Comparison of intrinsic dynamics of cytochrome p450 proteins using normal mode analysis

Abstract

Cytochrome P450 enzymes are hemeproteins that catalyze the monooxygenation of a widerange of structurally diverse substrates of endogenous and exogenous origin. These heme monooxygenases receive electrons from NADH/NADPH via electron transfer proteins. The cytochrome P450 enzymes, which constitute a diverse superfamily of more than 8,700 proteins, share a common tertiary fold but < 25% sequence identity. Based on their electron transfer protein partner, cytochrome P450 proteins are classified into six broad classes. Traditional methods of protein classification are based on the canonical paradigm that attributes proteins' function to their three-dimensional structure, which is determined by their primary structure that is the amino acid sequence. It is increasingly recognized that protein dynamics play an important role in molecular recognition and catalytic activity. As the mobility of a protein is an intrinsic property that is encrypted in its primary structure, we examined if different classes of cytochrome P450 enzymes display any unique patterns of intrinsic mobility. Normal mode analysis was performed to characterize the intrinsic dynamics of five classes of cytochrome P450 proteins. The present study revealed that cytochrome P450 enzymes share a strong dynamic similarity (root mean squared inner product > 55% and Bhattacharyya coefficient > 80%), despite the low sequence identity (< 25%) and sequence similarity (< 50%) across the cytochrome P450 superfamily. Noticeable differences in C a atom fluctuations of structural elements responsible for substrate binding were noticed. These differences in residue fluctuations might be crucial for substrate selectivity in these enzymes.

Incorporating modeling and simulations in undergraduate biophysical chemistry course to promote understanding of structure‐dynamics‐function relationships in proteins

“…Students conducted quantitative analyses of sequence, structure, and dynamic similarities in Cytochrome P450 proteins and other enzymes involved in primary metabolic pathways to have in‐depth understanding of the structure‐dynamics‐function relationships in proteins. From the NMA study, students have demonstrated that differences in local fluctuations modulate substrate specificity and catalytic function of enzymes . The two end‐of‐semester projects, conducted in Fall 2013 and 2014, are described in Supporting Information Appendix VI.…”

“…Protein dynamics and their impact on protein function have been the main focus of our research in the past several years [58,59,[61][62][63][64][65]. Several undergraduate researchers have collaborated in various projects dealing with fundamental questions on the role of protein motions in relation to their function.…”

“…We have been very pleased by our ability to provide a research environment where students collaborate and participate in challenging research problem, share their data, and finally, be a co‐author of a research paper. Two of their end‐of‐semester projects resulted in peer‐reviewed publications .…”

Molecular elucidation of a new allelic variation at the Sg-5 gene associated with the absence of group A saponins in wild soybean

“…Although all CYP450s have a similar structural fold, they commonly have less than 20% sequence identities [ 51 ]. There are only three amino acid residues that are completely conserved (Cys in the CXG motif, and Glu and Arg in the motif) in the CYP450 superfamily proteins across almost all the biological kingdom species [ 34 , 52 ]. The amino acids “E” and “R” in the motif are occasionally reported as being non-conserved [ 35 , 36 ].…”

Exploring the intrinsic dynamics of SARS-CoV-2, SARS-CoV and MERS-CoV spike glycoprotein through normal mode analysis using anisotropic network model

“…Detailed mathematical description about normal mode analysis and how it is applicable to protein molecule is given in many studies [ 20 , [25] , [26] , [27] ]. NMA is a technique to study vibrational motion of harmonic oscillating system near the equilibrium state.…”