Brownian dynamics of interactions between glyceraldehyde‐3‐phosphate dehydrogenase (GAPDH) mutants and F‐actin

Waingeh, Victor F.; Lowe, Stephen L.; Thomasson, Kathryn A.

doi:10.1002/bip.10560

Cited by 13 publications

(5 citation statements)

References 31 publications

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“…BD methodology and the program MacroDox have been used successfully to study the cyt f-PC and cyt f-cyt c 6 interactions (9)(10)(11)38,40) plus the interactions between other proteins (58,59). For a description of the MacroDox strengths and weaknesses, see Gross and Pearson (10), Haddadian and Gross (11), and Gross (40).…”

Section: Brownian Dynamics Simulationsmentioning

confidence: 99%

A Brownian Dynamics Study of the Effects of Cytochrome f Structure and Deletion of Its Small Domain in Interactions with Cytochrome c6 and Plastocyanin in Chlamydomonas reinhardtii

Haddadian

Gross

2006

Biophysical Journal

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The availability of seven different structures of cytochrome f (cyt f) from Chlamydomonas reinhardtii allowed us, using Brownian dynamics simulations, to model interactions between these molecules and their redox partners, plastocyanin (PC) and cytochrome c6 (cyt c6) in the same species to study the effect of cyt f structure on its function. Our results showed that different cyt f structures, which are very similar, produced different reaction rates in interactions with PC and cyt c6. We were able to attribute this to structural differences among these molecules, particularly to a small flexible loop between A-184 and G-191 (which has some of the highest crystallographic temperature factors in all of the cyt f structures) on the cyt f small domain. We also showed that deletion of the cyt f small domain affected cyt c6 more than PC, due to their different binding positions on cyt f. One function of the small domain in cyt f may be to guide PC or cyt c6 to a uniform dock with cyt f, especially due to electrostatic interactions with K-188 and K-189 on this domain. Our results could serve as a good guide for future experimental work on these proteins to understand better the electron transfer process between them. Also, these results demonstrated the sensitivity and the power of the Brownian dynamics simulations in the study of molecular interactions.

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Section: Brownian Dynamics Simulationsmentioning

confidence: 99%

A Brownian Dynamics Study of the Effects of Cytochrome f Structure and Deletion of Its Small Domain in Interactions with Cytochrome c6 and Plastocyanin in Chlamydomonas reinhardtii

Haddadian

Gross

2006

Biophysical Journal

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“…They are found externally projected and two of these side chains (that is, amino acid residues Lys-24 and Lys-69) form a patch. In a study using molecular dynamics simulations of computer models [20], the authors observed that single and double mutants (i.e. substitutions with alanyl residues) did not have a large effect on the average electrostatic binding energy, suggesting that the lysine residues act in concert.…”

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confidence: 98%

Functional Diversity

Seidler

2012

Advances in Experimental Medicine and Biology

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There is increasing evidence to support a gene economy model that is fully based on the principles of evolution in which a limited number of proteins does not necessarily reflect a finite number of biochemical processes. The concept of 'gene sharing' proposes that a single protein can have alternate functions that are typically attributed to other proteins. GAPDH appears to play this role quite well in that it exhibits more than one function. GAPDH represents the prototype for this new paradigm of protein multi-functionality. The chapter discusses the diverse functions of GAPDH among three broad categories: cell structure, gene expression and signal transduction. Protein function is curiously re-specified given the cell's unique needs. GAPDH provides the cell with the means of linking metabolic activity to various cellular processes. While interpretations may often lead to GAPDH's role in meeting focal energy demands, this chapter discusses several other very distinct GAPDH functions (i.e. membrane fusogenic properties) that are quite different from its ability to catalyze oxidative phosphorylation of the triose, glyceraldehyde 3-phosphate. It is suggested that a single protein participates in multiple processes in the structural organization of the cell, controls the transmission of genetic information (i.e. GAPDH's involvement may not be finite) and mediates intracellular signaling.

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“…GAPDH was demonstrated as tubulin-binding protein ( Tisdale et al, 2009 ; Landino et al, 2014 ). Similarly, GAPDH is also bound to actin ( Waingeh et al, 2004 ). In mouse cell lines, GAPDH interacts with lactoferrin ( Chauhan et al, 2015 ).…”

Section: Discussionmentioning

confidence: 99%

The uncommon function and mechanism of the common enzyme glyceraldehyde-3-phosphate dehydrogenase in the metamorphosis of Helicoverpa armigera

Zhao

Zhang

Geng

et al. 2022

Front. Bioeng. Biotechnol.

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Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), a key enzyme in glycolysis, is commonly used as an internal reference gene in humans, mice, and insects. However, the function of GAPDH in insect development, especially in metamorphosis, has not been reported. In the present study, Helicoverpa armigera and Spodoptera frugiperda ovarian cell lines (Sf9 cells) were used as materials to study the function and molecular mechanism of GAPDH in larval metamorphosis. The results showed that HaGAPDH was more closely related to GAPDH of S. frugiperda and Spodoptera litura. The transcript peaks of HaGAPDH in sixth instar larvae were 6L-3 (epidermal and midgut) and 6L-1 (fat body) days, and 20E and methoprene significantly upregulated the transcripts of HaGAPDH of larvae in qRT-PCR. HaGAPDH–GFP–His was specifically localized in mitochondria in Sf9 cells. Knockdown of HaGAPDH by RNA interference (RNAi) in sixth instar larvae resulted in weight loss, increased mortality, and decreases in the pupation rate and emergence rates. HaGAPDH is directly bound to soluble trehalase (HaTreh1) physically and under 20E treatment in yeast two-hybrid, coimmunoprecipitation, and colocalization experiments. In addition, knockdown of HaGAPDH increased the Treh1 activity, which in turn decreased the trehalose content but increased the glucose content in larvae. Therefore, these data demonstrated that GAPDH controlled the glucose content within the normal range to ensure glucose metabolism and metamorphosis by directly binding with HaTreh1.

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Brownian dynamics of interactions between glyceraldehyde‐3‐phosphate dehydrogenase (GAPDH) mutants and F‐actin

Cited by 13 publications

References 31 publications

A Brownian Dynamics Study of the Effects of Cytochrome f Structure and Deletion of Its Small Domain in Interactions with Cytochrome c6 and Plastocyanin in Chlamydomonas reinhardtii

A Brownian Dynamics Study of the Effects of Cytochrome f Structure and Deletion of Its Small Domain in Interactions with Cytochrome c6 and Plastocyanin in Chlamydomonas reinhardtii

Functional Diversity

The uncommon function and mechanism of the common enzyme glyceraldehyde-3-phosphate dehydrogenase in the metamorphosis of Helicoverpa armigera

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