at a Kavli Seminar about “Multiscale systems linking quantum chemistry, molecular dynamics and microfluid hydrodynamics at the Kavli Center of the British Royal Society in Chichester Hall, UK May, 2013 Reinhard gave an invited talk at the international CanBIC conference in Parry Sound, Canada; Leah presented a poster Siobhan received a ‘Highly Commended” in Drexel’s 2013 Research Award competition April 2013 Reinhard’s paper on the simulation of amide I band profile of disordered peptides got accepted for publication in JPC B. March, 2013 Reinhard gave an invited talk at PittCon 2013 February 2013 Ivona, Jonathan, Leah and Siobhan presented at the annual American Biophysical Socity meeting in Philadelphia February 2013 Alicia joins the group!

Book Spotlight

Schweitzer-Stenner, Reinhard ; Uversky, Vladimir

Peptide Folding, Misfolding, and Nonfolding

Wiley Series in Protein and Peptide Science


Edition - April 2012
2012. 576 Pages, Hardcover
ISBN-10: 0-470-59169-2
ISBN-13: 978-0-470-59169-7 - John Wiley & Sons


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Sample Chapter

Uversky, Vladimir N.; Dunker, A. Keith

Intrinsically Disordered Protein Analysis

Volume 1, Methods and Experimental Tools

Springer Series in Methods in Molecular Biology, Vol. 896


Edition - June 2012
2012. 470 Pages, Hardcover
ISBN-13: 978-1-61779-926-6 - Humana Press

Chapers 18 and 19 Contributed to the Series

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Egelman, E

Comprehensive Biophysics

1st Edition, Biophysical Techniques for Structural Characterization of Macromolecules

Elsevier

Edition - May 2012
2012. 3524 Pages, Hardcover
ISBN: 9780123749208 - Academic Press

Chaper 1.23 Contributed to the Series

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pH Dependence of Ferricytochrome c Conformational Transitions During Binding to Cardiolipin Membranes: Evidence for Histidine as the Distal Ligand at Neutral pH.


Bridget Milorey, Dmitry Malyshka and R. Schweitzer-Stenner, JPC Letters,8, 1993-1998, 2017

The conformational changes of ferricytochrome c upon binding to cardiolipin-containing small unilamellar vesicles were studied at slightly acidic pH using fluorescence, visible circular dichroism, UV–visible absorption, and resonance Raman spectroscopy. The obtained spectroscopic response data suggest a mode of interaction, which is clearly distinct from the binding process observed at neutral pH. Evidence of a reversible and electrostatic binding mechanism under these conditions is provided through binding inhibition in the presence of 150 mM NaCl. Moreover, UV–visible absorption and resonance Raman spectra reveal that the conformational ensemble of membrane bound cytochrome c is dominated by a mixture of conformers with pentacoordinated and hexacoordinated high-spin heme irons, which contrast with the dominance of low-spin species at neutral pH. While our results confirm the L-site binding proposed by Kawai et al., they point to the protonation of a histidine ligand (H33) as conformational trigger.

Probing the Conformation-Dependent Preferential Binding of Ethanol to Cationic Glycylalanylglycine in Water/Ethanol by Vibrational and NMR Spectroscopy

David DiGuiseppi, Bridget Milorey, Gabrielle Lewis, Nina Kubatova, Stefanie Farrell\, Harald Schwalbe and Reinhard Schweitzer-Stenner. JPC B2017, 121, 5744−5758

Anticooperative Nearest-Neighbor Interactions between Residues in Unfolded Peptides

and Proteins.


Reinhard Schweitzer-Stenner* and Siobhan E. Toal Biophys. J. 114, 1046, 2018

We investigated whether nearest neighbor interactions  in unloaded peptides lead to a breakdown of the isolated pair hypothesis of the Flory’s random coil model. To this end we analyzed the conformational propensities of the two guest residues (x,y) of GxyG tetrapeptides by means of a statistical mechanics model. To our surprise, we found that the nearest neighbor interactions between most of the central residues in the investigated GxyG peptides are anti-cooperative. We used the obtained interaction parameter in a Zimm-Bragg/Ising-type approach to reproduce the experimentally obtained temperature dependence of the UV circular dichroism of the MAX3 peptide, which is predominantly built by KV-repeats.

Is a cross-β-sheet structure of low molecular weight peptides necessary for the formation of fibrils and peptide hydrogels?

Nirnajan Ilawe, Reinhard Schweitzer-Stenner, David DiGuiseppi, and Bryan Wong. Phys. Chem.Chem.Phys. 20, 18158/18168, 2018, DOI:10.1039/c8cp00691a.

Short peptides have emerged as versatile building blocks for supramolecular structures and hydrogels. In particular, the presence of aromatic amino acid residues and/or aromatic end groups is generally considered to be a prerequisite for initiating aggregation of short peptides into nanotubes or cross β-sheet type fibrils. However, the cationic GAG tripeptide surprisingly violates these rules. Specifically, in water/ethanol mixtures, GAG peptides aggregate into very long crystalline fibrils at temperatures below 35 C where they eventually form a spanning network structure and, thus, a hydrogel. Two gel phases are formed in this network, and they differ substantially in chirality and thickness of the underlying fibrils, their rheological parameters, and the kinetics of oligomerization, fibrilization, and gel formation. The spectroscopic data strongly suggests that the observed fibrils do not exhibit canonical cross β sheetstructures and are indicative of a yet unknown secondary conformation. To complement our unusualexperimental observations in this perspective article, we performed large-scale DFT calculations toprobe the geometry and spectroscopic properties of these GAG oligomers. Most importantly, our experimental and computational results yield rather unconventional structures that are not reminiscent of classical cross-b-sheet structures, and we give two extremely likely candidates for oligomer structures that are consistent with experimental amide I0 profiles in IR and vibrational circular dichroism (VCD) spectra of the two gel phases.