Dynamics of unfolded polypeptide chains as model for the earliest steps in protein folding

The rate of formation of intramolecular interactions in unfolded proteins determines how fast conformational space can be explored during folding. Characterization of the dynamics of unfolded proteins is therefore essential for the understanding of the earliest steps in protein folding. We used triplet-triplet energy transfer to measure formation of intrachain contacts in different unfolded polypeptide chains. The time constants (1/k) for contact formation over short distances are almost independent of chain length, with a maximum value of about 5 ns for flexible glycine-rich chains and of 12 ns for stiffer chains. The rates of contact formation over longer distances decrease with increasing chain length, indicating different rate-limiting steps for motions over short and long chain segments. The effect of the amino acid sequence on local chain dynamics was probed by using a series of host-guest peptides. Formation of local contacts is only sixfold slower around the stiffest amino acid (proline) compared to the most flexible amino acid (glycine). Good solvents for polypeptide chains like EtOH, GdmCl and urea were found to slow intrachain diffusion and to decrease chain stiffness. These data allow us to determine the time constants for formation of the earliest intrachain contacts during protein folding.     

Prediction of probable pathways of folding in globular proteins

A method is described for the prediction of probable folding pathways of globular proteins, based on the analysis of distance maps. It is applicable to proteins of unknown spatial structure but known amino acid sequence as well as to proteins of known structure. It is based on an objective procedure for the determination of the boundary of compact regions that contain high densities of interresidue contacts on the distance map of a globular protein. The procedure can be used both with contact maps derived from a known three-dimensional protein structure and with predicted contact maps computed by means of a statistical procedure from the amino acid sequence alone. The computed contact map can also be used to predict the location of compact short-range structures, viz. -helices and -turns, thereby complementing other statistical predictive procedures. The method provides an objective basis for the derivation of a theoretically predicted pathway of protein folding, proposed by us earlier [Tanaka and Scheraga (1977) Macromolecules10, 291–304; Némethy and Scheraga (1979) Proc. Natl. Acad. Sci., U.S.A.76, 6050–6054].     

Fast Subdomain Folding Prior to the Global Refolding Transition of E. coli Adenylate Kinase: A Double Kinetics Study

The rate of folding of globular proteins depends on specific local and nonlocal intramolecular interactions. What is the relative role of these two types of interaction at the initiation of refolding? We address this question by application of a “double kinetics” method based on fast initiation of refolding of site specifically labeled protein samples and detection of the transient distributions of selected intramolecular distances by means of fast measurements of time‐resolved fluorescence resonance energy transfer. We determined the distribution of the distance between the ends of a 44‐chain segment that includes the AMP_bind domain, by labeling residues 28 and 71, in Escherichia coli adenylate kinase (AK) and the distribution of the distance between residues 18 and 203, which depends on the overall order of the molecule. That distribution shows two-state transition to the native intramolecular distance at the same rate as that of the cooperative refolding transition of the AK molecule. In sharp contrast, the distance distribution between residues 28 and 71 is already native like at the end of the dead-time of the mixing device. This fast formation of native short distance between two widely separated chain sections can be either dependent on fast folding of the AMP_bind domain or a result of a very effective nonlocal interaction between specific short clusters of hydrophobic residues. Further experiments on studying the kinetics of folding of selected structural elements in the protein will help determination of the driving force of this early folding event.     

Influence of chirality,amino acid sequence,and protecting groups on the intramolecular interaction behavior of dipeptide and tripeptide derivatives

The intramolecular interaction of protected dipeptides and tripeptides containing the amino acid units Ala, Phe, and Val was studied by means of ir spectroscopy. The NH and CO regions of the compounds dissolved in carbon tetrachloride clearly show the existence of different intramolecular hydrogen bonds. Using solvents with higher polarity such as chloroform and methylene chloride, the association bands disappear. Investigating the substances with the same amino acid sequence but opposite chirality of the central C atom in the peptide chain, we observed different band shapes in the CO and NH regions. Large effects were found when the chirality of the Phe unit in the second position was changed. This is probably due to the steric hindrance originated by the rotation of the aromatic ring in the side chain. The protecting groups, Z (benzyloxycarbonyl) or Boc (tert-butyloxycarbonyl) residues at the N-terminal group and methyl- or tert-butyl esters at the C-terminal group, influence the solubility of the substances in nonpolar solvent, as well as the NH and CO association band profiles in the methylene chloride solutions. The consequences of changing the sequence of the amino acids are discussed for the tripeptide derivatives. Besides a qualitative discussion, some quantitative considerations concerning the intramolecular interaction are also given to illustrate the different stabilities of the associates. © 1996 John Wiley & Sons, Inc.     

Protein Structures and Neutral Theory of Evolution

Abstract

The neutral theory of evolution is extended to the origin of protein molecules. Arguments are presented which suggest that the amino acid sequences of many globular proteins mainly represent “memorized” random sequences while biological evolution reduces to the “editing” these random sequences. Physical requirements for a functional globular protein are formulated and it is shown that many of these requirements do not involve strategical selection of amino acid sequences during biological evolution but are inherent also for typical random sequences. In particular, it is shown that random sequences of polar and unpolar amino acid residues can form α-helices and β-strands with lengths and arrangement along the chain similar to those in real globular proteins. These α- and β-regions in random sequences can form three-dimensional folding patterns also similar to those in real proteins. The arguments are presented suggesting that even the tight packing of side groups inside protein core do not require very strong biological selection of amino acid sequences either. Thus many structural features of real proteins can exist also in random sequences and the biological selection is needed mainly for the creation of active sites of proteins and for their stability under physiological conditions.     

Sequential resonance assignments in protein 1H nuclear magnetic resonance spectra: Computation of sterically allowed proton-proton distances and statistical analysis of proton-proton distances in single crystal protein conformations

Two different, theoretical studies of intramolecular proton-proton distances in polypeptide chains are described. Firstly, the distances between amide, C^α and C^β protons of neighbouring residues in the amino acid sequence, which correspond to the sterically allowed values for the dihedral angles φ_i, ψ_i and χ_i¹, were computed. Secondly, the frequency with which short distances occur between amide, C^α and C^β protons of neighbouring and distant residues in the amino acid sequence were statistically evaluated in a representative sample of globular protein crystal structures. Both approaches imply that semi-quantitative measurements of short, non-bonding proton-proton distances, e.g. by nuclear Overhauser experiments, should present a reliable and generally applicable method for sequential, individual resonance assignments in protein ¹H nuclear magnetic resonance spectra. Similar calculations imply that corresponding distance measurements can be used for resonance assignments in the side-chains of the aromatic amino acid residues, asparagine and glutamine, where the complete spin systems cannot usually be identified from through-bond spin-spin coupling connectivities.     

Dissecting the non-specific and specific components of the initial folding reaction of barstar by multi-site FRET measurements

Initial polypeptide chain collapse plays a major role in the development of subsequent structure during protein folding, but it has been difficult to elucidate the coupling between its cooperativity and specificity. To better understand this important aspect of protein folding, nine different intramolecular distances in the protein have been measured by fluorescence resonance energy transfer (FRET) in the product(s) of the initial, sub-millisecond collapse reaction during the folding of barstar, under different folding conditions. All nine distances contract in these initial folding products, when the denaturant concentration is reduced. Two of these distances were also measured in peptides corresponding to sequence segments 38-55 and 51-69 of the protein. Surprisingly, both distances do not contract in the peptides which remain fully unfolded when the denaturant concentration is reduced. This suggests that the contraction of at least some segments of the polypeptide chain may be facilitated only by contraction of other segments. In the case of the initial product of folding of the protein, the dependence on denaturant concentration of the relative change in each distance suggests that there are two components to the initial folding reaction. One is a nonspecific component, which appears to be driven by the change in denaturant concentration that is used to initiate refolding. This component corresponds to the collapse of completely unfolded protein (U) to unfolded protein in refolding conditions (U(C)). The extent of nonspecific collapse can be predicted by the response of completely unfolded protein to a change in denaturant concentration. All distances undergo such solvent-induced contraction, but each distance contracts to a different extent. There is also a specific component to initial sub-millisecond folding, in which some distances (but not all) contract more than that predicted by solvent-induced contraction. The observation that only some of the distances undergo contraction over and above solvent-induced contraction, suggest that this specific component is associated with the formation of a specific intermediate (I(E)). FRET efficiency and distance change differently for the different donor-acceptor pairs, with a change in denaturant concentration, indicating that the formation or dissolution of structure in U(C) and I(E) does not happen in a synchronized manner across different regions of the protein molecule. Also, all nine FRET efficiencies and intramolecular distances in the product(s) of sub-ms folding, change continuously with a change in denaturant concentration. Hence, it appears that the transitions from U to U(C) and to I(E) are gradual transformations, and not all-or-none structural transitions. Nevertheless, the product of these gradual transitions, I(E), possesses specific structure.     

Why do proteins divide into domains? Insights from lattice model simulations

It is known that larger globular proteins are built from domains, relatively independent structural units. A domain size seems to be limited, and a single domain consists of from few tens to a couple of hundred amino acids. Based on Monte Carlo simulations of a reduced protein model restricted to the face centered simple cubic lattice, with a minimal set of short-range and long-range interactions, we have shown that some model sequences upon the folding transition spontaneously divide into separate domains. The observed domain sizes closely correspond to the sizes of real protein domains. Short chains with a proper sequence pattern of the hydrophobic and polar residues undergo a two-state folding transition to the structurally ordered globular state, while similar longer sequences follow a multistate transition. Homopolymeric (uniformly hydrophobic) chains and random heteropolymers undergo a continuous collapse transition into a single globule, and the globular state is much less ordered. Thus, the factors responsible for the multidomain structure of proteins are sufficiently long polypeptide chain and characteristic, protein-like, sequence patterns. These findings provide some hints for the analysis of real sequences aimed at prediction of the domain structure of large proteins.     

YspD: A Potential Therapeutic Target for Drug Design to Combat Yersinia enterocolitica Infection

YspD is an annotated hydrophilic translocator of Ysa–Ysp type III secretion system of Yersinia enterocolitica. YspD has sequence, secondary structure and three-dimensional structure similar to other hydrophilic translocators. All hydrophilic translocators lack transmembrane region and possess intramolecular coiled-coil region. Disordered regions are mostly clustered at the N-terminal. Large loops provide flexibility, allowing conformational changes during oligomerization and protein–protein interaction. LcrV and PcrV have globular N-terminal and C-terminal domains, connected by intramolecular coiled-coil region. YspD, IpaD, SipD and BipD lack globular N-terminal and C-terminal domains. Their N-terminal and C-terminal domain have a bundle like structure connected by the intramolecular coiled-coil. The intramolecular coiled-coil regions (helix-5&9) of YspD showed maximum conservation, followed by helices at N-terminal. Polar interactions are mainly involved during dimerization of YspD, involving polar residues from helix-9 of both the YspD molecules. A methionine forms the boundary of interaction between the two YspD molecules. The two YspD molecules are arranged in antiparallel fashion to form the dimer. N-terminal of YspB interacted with C-terminal of YspD molecule to form a pentameric complex, consisting four YspD molecules and one YspB molecule. Sequence, structural similarity and presence of specific motifs in YspD (like chaperone protein) indicate the ability of N-terminal domain to show self-chaperoning activity and regulate folding and conformational state of YspD during its journey from the bacterial cytoplasm to the needle tip. Structural analysis of YspD and its mechanism of interaction with other proteins would enable us to design drugs against this hydrophilic protein to combat Yersinia infection.

     

Monte Carlo studies on equilibrium globular protein folding. I. Homopolymeric lattice models of beta-barrel proteins

Dynamic Monte Carlo studies have been performed on various diamond lattice models of β-proteins. Unlike previous work, no bias toward the native state is introduced; instead, the protein is allowed to freely hunt through all of phase space to find the equilibrium conformation. Thus, these systems may aid in the elucidation of the rules governing protein folding from a given primary sequence; in particular, the interplay of short- vs long-range interaction can be explored. Three distinct models (A? C) were examined. In model A, in addition to the preference for trans (t) over gauche states (g⁺ and g^?) (thereby perhaps favoring β-sheet formation), attractive interactions are allowed between all nonbonded, nearest neighbor pairs of segments. If the molecules possess a relatively large fraction of t states in the denatured form, on cooling spontaneous collapse to a well-defined β-barrel is observed. Unfortunately, in model A the denatured state exhibits too much secondary structure to correctly model the globular protein collapse transition. Thus in models B and C, the local stiffness is reduced. In model B, in the absence of long-range interactions, t and g states are equally weighted, and cooperativity is introduced by favoring formation of adjacent pairs of nonbonded (but not necessarily parallel) t states. While the denatured state of these systems behaves like a random coil, their native globular structure is poorly defined. Model C retains the cooperativity of model B but allows for a slight preference of t over g states in the short-range interactions. Here, the denatured state is indistinguishable from a random coil, and the globular state is a well-defined β-barrel. Over a range of chain lengths, the collapse is well represented by an all-or-none model. Hence, model C possesses the essential qualitative features observed in real globular proteins. These studies strongly suggest that the uniqueness of the globular conformation requires some residual secondary structure to be present in the denatured state.     

Kinetic analysis of local structure formations in protein folding

The protein folding process is described by a cluster model based on the assumption that local structures or clusters are formed at an early stage in different regions of the polypeptide chain. Possible local structural elements in a globular protein are helices, bends, and hydrophobic cores whose formation is presumably determined by the interaction with the environment. Thus the tendency of local structure formation is expressed by a surface free energy of the cluster, which is assigned to the interface between the cluster and its environment. The probability of finding the chain of N residues with k clusters and m residues in the cluster is represented by a cluster distribution map. The cluster model exhibits a distinct two-state-like equilibrium transition, which can be seen on this map as well-separated native and denatured populations at the midpoint of the transition. The native population is localized at k ≈ 1 and m ≈ N, while the position of the denatured population can vary significantly depending on the surface free energy of the cluster. If the surface free energy is strong, the denatured population is localized near k = 0 and m = 0. On the other hand, if the surface free energy is weak, the denatured population is localized at high k and m values. The dynamics of the cluster model are treated as a stochastic process involving the transition from a state (k,m) to one of its six neighbors. The transition probability for each transition is determined by the free energy difference between two states; thus no activation process is assumed. However, the conversion of the two macrostates, native and denatured populations, involves the free energy activation due to the cooperative interaction of the macrosystem. The dynamics are analyzed by following the time evolution of the population profile on the cluster distribution map. Kinetic schemes are proposed to describe the multistep mechanism of protein folding and unfolding.     

Stabilization of short helices by intramolecular cluster formation

The intramolecular formation of multiple clusters of interacting helices has been characterized in a homopolymer. The configuration partition function permits the formation of clusters in which the number of interacting helices may be as large as the greatest integer in n/2, where n denotes the number of amino acid residues in the chain. The theoretical formulation has its origin in a recent [Mattice, W. L. & Scheraga, H. A. (1984) Biopolymers 23 , 1701–1724], tractable matrix expression for the configuration partition function for intramolecular antiparallel β-sheet formation. Reassignment of the expression for one of the n(n+3)/2 elements in the sparse statistical weight matrix, along with a simple change in notation, converts that treatment into a matrix formulation of the configuration partition function for a chain containing multiple clusters of interacting antiparallel helices. The five statistical weights used are δ, f_l, w, and the Zimm-Bragg σ and s. Each tight bend that connects two interacting helices contributes a factor of δ, f_l is used in the weight for larger loops between interacting helices, and w arises from helix–helix interaction. The influence of the helix–helix interaction is well illustrated by two helix–coil transitions in a chain with n = 156 and σ = 0.001. In the absence of helix–helix interaction, the transition occurs by the nucleation and subsequent elongation of a small number of helices. When helix–helix interaction is attractive, the transition can occur by a different mechanism. Formation of a single pair of interacting helices is followed by addition of new helices to the initial cluster. In the latter process, individual helices experience relatively little growth after they are formed.     

Nonradiative energy transfer in oligopeptide chains generated by a monte-cralo mehod including long-range interactions

A Monte-Carlo method including long-range interactions is used to oligopeptide chains in random-coil state. The chains are composed of 4, 9, or 14 repeating units and are labeled with the luminopheres tyrosine or tryptophan. Interactions with a solvent (water) are taken into account in the calculations through modifications of the semiempirical potential-energy functions. The chains represent oligopeptides composed of hydrophobic or hydrophilic amino acid residues. Various properties relavent to the interpretaiton of nonradiative enrgy-transfer experiments, such as the average value of the orientation factor for dipole-dipole interaction of the luminophores, 〈k²〉, the distribution function of the distances between the luminophores f(r_l), the efficiences of energy transfer in the static and dyamic averaging regimes, 〈T〉_s amnd 〈T〉_d, as well as the fluorescence decay I(t) of the donor luminophore in various averaging conditions, are computed. It is shown that, for all chains considered, 〈k²〉 is not vary far form 0.67 and that 〈T〉_s and 〈T〉_d have completely different values. Due to the small extent of correlation between the distances r_l and the mutual orientations of the lumninophores, the decay kinetics 〈I(t)_s corresponding to a static averaging regime can be expressed in terms of distribution functions f(r_l). These results are in agrrement with those obtained previously for the unperturbed chain model.     

Single amino acid mutations block a late step in the folding of beta-lactamase from Staphylococcus aureus

Two single amino acid mutant proteins of beta-lactamase PC1 from Staphylococcus aureus, P2 Thr40----Ile and P54 Asp146----Asn, have been investigated using urea-gradient polyacrylamide gel electrophoresis, circular dichroism and sedimentation velocity. Investigation of the folded states of the mutants has shown that compared to wild-type PC1 they are slightly more expanded, and have reduced aromatic circular dichroism, but the same content of secondary structure as PC1. The mutants exhibit fast refolding kinetics to the folded state, in contrast to PC1, which refolds only slowly. We conclude from these results that the folded mutants are in a state close to but distinct from the native state of PC1 and have certain properties in common with the compact intermediate in the folding of beta-lactamase. Therefore, these single amino acid substitutions result in a folding pathway blocked at a point located after collapse of the already folded structural units into a globular shape, and close to the final reshuffling step that leads to the native state of the wild-type enzyme.     

Amino acid replacements can selectively affect the interaction energy of autonomous folding units in the alpha subunit of tryptophan synthase.

Amino acid replacements were made at the interface between two autonomous folding units in the alpha subunit of tryptophan synthase from Salmonella typhimurium to test their mutual interaction energy. The results of equilibrium studies of the urea-induced unfolding reaction of the wild-type and mutant proteins in which phenylalanine 22 is replaced by leucine, isoleucine, and valine can be understood in terms of a selective decrease in the interaction energy between the two folding units; the intrinsic stability of each folding unit is not significantly altered. Kinetic studies of the rate-limiting step in unfolding show that the interaction energy appears in the transition state preceding the native conformation. Comparisons of the individual effects of these nonpolar side chains show that both hydrophobic and steric effects play important roles in the interaction energy between the folding units. The implication of these results is that the high cooperativity observed in the folding of many globular proteins may be reduced by appropriate amino acid replacements.     

Functional unit of the Rapana thomasiana (grosse) (marine snail, gastropod) hemocyanin

The amino terminal functional unit (domain a) of the Rapana hemocyanin “heavy” structural subunit, designated as Rta, was obtained after limited trypsinolysis of the whole polypeptide chain. Mass spectrometric analysis showed a molecular mass of 49,698 daltons for the electrophoretically homogeneous fragment. Twenty-five amino acid residues were sequenced directly from the N-terminus of Rta, which allowed the location of the domain in the polypeptide chain of the subunit. Physicochemical parameters were determined by absorption and fluorescence spectroscopy and circular dichroism. Comparison with the respective parameters of the whole Rapana hemocyanin showed that the polypeptide backbone folding, binuclear active site and capability of oxygen binding of the isolated functional unit are identical to those of the native hemocyanin. Comparison of N-terminal sequences of functional units from different molluskan hemocyanins and located at different positions revealed some evolutionary relationships.     

Investigation of protein folding: uneven distribution of point mutations along polypeptide chains.

The distribution of point mutations accepted by natural selection in the amino acid sequences of 16 cytochrome-C, 7 lysozyme, 15 myoglobin, 10 ribonuclease, 12 short neurotoxin, 16 plant ferredoxin and 6 bacterial ferredoxin molecules have been investigated.The number of point mutations shows an increasing tendency from the NH₂-terminus towards the COON-terminus of these proteins or at least within their structural domains.Our results suggest that the continuous folding of polypeptide chain during biosynthesis may play an important role in the formation of globular protein structure.     

DNA Triplex‐Mediated Assembly of Polyaromatic Chromophores

The synthesis and characterization of intramolecular triple‐helical DNA structures containing polyaromatic pyrene and perylene (perylenetetracarboxylic acid diimide, PDI) building blocks are presented. Two 1,8‐dialkynylpyrene units are located in the Watson? Crick stem of the construct, while a PDI or a natural thymidine is present in the Hoogsteen strand. The triple helical structures were investigated by UV/VIS absorbance, fluorescence spectroscopy, and circular dichroism (CD) measurements. The folding of the intramolecular triple helix can be monitored by changes in the vibronic transition ratios, as well as by a change in the alkynylpyrene fluorescence (monomer vs. excimer). It is shown that thymine in the third strand has a pronounced influence on the interaction and, thus, on the fluorescence properties of two pyrene building blocks.     

Early Closure of a Long Loop in the Refolding of Adenylate Kinase: A Possible Key Role of Non-Local Interactions in the Initial Folding Steps

Most globular protein chains, when transferred from high to low denaturant concentrations, collapse instantly before they refold to their native state. The initial compaction of the protein molecule is assumed to have a key effect on the folding pathway, but it is not known whether the earliest structures formed during or instantly after collapse are defined by local or by non-local interactions—that is, by secondary structural elements or by loop closure of long segments of the protein chain. Stable closure of one or several long loops can reduce the chain entropy at a very early stage and can prevent the protein from following non-productive pathways whose number grows exponentially with the length of the protein chain. In Escherichia coli adenylate kinase (AK), about seven long loops define the topology of the native structure. We selected four loop-forming sections of the chain and probed the time course of loop formation during refolding of AK. We labeled the termini of the loop segments with tryptophan and cysteine-5-amidosalicylic acid. This donor-acceptor pair of probes used with fluorescence resonance excitation energy transfer spectroscopy (FRET) is suitable for detecting very short distances and thus is able to distinguish between random and specific compactions. Refolding of AK was initiated by stopped-flow mixing, followed simultaneously by donor and acceptor fluorescence, and analyzed in terms of energy transfer efficiency and distance. In the collapsed state of AK, observed after the 5-ms dead time of the instrument, one of the selected segments shows a native-like separation of its termini; it forms a loop already in the collapsed state. A second segment that includes the first but is longer by 15 residues shows an almost native-like separation of its termini. In contrast, a segment that is shorter but part of the second segment shows a distance separation of its termini as high as a segment that spans almost the whole protein chain. We conclude that a specific network of non-local interactions, the closure of one or several loops, can play an important role in determining the protein folding pathway at its early phases.