MISSENSE MEANDERINGS IN
SEQUENCE SPACE: A BIOPHYSICAL
VIEW OF PROTEIN EVOLUTION
Mark A. DePristo, Daniel M. Weinreich and Daniel L. Hartl
“Taken as a whole, recent findings from biochemistry and evolutionary biology indicate that our understanding of protein evolution is incomplete, if not fundamentally flawed.”
Abstract | Proteins are finicky molecules; they are barely stable and are prone to aggregate, but they must function in a crowded environment that is full of degradative enzymes bent on their destruction. It is no surprise that many common diseases are due to missense mutations that affect protein stability and aggregation. Here we review the literature on biophysics as it relates to molecular evolution, focusing on how protein stability and aggregation affect organismal fitness. We then advance a biophysical model of protein evolution that helps us to understand phenomena that range from the dynamics of molecular adaptation to the clock-like rate of protein evolution
Summary:
**In addition to functional properties, proteins have a wide range of biophysical characteristics, such as stability, propensity for aggregation and rate of degradation. These properties are at least as important as function for cellular and organismal fitness.
**Proteins tolerate only narrow ranges of stability, aggregation propensity and degradation rate. Many individual missense mutations perturb these traits by amounts that are on the same order as the permissible range of values, and are consequently common causes of human genetic disease.
**The narrow range of tolerance of deviations from optimum characteristics and the significant effects of mutations give rise to a substantial degree of epistasis for fitness. Moreover, mutations simultaneously affect function, stability, aggregation and degradation. For these reasons, mutations might be selectively beneficial on some genetic backgrounds and deleterious on others.
**Mutations that change function often do so at the cost of protein stability and aggregation. Compensatory mutations therefore function by relieving the biophysical strain that is introduced by adaptive mutations.
**We propose a new model of protein evolution that is reminiscent of a constrained ‘random walk’ through fitness space, which is based on the fitness consequences and distribution of mutational effects on function, stability, aggregation and degradation.
**This model can account for both the micro-evolutionary events that are studied by biochemists and the long-term patterns of protein evolution that are observed by evolutionary biologists.
—–
Taken as a whole, recent findings from biochemistry and evolutionary biology indicate that our understanding of protein evolution is incomplete, if not fundamentally flawed. The neutral theory of molecular evolution1, which states that all mutations that reach FIXATION in a population are selectively neutral, appeals to evolutionary geneticists in part because it can account for the approximately constant rate of protein evolution. However, its premise that most missense mutations are selectively neutral has been systematically rejected by protein biochemists, who recognize instead that almost all missense mutations have large biophysical effects2. Indeed, nucleotide sequence analyses have uncovered pervasive positive selection for amino-acid replacements3?5.
Another important challenge to evolutionary theory, which emphasizes the independent and additive effects of mutations, arises from studies of compensatory evolution. Here the deleterious effects of mutations are rapidly and effectively compensated by conditionally beneficial mutations. Compensatory mutations often occur in the same gene as the initial deleterious mutation, are common in ADAPTIVE EVOLUTION6?8 and have an important role in many human diseases9. There are currently no models that reconcile the constant rate of protein evolution with the biochemical reality that missense mutations have large, context-dependent effects and that few, if any, are selectively neutral.
There is a growing appreciation of the role that the biophysical properties of protein stability, aggregation and degradation have in FITNESS and disease10 TABLE 1. Moreover, these properties have been identified as significant factors in many cases of adaptive8,11,12 and compensatory evolution13?15. These properties ? and not function ? seem to be the forces driving much of protein evolution.
Here we review the literature on biophysics as it relates to molecular evolution, with a particular focus on how missense mutations affect protein stability and aggregation. We then develop a biophysical model of protein evolution that helps to explain such diverse phenomena as compensatory mutation, the dynamics of molecular adaptation and the rate of protein evolution. Throughout this review, we bring together the fields of protein biophysics and molecular evolution by highlighting the shared questions, complementary techniques and important results concerning protein evolution that have come from both fields.