James C. Patterson, Ph.D.
Assistant Professor, Department of Chemistry

Areas of focus: Computational Inorganic Chemistry, Computational Biophysics


Visit James' Lab

Contact Information
CHEM 256
(205) 975-9146
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My research uses computational methods to study the reaction mechanisms of metalloenzymes and the dynamics of membrane-associated proteins. The main goal of my research is to elucidate the underlying chemical and biophysical causes of age- and stress-related diseases.

Computational Inorganic Chemistry

Cupins are a class of proteins that are found in every kingdom of life and have a wide range of functions. Cysteine dioxygenase (CDO) belongs to this superfamily of proteins, and it catalyzes the conversion of cysteine to cysteine sulfinic acid. This is the first step in cysteine catabolism, which has implications for neurodegenerative disorders like Alzheimer's, Parkinson's diseases and ALS.

Crystal structures for mouse, rat and human CDO are known. Although   there are small structural differences in each, there are significant differences in the three proposed reaction mechanisms for how they function. These mechanisms were based on crystallographic and chemical intuition. My research uses density functional calculations to study these reaction mechanisms with the goal of identifying which reactive intermediates are energetically accessible, and which reaction pathways are most favorable.

Computational Biophysics

Alpha synuclein is a soluble presynaptic protein that has been found in the abnormal protein depositions of Lewy bodies and senile plaques of Parkinson’s and Alzheimer’s diseases, respectively. The aggregation (or oligomerization) of this protein are believed to play a critical role in the pathology of Parkinson's disease, but the mechanism by which this occurs is not well understood. 

Several researchers have suggested that transition metals play an important role in the pathogenesis of idiopathic Parkinson's disease.  While much critical experimental research continues in this area, very few computational studies have attempted to study á-synuclein dynamics.  My research combines molecular dynamics simulations and density functional theory calculations to study the dynamics of á-synuclein oligomerization, particularly in the presence of transition metals.


Dr. Patterson received his BA in chemistry from Carleton College in 1997; and went on to complete his Ph. D. degree in chemistry from the University of California in Santa Barbara in 2004.  He completed his Post-doctoral fellowship at UAB in from 2004-2007 with Dr. Jere Segrest while studying apolipoproteins.