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University of Colorado Denver


Protein Folding and Function: Dr. Mallela Research Laboratory

Research Interests

Project 1: Structure-function-disease relationship of dystrophin and utrophin in muscular dystrophy

Muscular dystrophy (MD) refers to a group of degenerative muscle diseases that cause progressive muscle weakness. MD affects all types of muscles. For example, decreased function of heart muscles causes heart diseases that include cardiomyopathy and congestive heart failure. At present there is no cure available for MD, although certain palliative treatments are available to ease the pain associated with MD. Duchenne MD (DMD) and Becker MD (BMD) are two prominent types of MD, which are caused by the deficiency of a vital muscle protein known as dystrophin. These dystrophin-related diseases physically weaken patients to a state of immobility, and often cause death at an early age. Dystrophin stabilizes the sarcolemma membrane against the mechanical forces associated with muscle contraction and stretch. Mutations in dystrophin trigger the disease. Although dystrophin was identified as a key molecular player in MD 25 years ago, little is known about the biophysical mechanisms that trigger the disease at the fundamental protein level.

Utrophin, the closest homologue of dystrophin (60% sequence similarity), has been shown to compensate the loss of functional dystrophin in animal studies, but its exact biological function is not known. It binds to actin, protects actin against its depolymerization, and interacts with dystrophin-related proteins. Utrophin is confined specifically to the sarcolemma in fetal and regenerating muscle cells. After down-regulation at birth, it is only found in the neuromuscular junctions in adult muscle cells to aid in optimal synapse transmission and to play a stabilizing role at these junctions.

In this project, we are trying to understand the biophysical and structural principles of how these two important proteins function and the effect thereon of disease-causing mutations.

Relevant Publications

S.M. Singh, S. Bandi, and K.M.G. Mallela, The N- and C-terminal domains differentially contribute to the structure and function of dystrophin and utrophin tandem calponin-homology domains, Biochemistry, 54 (2015) 6942-6950. PDF 

S. Bandi, S.M. Singh, and K.M.G. Mallela, Interdomain linker determines primarily the structural stability of dystrophin and utrophin tandem calponin-homology domains rather than their actin-binding affinity, Biochemistry, 54 (2015) 5480-5488. PDF 

S.M. Singh, S. Bandi, D.D. Shah, G. Armstrong, and K.M.G. Mallela, Missense mutation Lys18Asn in dystrophin that triggers X-linked dilated cardiomyopathy decreases protein stability, increases protein unfolding, and perturbs protein structure, but does not affect protein function, PLoS One, 9 (2014) e110439. PDF

S. Bandi, S.M. Singh, and K.M.G. Mallela, The C-terminal domain of the utrophin tandem calponin-homology domain appears to be thermodynamically and kinetically more stable than the full-length protein, Biochemistry, 53 (2014) 2209-2211. PDF

S.M. Singh, S. Bandi, S.J. Winder, and K.M.G. Mallela, The actin binding affinity of the utrophin tandem calponin-homology domain is primarily determined by its N-terminal domain, Biochemistry, 53 (2014) 1801-1809. PDF

S.M. Singh and K.M.G. Mallela, The N-terminal actin-binding tandem calponin-homology (CH) domain of dystrophin is in a closed conformation in solution and when bound to F-actin, Biophysical Journal, 103 (2012) 1970-1978. PDF Selected for a New & Notable: Biophysical Journal, 103 (2012) 1818-1819. PDF

S.M. Singh, J.F. Molas, N. Kongari, S. Bandi, G.S. Armstrong, S.J. Winder, and K.M.G. Mallela, Thermodynamic stability, unfolding kinetics, and aggregation of the N-terminal actin binding domains of utrophin and dystrophin, Proteins: Structure, Function, and Bioinformatics, 80 (2012) 1377-1392. PDF

S.M. Singh, N. Kongari, J. Cabello-Villegas, and K.M.G. Mallela, Mutations in dystrophin that trigger muscular dystrophy decrease protein stability and lead to cross-beta aggregates, Proceedings of the National Academy of Sciences of the United States of America, 107 (2010) 15069-15074. PDF

Project 2: Mechanisms of protein aggregation induced by alcohols and antimicrobial preservatives

Approximately one-third of pharmaceutical formulations are of multi-dose. Multi-dose protein formulations are desirable for reasons of economics, patient compliance, and safety. Because of the risk of microbial growth after the first dose has been removed from the product vial, multi-dose formulations require an effective antimicrobial preservative (AP). However, APs have been shown to cause protein aggregation and the underlying mechanisms are less understood. Such knowledge is required for developing approaches to inhibit AP-induced protein aggregation, and for choosing the right AP that causes less protein aggregation yet offers the desired antimicrobial function. In this project, we are studying the effect of various phenolic APs such as benzyl alcohol and m-cresol on protein aggregation using a model protein cytochrome c.

Alcohols form a major class of APs. Besides therapeutic proteins, alcohols were recently shown to aggregate disease-related and non-disease-related proteins. Alcohols have been traditionally used as "co-solvents" to probe the effect of various physical parameters of solvents on protein stability and folding, but the mechanisms of alcohol-induced protein aggregation were less understood. In this project, we are studying how the physical properties of alcohols affect protein aggregation.

Relevant Publications

R.L. Bis, S.M. Singh, J. Cabello-Villegas, and K.M.G. Mallela, Role of benzyl alcohol in the unfolding and aggregation of interferon alpha-2a, Journal of Pharmaceutical Sciences, 104 (2015) 407-415. PDF ​

R.L. Bis and K.M.G. Mallela, Antimicrobial preservatives induce aggregation of interferon alpha-2a: The order in which preservatives induce protein aggregation is independent of the protein, International Journal of Pharmaceutics, 472 (2014) 356-361. PDF

R.L. Bis, T.M. Stauffer, S.M. Singh, T.B. Lavoie, and K.M.G. Mallela, High yield soluble bacterial expression and streamlined purification of recombinant human interferon alpha-2a, Protein Expression and Purification, 99 (2014) 138-146. PDF

R.L. Hutchings, S.M. Singh, J. Cabello-Villegas, and K.M.G. Mallela, Effect of antimicrobial preservatives on partial protein unfolding and aggregation, Journal of Pharmaceutical Sciences, 102 (2013) 365-376. PDF

S.M. Singh, R.L. Hutchings, and K.M.G. Mallela, Mechanisms of m-cresol induced protein aggregation studied using a model protein cytochrome c, Journal of Pharmaceutical Sciences, 100 (2011) 1679-1689. PDF

S.M. Singh, J. Cabello-Villegas, R.L. Hutchings, and K.M.G. Mallela, Role of partial protein unfolding in alcohol-induced protein aggregation, Proteins: Structure, Function, and Bioinformatics, 78 (2010) 2625-2637. PDF