Role of water in protein folding, oligomerization, amyloidosis and miniprotein

The essential involvement of water in most fundamental extra-cellular and intracellular processes of proteins is critically reviewed and evaluated in this article. The role of water in protein behavior displays structural ambivalence; it can protect the disordered peptide-chain by hydration or helps the globular chain-folding, but promotes also the protein aggregation, as well (see: diseases). A variety of amyloid diseases begins as benign protein monomers but develops then into toxic amyloid aggregates of fibrils. Our incomplete knowledge of this process emphasizes the essential need to reveal the principles of governing this oligomerization. To understand the biophysical basis of the simpler in vitro amyloid formation may help to decipher also the in vivo way. Nevertheless, to ignore the central role of the water's effect among these events means to receive an uncompleted picture of the true phenomenon. Therefore this review represents a stopgap role, because the most published studies—with a few exceptions—have been neglected the crucial importance of water in the protein research. The following questions are discussed from the water's viewpoint: (i) interactions between water and proteins, (ii) protein hydration/dehydration, (iii) folding of proteins and miniproteins, (iv) peptide/protein oligomerization, and (v) amyloidosis

GIAO-PCM Calculations on Alanine Diamide Models Aimed at Predicting Protein Secondary Structures

In this paper we extend our theoretical studies dealing with the dependence of relative proton and carbon chemical shifts (CSs) of protein backbone atoms on their conformational position. In an earlier paper (A. Czajlik, I. Hudáky, A. Perczel, J Comp Chem 2011, 32, 3362) we reported on a fair agreement between calculated and observed backbone CSs as a function of backbone conformation. Applying the polarizable continuum model (PCM) in this work, we compare relative CSs of fully optimized alanine diamide conformers with gas phase calculations and experimental results. Along a path on the Ramachandran surface, we collated calculated relative CSs obtained with and without explicit water molecules, as well as with and without considering the PCM reaction field. Furthermore, we traced the energetically relevant reaction paths along the torsional angle ψ connecting the lowest energy minima (helical, extended, polyproline II and inverse γ-turn) on the Ramachandran plot, with the prospect to facilitate identifying them by their relative CSs. We found that consideration of the solvent effect of the environment around a diamide model improves the agreement with experimental findings on abundant conformers. This agreement is of the level achieved previously by a thorough gas phase investigation on considerably larger oligoalanine models. By relating DeltaδCα, DeltaδHα and DeltaδCβ values of polyproline II and inverse γ-turn to the experimentally well characterized helical and extended data, our calculations contribute to protein secondary structure prediction based on nuclear magnetic CS

Protein structure and dynamics

Proteins are essential components of biological processes, this explains why understanding their structure, function and dynamics is so important. In the following, we give an overview on various methods for the determination of three-dimensional structure and dynamics of proteins. We discuss the most important experimental methods, X-ray diffraction and NMR spectroscopy, as well as computer modelling techniques and their application to the construction of graphics models, which can be inspected visually. We also treat prediction as well as molecular graphics representation of protein structures. We devote special attention to dynamics, where time scales of protein movement, structures and interactions are discussed. We wish to demonstrate that protein structure determination and computer representation is now at a very high degree of sophistication and reliability

1H, 15N backbone assignment and comparative analysis of the wild type and G12C, G12D, G12V mutants of K-Ras bound to GDP at physiological pH

K-Ras protein is a membrane-bound small GTPase acting as a molecular switch. It plays a key role in many signal transduction pathways regulating cell proliferation, differentiation, survival, etc. It alternates between its GTP-bound active and the GDP-bound inactive conformers regulated by guanine nucleotide exchange factors and GTPase activating proteins. Its most frequent oncogenic mutants are G12C, G12D, and G12V that have impaired GTPase activity, thus induce malignant tumors. Here we report the resonance assignment of the backbone 1H and 15N nuclei of K-Ras wildtype, G12C, G12D and G12V proteins’ catalytic G domain (1–169 residues) in GDP-bound state, and 13C of backbone and side chains of G12C mutant at physiological pH 7.4. Triple resonance data were used to get secondary structure information and backbone dynamics of G12C, the best-known drug target among K-Ras mutants. Simultaneous investigation of G12C, G12D and G12V mutants, along with the wild type form at the very same conditions allowed us to perform a comprehensive analysis based on the combined chemical shifts to reveal the effect of mutation at G12 position on structure. Intriguingly, the G12C and G12V mutants found to be structurally very similar at the three most important regions of K-Ras (P-loop, Switch-I, Switch-II), while the G12D mutant significantly differs at P-loop and Switch-II from the wildtype as well as G12C and G12V mutants. However, in Switch-I it hardly deviates from the wildtype protein

The clear and dark sides of water: influence on the coiled coil folding domain

Abstract: The essential role of water in extra- and intra- cellular coiled coil structures of proteins is critically evaluated, and the different protein types incorporating coiled coil units are overviewed. The following subjects are discussed: i) influence of water on the formation and degradation of the coiled coil domain together with the stability of this conformer type; ii) the water’s paradox iii) design of coiled coil motifs and iv) expert opinion and outlook is presented. The clear and dark sides refer to the positive and negative aspects of the water molecule, as it may enhance or inhibit a given folding event. This duplic- ity can be symbolized by the Roman ‘Janus-face’ which means that water may facilitate and stimulate coiled coil structure formation, however, it may contribute to the fatal processes of oligomerization and amyloidosis of the very same polypeptide chain

A fehérjefeltekeredés alapjai: a feltekeredés, a letekeredés és az aggregáció vizsgálata atomi szintű kísérleti és számítási módszerekkel = Unifying principles of protein folding: understanding folding, unfolding and aggregation at atomic-level by experimental and computational methods

Célkitűzésünk a fehérjefeltekeredés és konformációs állapotváltozások mélyebb megértése, alkalmasan megválasztott modellrendszerek - azaz különböző méretű és belső dinamikájú fehérjék - vizsgálatán keresztül. A kémiailag vagy bakteriális úton előállított fehérjék szerkezeti és dinamikai paramétereinek meghatározását követően olyan új variánsokat tervezünk, amelyek vagy még rendezettebbek, vagy a belsőleg rendezetlen fehérjék esetében, még rendezetlenebbé váltak. A vizsgált mini-, moduláris fehérjék, valamint a funkcionálisan rendezetlen rendszerek körét olyan fontos molekulák alkották, amelyek közvetlen kapcsolatban állnak a cukorbetegség, az agyi neurodegeneratív elváltozások, vagy az immunológia különböző tárgykörével. Kutatásaink során mind a téralkat, mind a fehérjék belső mozgékonyságának explicit jellemzésén keresztül értettük meg jobban az adott makromolekulák biológiai szerepét, fiziológiás jelentőségét. A peptidek és fehérjék racionális tervezése során nem csak mutánsokat és variánsokat, de nem-természetes aminosavakból felépülő „foldamereket” is terveztünk, majd állítottunk elő. Vizsgáltuk a béta-aminosavak és béta-peptidek beépíthetőségét és felhasználhatóságát a téralkat és mozgékonyság függvényében. Eredményeinket 33 angol nyelvű közleményben (IF=116,984), webszervereken, és több mint 40 hazai és nemzetközi tudományos fórumon és konferencián adtuk közre. | Our aim was to decipher and better understand the molecular details of protein folding and conformational switching achieved via selected polyamide nanosystems of different size and internal dynamics. Once the structural parameters of the chemically synthesized or bacterially expressed proteins were determined, new variants and mutants were designed. Thus, the polypeptide chain was made either more ordered for globular proteins, or less structured for the disordered proteins (IDP). The investigated mini-, modular, globular and unstructured proteins are involved in biologically important cellular processes associated with either Diabetes Mellitus, neurodegenerative or immunological diseases. Our goal was to better understand the biological role and function of these proteins by monitoring both their structure (NMR and X-ray crystallography) and internal dynamics (NMR). The rational design of selected peptides and proteins resulted in not only mutants and variants of the parent macromolecule, but also foldamers. The applicability of beta amino acids and beta peptides were in focus. Our results were published in international journals (33 articles, IF=116,984), webservers, and presented on over 40 scientific meetings

Peptidek és moduláris fehérjék szerkezetvizsgálata NMR-spektroszkópiai és elméleti módszerek segítségével = Structure analysis of peptides and modular proteins by NMR-spectroscopy and theoretical methods

Munkánk során biológiai jelentőséggel bíró peptidek és fehérjék térszerkezetének és dinamikájának elemzését végeztük el NMR-spektroszkópiával. Megmutattuk, hogy az SGCI nevű proteázinhibitor egésze térszerkezeti/dinamikai változásokat szenved az enzimhez való kötődéskor. Valószínűsítettük a belső dinamika szerepét az immunrendszer egyik fehérjéjének (C1r) működésében. Racionális tervezéssel előállítottuk a Tc5b minifehérje stabilizált változatát. Feltérképeztük az SGTI proteázinhibitor esetében a fajspecifitást nem mutató változat térszerkezetét. Meghatároztuk továbbá a GnRHIII peptidhormon és néhány variánsa térszerkezetét. Kvantumkémiai számítások segítségével jellemeztük aminosavak (a metioinin és a hisztidin), valamint alfa- és béta-aminosavakból felépülő különböző peptidrendszerek stabilitását. Elemeztük a béta-redőzött és a poliprolin-II szerkezetek felépülésének energetikáját. Feltérképeztük az amiloid szerkezetek nagyfokú termodinamikai stabilitásának molekuláris szintű okait. Megmutattuk, hogy béta-peptidekből nanocső szerkezetek építhetőek, amelyek stabilitási viszonyai eltérnek az alfa-peptidekből felépülő ''béta-hordó'' szerkezetekétől. Feltérképeztük továbbá a kimotripszin enzim által katalizált reakció energetikai viszonyait kvantumkémiai módszerekkel. Elvégeztük 3 fehérjealkotó aminosav, a glicin, az alanin és a prolin diamidjának mátrixizolációs spektroszkópiai vizsgálatát is. | We have determined the structure and internal dynamics of biologically important peptides and proteins by NMR spectroscopy. We have shown that the portease inhibitor SGCI undergoes overal changes in ints tsructure/dynamics upon protease binding. Our results suggest important role of the internal dynamics in the immune proteins C1r. We have prepared a stabilized variant of the Tc5b miniprotein by rational design. We have solved the solution structure of an SGTI variant without taxon specificity. The structure of the peptide hormon GnRHIII and some of its variants were also determined. Using quantum chemical calculations, we have deciphered the conformational behaviour of amino acids (methionine and histidine) and alpha- and beta-peptide systems. We have analyzed the stability of beta-pleated sheet structures and collagen helices, and have deciphered the stability of amyloid structures. We have shown that beta-peptides are capable of forming nanotubes quite differently than alpha-peptide barrels. The catalytic mechanism of chymotrypsin was also investigated by quantum mechanics. We have also performed matrix isolation spectroscopy studies on three proteinogenic amino acids: glycin, alanine and proline

CoNSEnsX: an ensemble view of protein structures and NMR-derived experimental data

<p>Abstract</p> <p>Background</p> <p>In conjunction with the recognition of the functional role of internal dynamics of proteins at various timescales, there is an emerging use of dynamic structural ensembles instead of individual conformers. These ensembles are usually substantially more diverse than conventional NMR ensembles and eliminate the expectation that a single conformer should fulfill all NMR parameters originating from 10¹⁶- 10¹⁷molecules in the sample tube. Thus, the accuracy of dynamic conformational ensembles should be evaluated differently to that of single conformers.</p> <p>Results</p> <p>We constructed the web application CoNSEnsX (Consistency of NMR-derived Structural Ensembles with eXperimental data) allowing fast, simple and convenient assessment of the correspondence of the ensemble as a whole with diverse independent NMR parameters available. We have chosen different ensembles of three proteins, human ubiquitin, a small protease inhibitor and a disordered subunit of cGMP phosphodiesterase 5/6 for detailed evaluation and demonstration of the capabilities of the CoNSEnsX approach.</p> <p>Conclusions</p> <p>Our results present a new conceptual method for the evaluation of dynamic conformational ensembles resulting from NMR structure determination. The designed CoNSEnsX approach gives a complete evaluation of these ensembles and is freely available as a web service at <url>http://consensx.chem.elte.hu</url>.</p