Mn/Fe superoxide dismutase interaction fingerprints and prediction of oligomerization and metal cofactor from sequence

Abstract

Fe- and Mn-containing superoxide dismutase (sod) enzymes are closely related and similar in both amino acid sequence and structure, but differ in their mode of oligomerization and in their specificity for the Fe or Mn cofactor. The goal of the present work is to identify and analyze the sequence and structure characteristics that ensure the cofactor specificities and the oligomerization modes. For that purpose, 374 sod sequences and 17 sod crystal structures were collected and aligned. These alignments were searched for residues and inter-residue interactions that are conserved within the whole sod family, or alternatively, that are specific to a given sod subfamily sharing common characteristics. This led us to define key residues and inter-residue interaction fingerprints in each subfamily. The comparison of these fingerprints allows, on a rational basis, the design of mutants likely to modulate the activity and/or specificity of the target sod, in good agreement with the available experimental results on known mutants. The key residues and interaction fingerprints are furthermore used to predict if a novel sequence corresponds to a sod enzyme, and if so, what type of sod it is. The predictions of this fingerprint method reach much higher scores and present much more discriminative power than the commonly used method that uses pairwise sequence comparisons.

Using Amino Acid Correlation and Community Detection Algorithms to Identify Functional Determinants in Protein Families

“…Members of the family can be either dimeric or tetrameric, and usually selectively bind either Fe or Mn at the active site in a non-substitutable fashion in order to present catalytic activity. The clusters found seemed to be related to positions which were already described as determinants of oligomeric state and metal selectivity [12]. Therefore, instead of the previously postulated view that clusters of correlated positions would reflect routes of allosteric communication or energetic coupling, a much more reasonable hypothesis can be proposed from these results: if a given protein family is populated by proteins having distinct properties (e.g., binding or not a given ligand, having different oligomeric states, being able to interact or not with a given protein, etc.…”

Rat mitochondrial manganese superoxide dismutase: Amino acid positions involved in covalent modifications, activity, and heat stability

“…A previous analysis on several SOD2 primary structures pointed to the relevance of position 143 for the type of metal bound in the active site of the enzyme. 34 This position is semiconservatively occupied by Gln or His, and this difference is usually predictive of the active metal cofactor of SOD2, namely Mn or Fe with Gln or His, respectively. To exclude that the lower Mn content of SOD2(H143) with respect to SOD2(Q143) was due to its replacement by Fe, the iron content of both protein samples was determined.…”

Identificação dos determinantes estruturais de Fe/MnSODs necessários a especificidade por metal.

“…Superóxido dismutases são oxidorredutases que metabolizam o radical superóxido evitando o desencadeamento de reações oxidativas e prevenindo a formação de espécies reativas responsáveis por causar dano celular extensivo (2,13,39). A existência dessas enzimas era associada anteriormente apenas a organismos aeróbios (40), atualmente consideradas ubíquas, a presença dessas foi confirmada em anaeróbios como Mathanobacterium thermoautotrophicum (41).…”

“…Apesar das diferenças clássicas encontradas nestas SODs, alguns organismos possuem enzimas tetraméricas ligadas a ferro com características de MnSODs, como resistência a íons azoteto e peróxido de hidrogênio (41). Embora essa substituição de metais possa ser obtida, as atividades dismutásicas resultantes são muito reduzidas quando comparadas com as proteínas na presença dos metais próprios (39,64 Se o MSA é composto por um número suficientemente grande e diverso de sequências individuais, admite-se que se um resíduo l não contribui para a estrutura e função da proteína sua freqüência no MSA deve ser próxima do valor médio calculado para todas as proteínas. Entretanto, se resíduos i, j, k fazem alguma contribuição, suas distribuições deveriam desviar dos valores médios, e a extensão desses desvios quantificaria a pressão evolucionária recebida nestes sítios.…”