Detecting Repetitions and Periodicities in Proteins by Tiling the Structural Space

The notion of energy landscapes provides conceptual tools for understanding the complexities of protein folding and function. Energy Landscape Theory indicates that it is much easier to find sequences that satisfy the "Principle of Minimal Frustration" when the folded structure is symmetric (Wolynes, P. G. Symmetry and the Energy Landscapes of Biomolecules. Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 14249-14255). Similarly, repeats and structural mosaics may be fundamentally related to landscapes with multiple embedded funnels. Here we present analytical tools to detect and compare structural repetitions in protein molecules. By an exhaustive analysis of the distribution of structural repeats using a robust metric we define those portions of a protein molecule that best describe the overall structure as a tessellation of basic units. The patterns produced by such tessellations provide intuitive representations of the repeating regions and their association towards higher order arrangements. We find that some protein architectures can be described as nearly periodic, while in others clear separations between repetitions exist. Since the method is independent of amino acid sequence information we can identify structural units that can be encoded by a variety of distinct amino acid sequences

Computational Design Of Protein–ligand And Protein–protein Interactions

Central to the function of proteins is the concept of molecular recognition. Protein–ligand and protein–protein interactions make up the bulk of the chemical processes that give rise to living things. Realizing the full potential of protein design technology will therefore require an increased understanding of the design principles of molecular recognition. We have tackled problems involving molecular recognition by using computational methods to design novel protein-ligand and protein-protein interactions. Firstly, we set out to design a protein capable of recognizing lanthanide metal ions. Protein-lanthanide systems are of interest for their potential to serve as purification agents for use under biological conditions. We have designed a highly dense 6-coordinate lanthanide binding at the core of a de novo protein, and used the dynamical aspects of the protein to achieve a degree of differentiation between elements in the lanthanide series. Secondly, we investigated systems of homo-oligomeric protein complexes that self-assemble into hollow cages. We have studied the structural determinants of naturally occurring self-assembling ferritin cages and identified a single mutation that greatly increased the stability of the ferritin cage, as well as dramatically altered the overall structure of the assembly. We have also used the formulation of probabilistic protein design to arrive at novel sequences for α-helical peptides that can adjust their surfaces in accordance to different local environments. This formulation was used to identify a sequence for a peptide designed to self-assemble into a spherical particle with broken symmetry. Taken together, these efforts will lead to an increased understanding of the role of kinetics and structural plasticity in protein-ligand and protein-protein interactions

Frustration in Biomolecules

Biomolecules are the prime information processing elements of living matter. Most of these inanimate systems are polymers that compute their structures and dynamics using as input seemingly random character strings of their sequence, following which they coalesce and perform integrated cellular functions. In large computational systems with a finite interaction-codes, the appearance of conflicting goals is inevitable. Simple conflicting forces can lead to quite complex structures and behaviors, leading to the concept of "frustration" in condensed matter. We present here some basic ideas about frustration in biomolecules and how the frustration concept leads to a better appreciation of many aspects of the architecture of biomolecules, and how structure connects to function. These ideas are simultaneously both seductively simple and perilously subtle to grasp completely. The energy landscape theory of protein folding provides a framework for quantifying frustration in large systems and has been implemented at many levels of description. We first review the notion of frustration from the areas of abstract logic and its uses in simple condensed matter systems. We discuss then how the frustration concept applies specifically to heteropolymers, testing folding landscape theory in computer simulations of protein models and in experimentally accessible systems. Studying the aspects of frustration averaged over many proteins provides ways to infer energy functions useful for reliable structure prediction. We discuss how frustration affects folding, how a large part of the biological functions of proteins are related to subtle local frustration effects and how frustration influences the appearance of metastable states, the nature of binding processes, catalysis and allosteric transitions. We hope to illustrate how Frustration is a fundamental concept in relating function to structural biology.Comment: 97 pages, 30 figure

A creature with a hundred waggly tails: intrinsically disordered proteins in the ribosome

This article is made available for unrestricted research re-use and secondary analysis in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the World Health Organization (WHO) declaration of COVID-19 as a global pandemic.Intrinsic disorder (i.e., lack of a unique 3-D structure) is a common phenomenon, and many biologically active proteins are disordered as a whole, or contain long disordered regions. These intrinsically disordered proteins/regions constitute a significant part of all proteomes, and their functional repertoire is complementary to functions of ordered proteins. In fact, intrinsic disorder represents an important driving force for many specific functions. An illustrative example of such disorder-centric functional class is RNA-binding proteins. In this study, we present the results of comprehensive bioinformatics analyses of the abundance and roles of intrinsic disorder in 3,411 ribosomal proteins from 32 species. We show that many ribosomal proteins are intrinsically disordered or hybrid proteins that contain ordered and disordered domains. Predicted globular domains of many ribosomal proteins contain noticeable regions of intrinsic disorder. We also show that disorder in ribosomal proteins has different characteristics compared to other proteins that interact with RNA and DNA including overall abundance, evolutionary conservation, and involvement in protein–protein interactions. Furthermore, intrinsic disorder is not only abundant in the ribosomal proteins, but we demonstrate that it is absolutely necessary for their various functions

Thermodynamics and Kinetics of Iso-1-cytochrome c Denatured State

Various diseases result from protein misfolding. Curing these conditions requires understanding the principles governing folding. Efforts toward understanding how proteins fold have focused on the transition state rather than the earliest folding events. We study these initial events using the assumption that protein folding must involve the formation of the most primitive structure possible – a simple loop. Our laboratory has developed a system of studying simple loops in the denatured state using c-type cytochromes. New insights into how the properties of these loops impact the denatured state are outlined in this thesis. First, studies on a 22-residue loop revealed a previously unreported finding that equilibrium loop formation was not strongly affected by sequence composition. While loop formation rates depended only on sequence composition, loop breakage rates also depended on sequence order. Second, thermodynamic and kinetic studies on homopolymeric inserts in “poor” and “good” solvents revealed that homopolymeric non-foldable protein sequences behave like a random coil. However, heteropolymeric foldable sequences have scaling factors higher than those of a random coil, suggesting the presence of residual structure in denatured proteins. Thus, peptide models with homopolymeric sequences do not adequately describe the nature of foldable sequences. Third, we investigated the kinetics of reversible oligomerization in the denatured state using a P25A yeast iso-1-cytochrome c variant. The findings indicated that intermolecular aggregation in a denatured protein is extremely fast – 107-108 M-1s-1 and that the P25A mutation strongly affects intermolecular aggregation. This work suggests that equilibrium control of folding versus aggregation is advantageous for productive protein folding in vivo. Fourth, we use time-resolved FRET to follow compact and extended distributions of a protein under denaturing conditions. Our findings revealed three major populations in the unfolded state when no loop is present whereas only two populations remain when the loop forms. The most extended population is lost upon loop formation showing that simple loop formation dramatically constrains the denatured state. Thus, thermodyamic and kinetic studies on simple loops using a variety of spectroscopic techniques have enhanced understanding of the initial events of protein folding and the role of the denatured state in modulating protein aggregation

Hydrophobic forces and the length limit of foldable protein domains

To find the native conformation (fold), proteins sample a subspace that is typically hundreds of orders of magnitude smaller than their full conformational space. Whether such fast folding is intrinsic or the result of natural selection, and what is the longest foldable protein, are open questions. Here, we derive the average conformational degeneracy of a lattice polypeptide chain in water and quantitatively show that the constraints associated with hydrophobic forces are themselves sufficient to reduce the effective conformational space to a size compatible with the folding of proteins up to approximately 200 amino acids long within a biologically reasonable amount of time. This size range is in general agreement with the experimental protein domain length distribution obtained from approximately 1,200 proteins. Molecular dynamics simulations of the Trp-cage protein confirm this picture on the free energy landscape. Our analytical and computational results are consistent with a model in which the length and time scales of protein folding, as well as the modular nature of large proteins, are dictated primarily by inherent physical forces, whereas natural selection determines the native state

Phenotypic suppression caused by resonance with light-dark cycles indicates the presence of a 24-hours oscillator in yeast and suggests a new role of intrinsically disordered protein regions as internal mediators

The mutual interaction between environment and life is a main topic of biological sciences. An interesting aspect of this interaction is the existence of biological rhythms spanning all the levels of organisms from bacteria to humans. On the other hand, the existence of a coupling between external oscillatory stimuli and adaptation and evolution rate of biological systems is a still unexplored issue. Here we give the demonstration of a substantial increase of heritable phenotypic changes in yeast, an organism lacking a photoreception system, when growing at 12 h light/dark cycles, with respect to both stable dark (or light) or non-12 + 12 h cycling. The model system was a yeast strain lacking a gene whose product is at the crossroad of many different physiological regulations, so ruling out any simple explanation in terms of increase in reverse gene mutations. The abundance of intrinsically disordered protein regions (IDPRs) in both deleted gene product and in its vast ensemble of interactors supports the hypothesis that resonance with the environmental cycle might be mediated by intrinsic disorder-driven interactions of protein molecules. This result opens to the speculation of the effect of environment/biological resonance phenomena in evolution and of the role of protein intrinsically disordered regions as internal mediators. Communicated by Ramaswamy H. Sarma