Inter-residue Average Distance Statistics Research Articles

Analyses of the folding sites of irregular \u03b2-trefoil fold proteins through sequence-based techniques and G\u014d-model simulations

BackgroundThe details of the folding mechanisms have not yet been fully understood for many proteins, and it is believed that the information on the folding mechanism of a protein is encoded in its amino acid sequence. β-trefoil proteins are known to have the same 3D scaffold, namely, a three-fold symmetric scaffold, despite the proteins’ low sequence identity among superfamilies. In this study, we extract an initial folding unit from the amino acid sequences of irregular β-trefoil proteins by constructing an average distance map (ADM) and utilizing inter-residue average distance statistics to determine the relative contact frequencies for residue pairs in terms of F values. We compare our sequence-based prediction results with the packing between hydrophobic residues in native 3D structures and a Gō-model simulation.ResultsThe ADM and F-value analyses predict that the N-terminal and C-terminal regions are compact and that the hydrophobic residues at the central region can be regarded as an interaction center with other residues. These results correspond well to those of the Gō-model simulations. Moreover, our results indicate that the irregular parts in the β-trefoil proteins do not hinder the protein formation. Conserved hydrophobic residues on the β5 strand are always the interaction center of packing between the conserved hydrophobic residues in both regular and irregular β-trefoil proteins.ConclusionsWe revealed that the β5 strand plays an important role in β-trefoil protein structure construction. The sequence-based methods used in this study can extract the protein folding information from only amino acid sequence data, and well corresponded to 3D structure-based Gō-model simulation and available experimental results.

Prediction of the initial folding sites and the entire folding processes for Ig-like beta-sandwich proteins.

Describing the whole story of protein folding is currently the main enigmatic problem in molecular bioinformatics study. Protein folding mechanisms have been intensively investigated with experimental as well as simulation techniques. Since a protein folds into its specific 3D structure from a unique amino acid sequence, it is interesting to extract as much information as possible from the amino acid sequence of a protein. Analyses based on inter-residue average distance statistics and a coarse-grained Gō-model simulation were conducted on Ig and FN3 domains of a titin protein to decode the folding mechanisms from their sequence data and native structure data, respectively. The central region of all domains was predicted to be an initial folding unit, that is, stable in an early state of folding. This common feature coincides well with the experimental results and underscores the significance of the β-sandwich proteins' common structure, namely, the key strands for folding and the Greek-key motif, which is located in the central region. We confirmed that our sequence-based techniques were able to predict the initial folding event just next to the denatured state and that a 3D-based Gō-model simulation can be used to investigate the whole process of protein folding.

A new technique for predicting intrinsically disordered regions based on average distance map constructed with inter-residue average distance statistics

BackgroundIt had long been thought that a protein exhibits its specific function through its own specific 3D-structure under physiological conditions. However, subsequent research has shown that there are many proteins without specific 3D-structures under physiological conditions, so-called intrinsically disordered proteins (IDPs). This study presents a new technique for predicting intrinsically disordered regions in a protein, based on our average distance map (ADM) technique. The ADM technique was developed to predict compact regions or structural domains in a protein. In a protein containing partially disordered regions, a domain region is likely to be ordered, thus it is unlikely that a disordered region would be part of any domain. Therefore, the ADM technique is expected to also predict a disordered region between domains.ResultsThe results of our new technique are comparable to the top three performing techniques in the community-wide CASP10 experiment. We further discuss the case of p53, a tumor-suppressor protein, which is the most significant protein among cell cycle regulatory proteins. This protein exhibits a disordered character as a monomer but an ordered character when two p53s form a dimer.ConclusionOur technique can predict the location of an intrinsically disordered region in a protein with an accuracy comparable to the best techniques proposed so far. Furthermore, it can also predict a core region of IDPs forming definite 3D structures through interactions, such as dimerization. The technique in our study may also serve as a means of predicting a disordered region which would become an ordered structure when binding to another protein.

Prediction of folding mechanisms for Ig-like beta sandwich proteins based on inter-residue average distance statistics methods.

To understand the folding mechanism of a protein is one of the goals in bioinformatics study. Nowadays, it is enigmatic and difficult to extract folding information from amino acid sequence using standard bioinformatics techniques or even experimental protocols which can be time consuming. To overcome these problems, we aim to extract the initial folding unit for titin protein (Ig and fnIII domains) by means of inter-residue average distance statistics, Average Distance Map (ADM) and contact frequency analysis (F-value). TI I27 and TNfn3 domains are used to represent the Ig-domain and fnIII-domain, respectively. Beta-strands 2, 3, 5, and 6 are significant for the initial folding processes of TI I27. The central strands of TNfn3 were predicted as a primary folding segment. Known 3D structure and unknown 3D structure domains were investigated by structure or non-structure based multiple sequence alignment, respectively, to learn the conserved hydrophobic residues and predicted compact region relevant to evolution. Our results show good correspondence to experimental data, phi-value and protection factor from H-D exchange experiments. The significance of conserved hydrophobic residues near F-value peaks for structural stability using hydrophobic packing is confirmed. Our prediction methods once again could extract a folding mechanism only knowing the amino acid sequence.

Detection of Folding Sites of β-Trefoil Fold Proteins Based on Amino Acid Sequence Analyses and Structure-Based Sequence Alignment

The information on the 3D structure of a protein including its folding mechanism is encoded in its amino acid sequence. A β-trefoil protein is well known to have a remarkable 3D structure property, that is, the pseudo three-fold symmetry without clear hydrophobic packing. It is interesting to investigate how information on the folding mechanism to form such a topology is encoded in the amino acid sequence of a protein. In this study, analyses based on inter-residue average distance statistics and the conservation of hydrophobic residues are performed for sequences of 26 β-trefoil proteins to identify significant sites for the initial folding. Results are compared with the native 3D structures. The conserved hydrophobic residues are defined by multiple sequence alignment based on the 3D structures. It is confirmed that a conserved hydrophobic residue is always located in a β-strand. In particular, β-strands 5 and 6 are significant for the initial folding from the analyses based on the inter-residue average distance statistics. These results coincide well with the experimental data obtained so far for folding of some of the β-trefoil proteins. It is also confirmed that the conserved hydrophobic residues defined in this study contribute to form hydrophobic packing in β-trefoil proteins in general. Twelve conserved hydrophobic residue pairs are almost always observed to form packing in the 26 β-trefoil proteins from different superfamilies. We elucidate how the conserved hydrophobic residues in β-strands 5 and 6 contribute to the initial stage of folding of a β-trefoil protein. The common packing of the 12 conserved hydrophobic residue pairs are significant to form the whole β-trefoil fold structure.

Properties of Amino Acid Sequences of Lysozyme-Like Superfamily Proteins Relating to Their Folding Mechanisms

It is expected that we can predict the mechanism of folding of a protein from only its sequence if the information about the folding is encoded in the sequence. This is a long standing problem in molecular biophysics and molecular bioinformatics. In this study, we examine the folding of the lysozyme-like superfamily proteins that diverged from a common ancestor protein and show the common function and partially common 3D topology. We use methods based on inter-residue average distance statistics and evolutionary analysis to identify the location of the folding region from only their amino acid sequence. The properties of these sequences indicate that the general folding mechanisms are common among proteins in the same family. The difference in the folding mechanisms between the lysozymes in the animal kingdom and that in λ-phage are also suggested. We compare the hydrophobic packing observed in the actual 3D structures of the lysozymes with the results of the present study. We confirmed that the possible significant residues predicted in this study form hydrophobic packing in the 3D structures of the examined lysozymes. The sequence properties in the partially common 3D topology of these proteins imply that these parts are highly involved in the folding mechanisms in each family. We also find out that hydrophobic interactions of partially common 3D topology appeared in all families are conserved. These conserved hydrophobic contacts may be significant for forming the common topology; these contacts can be regarded as significant for the common function.

Validation of the Conservation and Robustness of Folding Initiation Sites in Evolutionarily Related Proteins

Despite the recent progress in the protein folding field, how a given amino acid sequence folds into its unique structure is still unclear. According to KA Scott et. al., for Immunoglobulin and Fibronectin-like fold, which are evolutionarily unrelated but have the same topology, share a folding mechanism consisting of 4 key residues and their peripheral residues. However, there are also some cases that two evolutionarily related proteins have different folding mechanisms (for example, PDZ2 and PDZ3 whose sequence identity is nearly 30%). In this study, we aim to investigate whether such folding segments (i.e., folding initiation sites playing important roles for the folding from the denatured state to the transition state) really exist in evolutionarily related proteins by our sequence analysis methods and validate the results with the experimental phi values that provide a degree of the contribution for the structural formation in the transition state for each residue. Our sequence analysis methods are based on the inter-residue average distance statistics and already applied to several proteins, like leghemoglobin, FABP, azurin, and TIM-barrel proteins; they returned reasonable results with HD exchange experiments or phi-value analyses. According to the current study, for the Ferredoxin-like proteins we treat here, the predicted folding initiation sites have good agreements with experimental phi values, and the application to their evolutionarily related proteins returns a suggestion that the location of folding initiation sites are more conservative than sequence. In addition to these analyses, we also investigate the robustness of folding initiation sites by comparing the results of our analyses between naturally evolved proteins, which are under the pressure of nature, and artificially evolved proteins, which are not under the pressure of nature. The details will be reported in the conference.

The Analysis of the Conservation of Folding Cores Among Highly Diverse Proteins in the Lysozyme Superfamily

For understanding a protein folding mechanism it is important to know whether folding mechanisms of evolutionary related proteins are conserved during biological evolution. However, the relationships between evolution of proteins and protein folding mechanisms are not completely elucidated. How the information of folding mechanisms reflects on amino acid sequences is an unsolved problem. The trace of this information of an ancestral protein during sequence divergence should be found on a sequence. In the lysozyme superfamily the structural similarity suggests they have a common ancestor despite their low sequence similarity. In this study, we analyze the folding mechanism of each protein in the lysozyme superfamily only from their amino acid sequences by means of the inter-residue average distance statistics. In these analyses we predict possible folding initiation sites as predicted folding core by analyzing contact maps based on the statistics. If the distributions of predicted folding cores among homologous proteins are similar, homologous proteins have robust folding cores not altered by amino acid substitutions. Multiple sequence alignment is used to check the existence of robust folding cores in each family of lysozyme whose sequences are not so diverged. Structural alignment is also used to investigate the correspondence of robust folding cores to common structural units among highly diverged sequences in the lysozyme superfamily. From the comparison of robust folding cores corresponding to structurally similar regions, we examine the existence of robust folding cores among distantly related proteins. The results suggest that predicted robust folding cores in closely related sequences of each family of lysozyme tend to correspond to common structural units. Thus it is indicated the existence of robust folding cores among the lysozyme superfamily although they lost sequence homology.

3P263 beta-Trefoilタンパクのフォールディングコアの残基間平均距離統計に基づく解析(22A.生命情報科学:構造ゲノミクス,ポスター,日本生物物理学会年会第51回(2013年度))

3P263 beta-Trefoilタンパクのフォールディングコアの残基間平均距離統計に基づく解析(22A.生命情報科学:構造ゲノミクス,ポスター,日本生物物理学会年会第51回(2013年度))

Analyses of Protein Sequences Using Inter-Residue Average Distance Statistics to Study Folding Processes and the Significance of Their Partial Sequences

One of the goals of molecular bioinformatics is decoding amino acid sequences to extract information on the principles of protein folding. However, this is difficult to perform with standard bioinformatics techniques such as multiple sequence alignment and so on. Thus, we propose a technique based on inter-residue average distance statistics to make predictions regarding the protein folding mechanisms of amino acid sequences. Our method involves constructing a kind of predicted contact map called an Average Distance Map (ADM) based on average distance statistics to pinpoint regions of possible folding nuclei for proteins. Only information on the amino acid sequence of a given protein is required for the present method. In this article, we summarize the results of studies using our method to analyze how specific protein sequences affect folding properties. In particular, we present studies on proteins in the phage lysozyme, such as the globin, fatty acid binding protein-like, and the cupredoxin-like fold families. In the present review, we characterize the 3D architectures of these proteins through the properties of the protein ADMs. Furthermore, we combine the information on the conserved residues within the regions predicted by the ADMs with our results obtained so far. Such information may help identify the folding characteristics of each protein. We discuss this possibility in the present review.

Analysis of the Local Sequences of Folding Sites in β Sandwich Proteins with Inter-Residue Average Distance Statistics

The sequences of azurin and titin,  sandwich proteins, are analyzed based on inter-residue average distance statistics. A kind of predicted contact map based on inter-residue average distance statistics (Average Distance Map, ADM) is used to pinpoint regions of possible compact regions for two proteins. We compare predicted compact regions with the positions of the residues with experimental high  values for these proteins reported in the literature. The results reveal that the regions predicted by ADMs correspond to the positions of residues with the high  value. Furthermore, we perform random sampling of 3D conformations using these protein sequences with a potential derived from inter-residue average distance statistics. It is demonstrated that the residues with highest contact frequency during the simulations quali- tatively correspond to the residues with the highest  values for these proteins. Importantly, analysis with inter-residue av- erage distance statistics predicts the properties of folding processes of the  sandwich proteins starting from only sequence information.

2H1624 The study of the folding units in the TIM-Barrel fold based on the inter-residue average distance statistics(Protein: Property 3,The 48th Annual Meeting of the Biophysical Society of Japan)

2H1624 The study of the folding units in the TIM-Barrel fold based on the inter-residue average distance statistics(Protein: Property 3,The 48th Annual Meeting of the Biophysical Society of Japan)

2P020 残基間平均距離統計に基づくフェレドキシン様フォールドのフォールディング機構の解析(蛋白質-構造,第48回日本生物物理学会年会)

2P020 残基間平均距離統計に基づくフェレドキシン様フォールドのフォールディング機構の解析(蛋白質-構造,第48回日本生物物理学会年会)

3P-019 Goモデルによるタンパク質のフォールディングシミュレーションと残基間平均距離統計に基づくフォールディング機構予測との比較(蛋白質-構造,第47回日本生物物理学会年会)

3P-019 Goモデルによるタンパク質のフォールディングシミュレーションと残基間平均距離統計に基づくフォールディング機構予測との比較(蛋白質-構造,第47回日本生物物理学会年会)

Analysis of 3D structural differences in the IgG-binding domains based on the interresidue average-distance statistics

It is well-known that the IgG-binding domain from staphylococcal protein A folds into a 3 alpha helix bundle structure, while the IgG-binding domain of streptococcal protein G forms an (alpha + beta) structure. Recently, He et al. (Biochemistry 44:14055-14061, 2005) made mutants of these proteins from the wild types of protein A and protein G strains. These mutants are referred to as protein A219 and protein G311, and it was showed that these two mutants have different 3D structures, i.e., the 3 alpha helix bundle structure and the (alpha + beta) structure, respectively, despite the high sequence identity (59%). The purpose of our study was to clarify how such 3D structural differences are coded in the sequences with high homology. To address this problem, we introduce a predicted contact map constructed based on the interresidue average-distance statistics for prediction of folding properties of a protein. We refer to this map as an average distance map (ADM). Furthermore, the statistics of interresidue distances can be converted to an effective interresidue potential. We calculated the contact frequency of each residue of a protein in random conformations with this effective interresidue potential, and then we obtained values similar to phi values. We refer to this contact frequency of each residue as a p(mu) value. The comparison of the p(mu) values to the phi values for a protein suggests that p(mu) values reveal the information on the folding initiation site. Using these techniques, we try to extract the information on the difference in the 3D structures of protein A219 and protein G311 coded in their amino acid sequences in the present work. The results show that the ADM analyses and the p(mu) value analyses predict the information of folding initiation sites, which can be used to detect the 3D difference in both proteins.

1P-014 グロビンフォールドヘリックスE-H単位の立体構造の普遍性 : 残基間平均距離統計を用いた解析(蛋白質・構造(1),第46回日本生物物理学会年会)

1P-014 グロビンフォールドヘリックスE-H単位の立体構造の普遍性 : 残基間平均距離統計を用いた解析(蛋白質・構造(1),第46回日本生物物理学会年会)

1P014 IgG結合ドメインの立体構造の違いについて : 残基間平均距離統計に基づく解析(蛋白質(構造・構造機能相関),ポスター発表,第45回日本生物物理学会年会)

1P014 IgG結合ドメインの立体構造の違いについて : 残基間平均距離統計に基づく解析(蛋白質(構造・構造機能相関),ポスター発表,第45回日本生物物理学会年会)

3P008 残基間平均距離統計ポテンシャルによる残基対相関関数の特性の解析(蛋白質 A) 構造))

3P008 残基間平均距離統計ポテンシャルによる残基対相関関数の特性の解析(蛋白質 A) 構造))

残基間平均距離に基づくコンタクトマップによるリボゾームタンパクS6の円順列変異タンパクのフォールディング機構の解析

残基間平均距離に基づくコンタクトマップによるリボゾームタンパクS6の円順列変異タンパクのフォールディング機構の解析

残基間平均距離統計の基づくコンタクトマップによるβバレルタンパク構造の解析

残基間平均距離統計の基づくコンタクトマップによるβバレルタンパク構造の解析