Optimal ratio between the average conformational entropy and the average energy of interaction between residues for fast protein folding

Based on available experimental data and using a theoretical model of protein folding, we demonstrate that there is an optimal ratio between the average conformational entropy and the average contact energy per residue for fast protein folding. A statistical analysis of the conformational entropy and the number of contacts per residue for 5829 protein domains from four main classes (α, β, α/β, α+β) shows that each class has its own characteristic average number of contacts per residue and average conformational entropy per residue. These class-specific characteristics determine the protein folding rates: α-proteins are the fastest to fold, β-proteins are the second fastest, α+β-proteins are the third, and α/β-proteins are the last to fold.     

A novel structural tree for wrap-proteins,a subclass of (α+β)-proteins

In this paper, a novel structural subclass of (α+β)-proteins is presented. A characteristic feature of these proteins and domains is that they consist of strongly twisted and coiled β-sheets wrapped around one or two α-helices, so they are referred to here as wrap-proteins. It is shown that overall folds of the wrap-proteins can be obtained by stepwise addition of α-helices and/or β-strands to the strongly twisted and coiled β-hairpin taken as the starting structure in modeling. As a result of modeling, a structural tree for the wrap-proteins was constructed that includes 201 folds of which 49 occur in known nonhomologous proteins.     

Radius of gyration is indicator of compactness of protein structure

Search and study of the general principles that govern kinetics and thermodynamics of protein folding generate a new insight into the factors controlling this process. Statistical analysis of radii of gyration for 3769 protein structures from four general structural classes (all-alpha, all-beta, alpha/beta, alpha + beta) demonstrates that each class of proteins has its own class-specific radius of gyration, which determines compactness of protein structures: alpha-proteins have the largest radius of gyration. This indicates that they are less tightly packed than beta- and alpha + beta-proteins. Finally, alpha/beta-proteins are the most tightly packed proteins with the least radius of gyration. It should be underlined that radius of gyration normalized on the radius of gyration of ball with the same volume, is independent of the length in comparison with such parameters as compactness and number of contacts per residue.     

Origins of structural diversity within sequentially identical hexapeptides

Efforts to predict protein secondary structure have been hampered by the apparent structural plasticity of local amino acid sequences. Kabsch and Sander (1984, Proc. Natl. Acad. Sci. USA 81, 1075–1078) articulated this problem by demonstrating that identical pentapeptide sequences can adopt distinct structures in different proteins. With the increased size of the protein structure database and the availability of new methods to characterize structural environments, we revisit this observation of structural plasticity. Within a set of proteins with less than 50% sequence identity, 59 pairs of identical hexapeptide sequences were identified. These local structures were compared and their surrounding structural environments examined. Within a protein structural class (α/α, β/β, α/β, α + β), the structural similarity of sequentially identical hexapeptides usually is preserved. This study finds eight pairs of identical hexapeptide sequences that adopt β-strand structure in one protein and α-helical structure in the other. In none of the eight cases do the members of these sequence pairs come from proteins within the same folding class. These results have implications for class dependent secondary structure prediction algorithms.     

Structural trees for protein superfamilies

Structural trees for large protein superfamilies, such as β proteins with the aligned β sheet packing, β proteins with the orthogonal packing of α helices, two-layer and three-layer α/β proteins, have been constructed. The structural motifs having unique overall folds and a unique handedness are taken as root structures of the trees. The larger protein structures of each superfamily are obtained by a stepwise addition of α helices and/or β strands to the corresponding root motif, taking into account a restricted set of rules inferred from known principles of the protein structure. Among these rules, prohibition of crossing connections, attention to handedness and compactness, and a requirement for α helices to be packed in α-helical layers and β strands in β layers are the most important. Proteins and domains whose structures can be obtained by stepwise addition of α helices and/or β strands to the same root motif can be grouped into one structural class or a superfamily. Proteins and domains found within branches of a structural tree can be grouped into subclasses or subfamilies. Levels of structural similarity between different proteins can easily be observed by visual inspection. Within one branch, protein structures having a higher position in the tree include the structures located lower. Proteins and domains of different branches have the structure located in the branching point as the common fold. Proteins 28:241–260, 1997. © 1997 Wiley-Liss Inc.     

Comparing atomistic molecular mechanics force fields for a difficult target: a case study on the Alzheimer’s amyloid β-peptide

Macromolecular function arises from structure, and many diseases are associated with misfolding of proteins. Molecular simulation methods can augment experimental techniques to understand misfolding and aggregation pathways with atomistic resolution, but the reliability of these predictions is a function of the parameters used for the simulation. There are many biomolecular force fields available, but most are validated using stably folded structures. Here, we present the results of molecular dynamics simulations on the intrinsically disordered amyloid β-peptide (Aβ), whose misfolding and aggregation give rise to the symptoms of Alzheimer’s disease. Because of the link between secondary structure changes and pathology, being able to accurately model the structure of Aβ would greatly improve our understanding of this disease, and it may facilitate application of modeling approaches to other protein misfolding disorders. To this end, we compared five popular atomistic force fields (AMBER03, CHARMM22 + CMAP, GROMOS96 53A6, GROMOS96 54A7, and OPLS-AA) to determine which could best model the structure of Aβ. By comparing secondary structure content, NMR shifts, and radius of gyration to available experimental data, we conclude that AMBER03 and CHARMM22 + CMAP over-stabilize helical structure within Aβ, with CHARMM22 + CMAP also producing elongated Aβ structures, in conflict with experimental findings. OPLS-AA, GROMOS96 53A6, and GROMOS96 54A7 produce very similar results in terms of helical and β-strand content, calculated NMR shifts, and radii of gyration that agree well with experimental data.     

Folding type-specific secondary structure propensities of amino acids,derived from α-helical, β-sheet, α/β, and α+β proteins of known structures

Folding type-specific secondary structure propensities of 20 naturally occurring amino acids have been derived from α-helical, β-sheet, α/β, and α+β proteins of known structures. These data show that each residue type of amino acids has intrinsic propensities in different regions of secondary structures for different folding types of proteins. Each of the folding types shows markedly different rank ordering, indicating folding type-specific effects on the secondary structure propensities of amino acids. Rigorous statistical tests have been made to validate the folding type-specific effects. It should be noted that α and β proteins have relatively small α-helices and β-strands forming propensities respectively compared with those of α+β and α/β proteins. This may suggest that, with more complex architectures than α and β proteins, α+β and α/β proteins require larger propensities to distinguish from interacting α-helices and β-strands. Our finding of folding type-specific secondary structure propensities suggests that sequence space accessible to each folding type may have differing features. Differing sequence space features might be constrained by topological requirement for each of the folding types. Almost all strong β-sheet forming residues are hydrophobic in character regardless of folding types, thus suggesting the hydrophobicities of side chains as a key determinant of β-sheet structures. In contrast, conformational entropy of side chains is a major determinant of the helical propensities of amino acids, although other interactions such as hydrophobicities and charged interactions cannot be neglected. These results will be helpful to protein design, class-based secondary structure prediction, and protein folding. © 1998 John Wiley & Sons, Inc. Biopoly 45: 35–49, 1998     

Probing protein fold space with a simplified model

We probe the stability and near-native energy landscape of protein fold space using powerful conformational sampling methods together with simple reduced models and statistical potentials. Fold space is represented by a set of 280 protein domains spanning all topological classes and having a wide range of lengths (33-300 residues) amino acid composition and number of secondary structural elements. The degrees of freedom are taken as the loop torsion angles. This choice preserves the native secondary structure but allows the tertiary structure to change. The proteins are represented by three-point per residue, three-dimensional models with statistical potentials derived from a knowledge-based study of known protein structures. When this space is sampled by a combination of parallel tempering and equi-energy Monte Carlo, we find that the three-point model captures the known stability of protein native structures with stable energy basins that are near-native (all α: 4.77 Å, all β: 2.93 Å, α/β: 3.09 Å, α+β: 4.89 Å on average and within 6 Å for 71.41%, 92.85%, 94.29% and 64.28% for all-α, all-β, α/β and α+β, classes, respectively). Denatured structures also occur and these have interesting structural properties that shed light on the different landscape characteristics of α and β folds. We find that α/β proteins with alternating α and β segments (such as the β-barrel) are more stable than proteins in other fold classes.     

Balancing the Production of Two Recombinant Proteins inEscherichia coliby Manipulating Plasmid Copy Number: High-Level Expression of Heterodimeric Ras Farnesyltransferase

The native Ras farnesyltransferase heterodimer (αβ) and a heterodimer with a truncated α subunit (α′β) were overproduced at a high level and in a soluble form inEscherichia coli.The α, α′, and β subunits were synthesized from individual plasmid vectors under the control of bacteriophage T7 promoters. Although each subunit could be expressed at a high level by itself, when either the α or α′ and the β plasmid were present in cells at the same time, the α and α′ subunits were preferentially expressed to such a degree that little or none of the β subunit accumulated. A satisfactory balance between both combinations of subunits (αβ and α′β) was achieved by making incremental adjustments in the copy number of the β-encoding plasmid. As the copy number of the β plasmid increased, so did the ratio of β:α or β:α′, but there was little difference in the total amount of recombinant protein (α + β or α′ + β) that was produced. This may be a generally useful method for balancing the production of two recombinant polypeptides inE. coli.A noteworthy advantage of this approach is that it can be undertaken without first determining the cause of the imbalance.     

α-Helical burst on the folding pathway of FHA domains from Rad53 and Ki67

We investigated refolding processes of β-sheeted protein FHA domains (FHA1 domain of Rad53 and Ki67 FHA domain) by cryo-stopped-flow (SF) method combined with far-ultraviolet (far-UV) circular dichroism (CD, the average secondary structure content) and small angle X-ray scattering (SAXS, measuring the radius of gyration). In case of FHA1 domain of Rad53, no detectable time course was observed except the initial burst on its refolding process at 4 °C, suggesting that the FHA1 domain of Rad53 was already refolded to its native state within the dead time of the SF apparatus and the rate of the refolding is too fast to be observed at this temperature. In contrast, there was an observable α-helical burst at −15 °C and −20 °C in the presence of 45% ethylene glycol (EGOH) by CD-SF. Besides, the radius of gyration (Rg) of the burst phase intermediate at −20 °C shows the intermediate is already compact, and the compaction process was accompanied with the decrease of α-helical content at the same temperature.     

A Transmembrane Polar Interaction Is Involved in the Functional Regulation of Integrin αLβ2

Integrins are heterodimeric transmembrane (TM) receptors formed by noncovalent associations of α and β subunits. Each subunit contains a single α-helical TM domain. Inside-out activation of an integrin involves the separation of its cytoplasmic tails, leading to disruption of αβ TM packing. The leukocyte integrin αLβ2 is required for leukocyte adhesion, migration, proliferation, cytotoxic function, and antigen presentation. In this study, we show by mutagenesis experiments that the packing of αLβ2 TMs is consistent with that of the integrin αIIbβ3 TMs. However, molecular dynamics simulations of αLβ2 TMs in lipids predicted a polar interaction involving the side chains of αL Ser1071 and β2 Thr686 in the outer-membrane association clasp (OMC). This is supported by carbonyl vibrational shifts observed in isotope-labeled αLβ2 TM peptides that were incorporated into lipid bilayers. Molecular dynamics studies simulating the separation of αLβ2 tails showed the presence of polar interaction during the initial perturbation of the inner-membrane association clasp. When the TMs underwent further separation, the polar interaction was disrupted. OMC polar interaction is important in regulating the functions of β2 integrins because mutations that disrupt the OMC polar interaction generated constitutively activated αLβ2, αMβ2, and αXβ2 in 293T transfectants. We also show that the expression of mutant β2 Thr686Gly in β2-deficient T cells rescued cell adhesion to intercellular adhesion molecule 1, but the cells showed overt elongated morphologies in response to chemokine stromal-cell-derived factor 1α treatment as compared to wild-type β2-expressing cells. These two TM polar residues are totally conserved in other members of the β2 integrins in humans and across different species. Our results provide an example of the stabilizing effect of polar interactions within the low dielectric environment of the membrane interior and demonstrate its importance in the regulation of αLβ2 function.     

Leukocyte integrin αLβ2 transmembrane association dynamics revealed by coarse-grained molecular dynamics simulations

Integrins are transmembrane (TM) proteins that mediate bidirectional mechanical signaling between the extracellular matrix and the cellular cytoskeletal network. Each integrin molecule consists of non-covalently associated α- and β-subunits, with each subunit consisting of a large ectodomain, a single-pass TM helix, and a short cytoplasmic tail. Previously we found evidence for a polar interaction (hydrogen bond) in the outer membrane clasp (OMC) of the leukocyte integrin αLβ2 TMs that is absent in the platelet integrin αIIβ3 OMC. Here, we compare the self-assembly dynamics of αLβ2 and αIIβ3 TM helices in a model membrane using coarse-grained molecular dynamics simulations. We found that although αIIβ3 TM helices associate more easily, packing is suboptimal. In contrast, αLβ2 TM helices achieve close-to-optimal packing. This suggests that αLβ2 TM packing is more specific, possibly due to the interhelix hydrogen bond. Theoretical association free energy profiles show a deeper minimum at a smaller helix-helix separation for αLβ2 compared with αIIβ3. The αIIβ3 profile is also more rugged with energetic barriers whereas that of αLβ2 is almost without barriers. Disruption of the interhelix hydrogen bond in αLβ2 via the β2T686G mutation results in poorer association and a similar profile as αIIβ3. The OMC polar interaction in αLβ2 thus plays a significant role in the packing of the TM helices.     

Novel structural tree of (α + β)-proteins containing abCd units

A database of 926 (α + β)-proteins and (α + β)-domains containing abCd units, including 401 non-homologous, was compiled from the Protein Data Bank (total of 2636 PDB entries). A novel structural tree of this structural class of proteins was constructed to include 286 possible polypeptide chain folds. A structural classification of (α + β)-proteins containing abCd unit was developed on the basis of the structural tree. The database and the structural tree are available at http://strees.protres.ru/.     

Analysis and prediction of the packing of α-helices against a β-sheet in the tertiary structure of globular proteins

The packing of α-helices and β-sheets in six $\text{α}\text{β}$ proteins (e.g. flavodoxin) has been analysed. The results provide the basis for a computer algorithm to predict the tertiary structure of an $\text{α}\text{β}$ protein from its amino acid sequence and actual assignment of secondary structure.The packing of an individual α-helix against a β-sheet generally involves two adjacent ± 4 rows of non-polar residues on the α-helix at the positions i, i + 4, i + 8, i + 1, i + 5, i + 9. The pattern of interacting β-sheet residues results from the twisted nature of the sheet surface and the attendant rotation of the side-chains. At a more detailed level, four of the α-helical residues (i + 1, i + 4, i + 5 and i + 8) form a diamond that surrounds one particular β-sheet residue, generally isoleucine, leucine or valine. In general, the α-helix sits 10 Å above the sheet and lies parallel to the strand direction.The prediction follows a combinational approach. First, a list of possible β-sheet structures (10⁶ to 10¹⁴) is constructed by the generation of all β-sheet topologies and β-strand alignments. This list is reduced by constraints on topology and the location of non-polar residues to mediate the sheet/helix packing, and then rank-ordered on the extent of hydrogen bonding. This algorithm was uniformly applied to 16 $\text{α}\text{β}$ domains in 13 proteins. For every structure, one member of the reduced list was close to the crystal structure; the root-mean-square deviation between equivalenced C^α atoms averaged 5.6 Å for 100 residues. For the $\text{α}\text{β}$ proteins with pure parallel β-sheets, the total number of structures comparable to or better than the native in terms of hydrogen bonds was between 1 and 148. For proteins with mixed β-sheets, the worst case is glyceraldehyde-3-phosphate dehydrogenase, where as many as 3800 structures would have to be sampled. The evolutionary significance of these results as well as the potential use of a combinatorial approach to the protein folding problem are discussed.     

Recognition of nucleoplasmin by its nuclear transport receptor importin α/β: insights into a complete import complex

Nuclear import of the pentameric histone chaperone nucleoplasmin (NP) is mediated by importin α, which recognizes its nuclear localization sequence (NLS), and importin β, which interacts with α and is in charge of the translocation of the NP/α/β complex through the nuclear pore. Herein, we characterize the assembly of a functional transport complex formed by full-length NP with importin α/β. Isothermal titration calorimetry (ITC) was used to analyze the thermodynamics of the interactions of importin α with β, α with NP, and the α/β heterodimer with NP. Our data show that binding of both importin α and α/β to NP is governed by a favorable enthalpic contribution and that NP can accommodate up to five importin molecules per NP pentamer. Phosphomimicking mutations of NP, which render the protein active in histone chaperoning, do not modulate the interaction with importin. Using small-angle X-ray scattering, we model the α/β heterodimer, NP/α, and NP/α/β solution structures, which reveal a glimpse of a complete nuclear import complex with an oligomeric cargo protein. The set of alternative models, equally well fitting the scattering data, yields asymmetric elongated particles that might represent consecutive geometries the complex can adopt when stepping through the nuclear pore.     

一个α,β地中海贫血复合家系β珠蛋白基因的进一步研究

 前文~[1]曾报道广西一个α,β地中海贫血复合家系的血红蛋白组成及α珠蛋白基因分析结果,并讨论了各成员可能的β珠蛋白基因结构情况。本文利用先进的PCR即基因扩增技术,结合特异寡核苷酸探针斑点杂交及扩增后直接测定DNA序列的技术,进一步研究并彻底搞请了该家系各成员的β珠蛋白基因结构情况。结果显示:母亲及两个弟弟都是编码子41—42TTCT四个碱基缺失造成框架位移所致β地中海贫血的杂合子。父亲与先证者的β基因均属正常。前三个成员均为α地贫复合β地贫,其α与β珠蛋白链合成的不均衡状态得到改善,贫血症状也明显轻。     

Subunit isoform selectivity in assembly of Na,K-ATPase α-β heterodimers

To catalyze ion transport, the Na,K-ATPase must contain one α and one β subunit. When expressed by transfection in various expression systems, each of the four α subunit isoforms can assemble with each of the three β subunit isoforms and form an active enzyme, suggesting the absence of selective α-β isoform assembly. However, it is unknown whether in vivo conditions the α-β assembly is random or isoform-specific. The α(2)-β(2) complex was selectively immunoprecipitated by both anti-α(2) and anti-β(2) antibodies from extracts of mouse brain, which contains cells co-expressing multiple Na,K-ATPase isoforms. Neither α(1)-β(2) nor α(2)-β(1) complexes were detected in the immunoprecipitates. Furthermore, in MDCK cells co-expressing α(1), β(1), and β(2) isoforms, a greater fraction of the β(2) subunits was unassembled with α(1) as compared with that of the β(1) subunits, indicating preferential association of the α(1) isoform with the β(1) isoform. In addition, the α(1)-β(2) complex was less resistant to various detergents than the α(1)-β(1) complex isolated from MDCK cells or the α(2)-β(2) complex isolated from mouse brain. Therefore, the diversity of the α-β Na,K-ATPase heterodimers in vivo is determined not only by cell-specific co-expression of particular isoforms, but also by selective association of the α and β subunit isoforms.     

Folding simulations of three proteins having all α-helix,all β-strand and α/β-structures

We performed folding simulations of three proteins using four force fields, AMBER parm96, AMBER parm99, CHARMM 27 and OPLS-AA/L, in order to examine the features of these force fields. We studied three proteins, protein A (all α-helix), cold-shock protein (all β-strand) and protein G (α/β-structures), for the folding simulations. For the simulation, we used the simulated annealing molecular dynamics method, which was performed 50 times for each protein using the four force fields. The results showed that the secondary-structure-forming tendencies are largely different among the four force fields. AMBER parm96 favours β-bridge structures and extended β-strand structures, and AMBER parm99 favours α-helix structures and 3₁₀-helix structures. CHARMM 27 slightly favours α-helix structures, and there are also π-helix and β-bridge structures. OPLS-AA/L favours α-helix structures and 3₁₀-helix structures.