Publications prior to 2018

Publications 2018-2023 • Publications prior to 2018

*denotes Haverford students/alumni

Cookmeyer, David L.*,Winesett, Emily S.*, Kokona, Bashkim, Aliev, Sabina*, Bloch, Noah, B.*, Bulos, Joshua A.*, Evans, Irene L.*, Fagre, Christian R.*, Godbe, Kerilyn N.*, Khromova, Maryna*, Konstantinovsky, Daniel M.*, Lafrance, Alexander E.*, Lamacki, Alexandra J.*, Parry, Robert C.*, Quinn, Jeanne M.*, Thurston, Alana M.*, Tsai, Kathleen J. S.-C.*, Cryle, Max J., Fairman, Robert and Charkoudian, Louise K.  2017.  Uncovering Protein-Protein Interactions through a Team-based Undergraduate Biochemistry Course. PLoS Biol, 15(11):11:e2003145.

Kim, Surin*, D’Acunto, Victoria F.*, Kokona, Bashkim, Hofmann, Jennifer, Cunningham, Nicole R., Bistline, Emily M.*, Garcia, F. Jay*, Akhtar, Nabeel M.*, Hoffman, Susanna H.*, Doshi, Seema H.*, Ulrich, Kathleen M.*, Jones, Nicholas M., Bonini, Nancy M., Roberts, Christine M., Link, Christopher D., Laue, Thomas M., and Fairman, Robert. 2017. Sedimentation velocity analysis with fluorescence detection of mutant huntingtin exon 1 aggregation in Drosophila Melanogaster and Caenorhabditis Elegans.Biochemistry 56:4676. doi: 10.1021/acs.biochem.7b00518.

Fairman, Robert. May 17, 2017, Twists and Turns in Protein Assembly. Not peer reviewed. http://www.scientia.global/professor-robert-fairman-twists-turns-protein-assembly/

Glaubman, Jessica, Hofmann, Jennifer, Bonney, Megan E.*, Park, Sumin*, Thomas, Jessica M.*, Kokona, Bashkim, Fairman, Robert, Ramos-Falcón, Laura I.*, Chung, Yoonjie K.*, and Okeke, Iruka N.  2016. Self-association motifs in the Escherichia coli heat-resistant agglutinin 1. Microbiology 162:1091.

Boyachi, H., Shah, T., Hurley, A., Kokona, B., Li, Z., Ventocilla, C. Jeffrey, P.D., Semmelhack, M.F., Fairman, Robert, Bassler, Bonnie L., and Hughson, Frederick M. 2016. Structure, regulation, and inhibition of the quorum-sensing signal integrator, LuxO. PLoS Biol 14:e1002464.

Kokona, Bashkim, May, Carrie A., Cunningham, Nicole R., Richmond, Lynne*, Garcia, Franklin J.*, Durante, Julia C.*, Ulrich, Kathleen M.*, Roberts, Christine M., Link, Christopher D., Stafford, Walter F., Laue, Thomas M., and Fairman, Robert.  2016. Applying an analytical ultracentrifuge equipped with fluorescence detection to the study of polyglutamine aggregation in Caenorhabditis elegans.  Protein Science 25:605.

Kokona, Bashkim, Winesett, Emily S.*, von Krusenstiern, Alfred N.*, Cryle, Max J., Fairman, Robert, and Charkoudian, Louise K.  2016.  Probing the selectivity of beta-hydroxylation reactions in non-ribosomal peptide synthesis using analytical ultracentrifugation.  Analyt. Biochem. 495:42.

Little, Wheaton*, Robblee, James*, Dahlberg, Caroline*, Kokona, Bashkim, and Fairman, Robert.  2015. Effect of helical length on the stability of the Lac repressor antiparallel coiled coil. Biopolymers,104:395.

Zhao, et al., 2015. A Multilaboratory Comparison of Calibration Accuracy and the Performance of External References in Analytical Ultracentrifugation.  PLOS ONE, DOI: 10.1371/journal.pone.0126420.

Taggart, James C.*, Welch, Elizabeth Z.*, Mulqueen, Mary F.*, Dioguardi, Vincent B.*, Cauer, Alexandra G.*, Kokona, Bashkim, and Fairman, Robert.  2014. Testing the role of charge and structure on the stability of peptide-porphyrin complexes. Biomacromolecules, 15:4544.

Kokona, Bashkim, Johnson, Karl A., and Fairman, Robert. 2014. Effect of helical flanking sequences on the morphology of polyglutamine-containing fibrils. Biochemistry, 53:6747.

Kokona, Bashkim, Rosenthal, Zachary P.*, and Fairman, Robert. 2014.  The role of the coiled-coil structural motif in polyglutamine aggregation. Biochemistry, 53:6738.

Cheng, Richard P., Wang, Wei-Ren, Girinath, Prashant, Yang, Po-An, Ahmad, Raheel, Li, Jhe-Hao, Hart, Pier*, Kokona, Bashkim, Fairman, Robert,  Kilpatrick, Casey, Argiros, Annmarie. 2012. Effect of charged residue side chain length on intrahelical glutamate-lysine ion pairing interactions. Biochemistry, 51:7157.

Pepe-Mooney, Brian J.* Kokona, Bashkim, and Fairman, Robert.  2011. Characterization of mesoscale coiled-coil peptide-porphyrin complexes.  Biomacromolecules, 12:4196.

Tsang, Betty*, Bretscher, Heidi S.*, Kokona, Bashkim, Manning, Robert S., and Fairman, Robert. 2011. Thermodynamic analysis of self-assembly in coiled-coil biomaterials. Biochemistry, 50:8548.

Smith, Melanie H.*, Miles, Timothy F.*, Sheehan, Molly*, Alfieri, Katherine N.*, Kokona, Bashkim, and Fairman, Robert. 2010. Polyglutamine fibrils are formed using a simple designed beta-hairpin model. Proteins: Struct. Funct. Bioinf., 78:1971.

Cheng , Richard P., Girinath, Prashant, Suzuki, Yuta, Kuo, Hsiu-Ting, Hsu, Hao-Chun, Wang, Wei-Ren, Yang, Po-An, Gullickson, Donald, Wu, Cheng-Hsun, Koyack, Marc J.,  Chiu, Hsien-Po, Weng, Yi-Jen, Hart, Pier,* Kokona, Bashkim, Fairman, Robert, Lin, Tzu-En, Barrett, Olivia. 2010. Positional Effects on Helical Ala-Based Peptides. Biochemistry, 49:9372.

Chiu, Hsien-Po, Kokona, Bashkim, Fairman, Robert, and Cheng, Richard P. 2009. Effect of highly fluorinated amino acids on protein stability at a solvent-exposed position on an internal strand of protein G B1 domain. J. Am. Chem. Soc., 131:13192.

Pepe-Mooney, Brian J.* and Fairman, Robert. 2009. Peptides as materials. Curr. Opin. Struct. Biol., 19:483.

Kokona, Bashkim, Kim, Andrew M.*, Daniels, Joshua P.*, Pepe-Mooney, Brian J.*, Kovaric, Brian C.*, de Paula, Julio C., Johnson, Karl A., and Fairman, Robert. 2009. Self-assembly of coiled-coil peptide-porphyrin complexes. Biomacromolecules, 10:1454

Root, Benjamin C.*, Pellegrino, Laurel*, Crawford, Emily D.*, Kokona, Bashkim, Fairman, Robert. Design of a heterotetrameric coiled coil. 2009. Protein Sci., 18:329.

Salinger, Nina*, Kokona, Bashkim, Fairman, Robert, and Okeke, Iruka N. The plasmid-encoded regulator activates factors conferring lysozyme resistance on enteropathogenic Escherichia coli. 2009. Appl. Environ. Microbiol.,75:275.

Kokona, Bashkim, Rigotti, Daniel J., Wasson, Andrew S.*, Lawrence, Sarah H., Jaffe, Eileen K., and Fairman, Robert. 2008. Probing the oligomeric assemblies of pea porphobilinogen synthase by analytical ultracentrifugation. Biochemistry, 48:10649.

Chiu, Hsien-Po, Suzuki, Yuta, Gullickson, Donald, Ahmad, Raheel, Kokona, Bashkim, Fairman, Robert, Cheng, Richard P. 2006. Helix propensity of highly fluorinated amino acids. J. Am. Chem. Soc., 128:15556.

Kovaric, Brian C.*, Kokona, Bashkim, Schwab, Alexander D., Twomey, Margaret A.*, de Paula, Julio C. and Fairman, Robert. 2006. Self-assembly of peptide porphyrin complexes: towards the development of smart biomaterials. J. Am. Chem. Soc., 128:4166. <supplementary material>

Tang, Lei, Brenig, Sabine, Stith, Linda, Mischel, Adele, Tannir, Justin, Kokona, Bashkim, Fairman, Robert, and Jaffe, Eileen. 2006. Single amino acid mutations alter the distribution of human porphobilinogen synthase quaternary structure isoforms (morpheeins). J. Biol. Chem., 281:6682.

Lehtiö, Lari, Grossmann, J. Günter, Kokona, Bashkim, Fairman, Robert, and Goldman, Adrian. 2006. Crystal structure of a glycyl radical enzyme from Archaeoglobus fulgidus. J. Mol. Biol., 35:221.

Rigotti, Daniel J., Kokona, Bashkim, Horne, Theresa*, Acton, Eric K.*, Lederman, Carl D.*, Johnson, Karl A., Manning, Robert S., Amador Kane, Suzanne, Smith, Walter F., and Fairman, Robert. 2005. Quantitative AFM image analysis of unusual filaments formed by the Acanthamoeba castellanii myosin II rod domain. Analyt. Biochem., 346:189.

Cedervall, Tommy, André, Ingemar, Selah, Cheryl, Robblee, James*, Krecioch, Peter C.*, Fairman, Robert, Linse, Sara, Åkerfeldt, Karin S. 2005. Calbindin D28k EF-hand ligand binding and oligomerization: four high-affinity sites-three modes of action. Biochemistry, 44:13522.

Wagner, Daniel E.*, Phillips, Charles L.*, Ali, Wasif M.*, Nybakken, Grant E.*, Crawford, Emily D.*, Schwab, Alexander D., Smith, Walter F., and Fairman, Robert. 2005. Towards the development of peptide nanfilaments and nanoropes as smart materials. Proc. Natl. Acad. Sci., USA, 102:12656.

Fairman, Robert and Åkerfeldt, Karin S. 2005. Peptides as smart materials. Curr. Opin. Struct. Biol., 15:453.

Dunetz, Joshua*, Sandstrom, Clair*, Young, Elizabeth R.*, Baker, Paul*, VanName, Steven*, Cathopolous, Terry*, Fairman, Robert, de Paula, Julio C. and Åkerfeldt, Karin S. 2005. Self-assembly of a porphyrin-derivatized peptide: toward the design of chromophore aggregates for light-harvesting applications. Org. Lett., 7:2559.

Chao, Yang, Shiozaki, Eric N., Srinivasula, Srinivasa M., Rigotti, Daniel J., Fairman, Robert, and Shi, Yigong. 2005. Engineering a dimeric caspase-9: a re-evaluation of the induced proximity model for caspase activation. PLoS-Biology, 3:e183.

Bollivar, David W., Clauson, Cheryl, Lighthall, Rachel, Kokona, Bashkim, Fairman, Robert, Forbes, Siiri, Kundrat, Leuka, and Jaffe, Eileen K. 2004. Rhodobacter capsulatus porphobilinogen synthase, a high activity metal ion independent hexamer. BMC Biochemistry, 5:17.

Chowdhury FA, Fairman R, Bi Y, Rigotti DJ, Raleigh DP. 2004. Protein dissection experiments reveal key differences in the equilibrium folding of alpha-lactalbumin and the calcium binding lysozymes. Biochemistry, 43:9961.

Tang, Yuefeng, Rigotti, Daniel J., Fairman, Robert, and Raleigh, Daniel P. 2004. Significant structure in the denatured state of a rapid folding protein: Characterization of peptide fragments derived from the villin headpiece subdomain. Biochemistry, 43:3264.

Breinig, Sabine, Kervinen, Jukka, Stith, Linda, Wasson, Andrew S.*, Fairman, Robert, Wlodawer, Alexander, Zdanov, Alexander, and Jaffe, Eileen K. 2003. Control of tetrapyrrole biosynthesis by alternate quaternary forms of porphobilinogen synthase. Nature: Struct. Biol., 10:757.

Joglekar, Ashwini P., Xu, Dalu, Rigotti, Daniel J., Fairman, Robert and Hay, Jesse C. 2003. The SNARE Motif Contributes to rbet1 Intracellular Targeting and Dynamics Independently of SNARE Interactions. J. Biol. Chem., 278:14121.

Shiozaki EN, Chai J, Rigotti DJ, Riedl SJ, Li P, Srinivasula SM, Alnemri ES, Fairman R, Shi Y. 2003. Mechanism of XIAP-mediated inhibition of caspase-9. Mol Cell. 11:519.

Solan, Amy*, Ratia, Kiira*, and Fairman, Robert. 2002. Exploring the role of alanine in the structure of the Lac repressor tetramerization domain, a ferritin-like ala-coil. J. Mol. Biol. 317:627.

Horng, Jia-Cherng, Moroz, Viktor, Rigotti, Daniel J., Fairman, Robert, and Raleigh, Daniel P. 2002. Characterization of large peptide fragments derived from the N-terminal domain of the ribosomal protein L9: Definition of the minimum folding motif and characterization of local electrostatic interactions. Biochemistry, 41:13360.

Julenius, Karin, Thulin, Eva, Robblee, James*, Fairman, Robert, Finn, Bryan E. and Linse, Sara. 2002. Isolated EF-hands from calbindin D9k: Coupling between Ca2+-binding and dimerization. Proteins, 47:323.

Wu, Jia-Wei, Hu, Min, Chai, Jijie, Seoane, Joan, Huse, Morgan, Li, Carey, Rigotti, Daniel J., Kyin, Saw, Muir, Tom W., Fairman, Robert, Massagué, Joan, and Shi, Yigong. 2001. Crystal Structure of a Phosphorylated Smad2: Recognition of Phosphoserine by the MH2 Domain and Insights on Smad Function in TGF-beta Signaling. Mol. Cell, 8:1277.

Szwajkajzer, Danuta, Dai, Lizhong, Fukayama, June W., Abramczyk, Bozena, Fairman, Robert, and Carey, Jannette. 2001. Quantitative analysis of DNA binding by the E. coli arginine repressor. J. Mol. Biol. 312:949.

Wu, Jia-Wei, Buczek, Jessica, Fairman, Robert, and Shi, Yigong. 2001. Formation of a stable hetero-dimer between Smad2 and Smad4. J. Biol. Chem. 276:20688.

Vu, Colynda*, Robblee, James*, Werner, Karin*, and Fairman, Robert. 2001. Effects of charged amino acids at b and c heptad positions on specificity and stability of four-chain coiled coils. Protein Science, 10:631.

Demarest, Stephen J., Zhou, Shui-Qin, Robblee, James*, Fairman, Robert, Chu, Benjamin, and Raleigh, Daniel P. 2001. Factors which contribute to the ability of a-lactalbumin and lysozyme to form partially folded states: A comparative study of peptide models of the a -domain of a-lactalbumin, lysozyme and a-lactalbumin/lysozyme chimeras. Biochemistry, 40:2138.

Lerman, Jeffrey C., Robblee, James*, Fairman, Robert, and Hughson, Frederick M. 2000. Structural analysis of the neuronal SNARE protein syntaxin-1A. Biochemistry, 39:8470.

Spector, Shari, Wang, Minghui, Carp, Stefan, Robblee, James*, Fairman, Robert, Tidor, Bruce and Raleigh, Daniel P. 2000. Rational modification of protein stability by the mutation of charged surface residues. Biochemistry, 39:872.

Moriarty, Daniel F., Demarest, Stephen J., Robblee, James*, Fairman, Robert and Raleigh, Daniel P. 2000. Local interactions and the role of the 6-120 disulfide bond in alpha-lactalbumin: Implications for formation of the molten globule state. Biochim. Biophys. Acta, 1476:9.

Demarest, Stephen J., Boice, Judith A., Fairman, Robert, and Raleigh, Daniel P. 1999. Defining the core structure of the alpha-lactalbumin molten globule state. J. Mol. Biol., 294:213

Fairman, Robert, Fenderson, William, Hail, Mark E., Wu, Youling, Shaw, Shyh-Yu. 1999. Molecular weights of CTLA-4 and CD80 by Sedimentation Equilibrium Ultracentrifugation. Analyt. Biochem., 270:286.

Nicholson, Karin L., Munson, Mary, Miller, Rebecca B., Filip, Thomas J.*, Fairman, Robert, Hughson, Frederick M. 1998. Regulation of SNARE complex assembly by an N-terminal domain of the t-SNARE Sso1p.Nature: Struct. Biol., 5:79.

Grandori, Rita, Boice, Judith A., Fairman, Robert, and Carey, Jannette. 1998. Biochemical characterization of WrbA, founding member of a new class of flavodoxin-like proteins. J. Biol. Chem., 273:20960.

Demarest, Stephen J., Fairman, Robert, Raleigh, Daniel P. 1998. Peptide models of local and long range interactions in the molten globule state of human a-lactalbumin. J. Mol. Biol., 28:279.

Kuhlman, Brian, Boice, Judith A., Fairman, Robert, and Raleigh, Daniel P. 1998. Structure and stability of the N-terminal domain of the ribosomal protein L9: Evidence for rapid two-state folding. Biochemistry, 37:1025.

Spector, Shari, Kuhlman, Brian, Fairman, Robert, Wong, Elsa, Boice, Judith A., and Raleigh, Daniel P. 1998. Cooperative folding of a protein mini domain: The peripheral subunit-binding domain of the pyruvate dehydrogenase multienzyme complex. J. Mol. Biol., 276:479.

Fairman, Robert, Beran-Steed, Rita K., and Handel, Tracy M. 1997. Assignment of 1H, 15N, and 13C resonances and identification of secondary structure for the helix-loop-helix domain of E47. Protein Science 6:175.

Kuhlman, Brian, Yang, Hui Y., Boice, Judith A., Fairman, Robert, and Raleigh, Daniel P. 1997. An exceptionally stable helix from the ribosomal protein L9: implications for protein folding and stability. J. Mol. Biol. 270:640.

Roy, Sushmita, Ratnaswamy, Gayathri, Boice, Judith A., Fairman, Robert, McLendon, George, and Hecht, Michael H. 1997. Native-like properties in a protein designed by binary patterning of polar and nonpolar amino acids. J. Am. Chem. Soc., 119:5302.

Kuhlman, Brian, Boice, Judith A., Wu, Wen-Jin, Fairman, Robert, and Raleigh, Daniel P. 1997. Calcium binding peptides from a-lactalbumin: implications for protein folding and stability. Biochemistry 36:4607.

Axley, Milton J., Fairman, Robert, Yanchunas, Joseph, Villafranca, Joseph J., and Robertson, James G. 1997. Spectroscopic properties of E. coli UDP-N-acetylenolpyruvylglucosamine reductase. Biochemistry 36:812.

Boice, Judith A., Dieckmann, Gregg R., DeGrado, William F., Fairman, Robert. 1996. Thermodynamic analysis of a designed three-stranded coiled coil. Biochemistry 35:14480.

Boice, Judith A. and Fairman, Robert. 1996. Structural characterization of p16, a tumor suppressor protein. Protein Science 5:1776.

Fairman, Robert, Chao, Hann-Guang, Lavoie, Thomas B., Villafranca, Joseph J., Matsueda, Gary R. and Novotny, Jiri. 1996. Design of heterotetrameric coiled coils: Evidence for increased stabilization by Glu--Lys+ ion pair interactions. Biochemistry 35:2824.

Jin, Haiyong, Emanuele, John, Fairman, Robert, Robertson, James G., Hail, Mark, Ho, Hsu-Tso, Flak, Paul, and Villafranca, Joseph. 1996. Studies of E. coli UDP-N-acetyl-muramate:L-alanine ligase. Biochemistry 35:1423.

Fairman, Robert, Chao, Hann-Guang, Mueller, Luciano, Lavoie, Thomas B., Shen, Liyang, Novotny, Jiri, and Matsueda, Gary, R. 1995. Characterization of a new four-chain coiled-coil: Influence of chain length on stability. Protein Science 4:1457.

Grandori, Rita, Lavoie, Teresa A., Pflumm, M., Tian, Guoling, Niersbach, Helmut, Maas, Werner K., Fairman, Robert, Carey, Jannette. 1995. The DNA-binding domain of the hexameric arginine repressor. J. Mol. Biol. 254:150.

Betz, Stephen, Fairman, Robert, O'Neil, Karyn T., Lear, James D., and Degrado, William F. 1995. Design of Two-Stranded and Three-Stranded Coiled Coil Peptides. Phil. Trans. R. Soc. 348:81.

Fairman, Robert, Beran-Steed, Rita K., Anthony-Cahill, Spencer J., Stafford, Walter F., Lear, James D. DeGrado, William F., Benfield, Pamela A., and Brenner, Stephen L. 1993. Multiple Oligomerization States of HLH Proteins: Novel Mechanism of Regulation. Proc. Natl. Acad. Sci., 90:10429.

Armstrong, Katherine M., Fairman, Robert, and Baldwin, Robert L. 1993. Mechanism of Interaction Between Phe and His Spaced (i,i+4) in an Alanine-Based a-Helix. J. Mol. Biol., 230:284.

Fairman, Robert, Anthony-Cahill, Spencer J., and DeGrado, William F. 1992. Free Energy Describing the Helix-Forming Propensity of D-Alanine. J. Am. Chem Soc., 114:5458.

Anthony-Cahill, Spencer J., Benfield, Pamela A., Fairman, Robert, Wasserman, Zelda R., Brenner, Stephen L., Altenbach, Christian, Hubbell, Wayne L., Stafford, Walter F. III, and DeGrado, William F. 1992. Molecular Characterization of Helix-Loop-Helix Peptides. Science, 255:979.

Fairman, Robert, Armstrong, Katherine M., Shoemaker, Kevin R., York, Eunice J., Stewart, John M., and Baldwin, Robert L. 1991. Position Effect on Apparent Helix Propensities in the C-peptide Helix. J. Mol. Biol., 221:1395.

Fairman, Robert, Shoemaker, Kevin R., York, Eunice J., Stewart, John M., and Baldwin, Robert L. 1990. The Glu 2^-...Arg 10⁺ Side-chain Interaction in the C-peptide Helix of Ribonuclease A. Biophys. Chem., 37:107.

York, Eunice J., Stewart, John M., Fairman, Robert, and Baldwin, Robert L. 1990. Effects of a Disulfide Bridge on the Helix in C-peptide Analogs. Proc. Am. Peptide Symp. 11th, pp. 635-636.

Shoemaker, Kevin R., Fairman, Robert, Schultz, David A., Robertson, Andrew, York, Eunice J., Stewart, John M., and Baldwin, Robert L. 1990. Sidechain Interactions in the C-peptide Helix: Phe 8^...His 12⁺. Biopolymers. 29:1.

Fairman, Robert, Shoemaker, Kevin R., York, Eunice J., Stewart, John M., and Baldwin, Robert L. 1989. Further Studies of the Helix Dipole Model: Efects of a Free a-NH3⁺ or a -COO^- Group on Helix Stability. Proteins. 5:1.

Fairman, Robert and Brutlag, Douglas L. 1988. Expression of the Drosophila Type II Topoisomerase is Developmentally Regulated. Biochemistry. 27: 560.

Shoemaker, Kevin R., Fairman, Robert, York, Eunice J., Stewart, John M., and Baldwin, Robert L. 1988. Circular Dichroism Measurement of Peptide Helix Unfolding. Proc. Am. Peptide Symp. 10th, pp. 5-20.

Shoemaker, Kevin R., Fairman, Robert, Kim, Peter S., York, Eunice J., Stewart, John M., and Baldwin, Robert L. 1987. The C-peptide Helix from Ribonuclease A Considered as an Autonomous Folding Unit. Cold Spring Harbor Symp. Quant. Biol. LII: 391.