Influence of medium and long range interactions in different structural classes of globular proteins

Importance of mutant position in Ramachandran plot for predicting protein stability of surface mutations

Understanding the mechanisms by which mutations affect protein stability is one of the most important problems in molecular biology. In this work, we analyzed the relationship between changes in protein stability caused by surface mutations and changes in 49 physicochemical, energetic, and conformational properties of amino acid residues. We found that the hydration entropy was the major contributor to the stability of surface mutations in helical segments; other properties responsible for size and volume of molecule also correlated significantly with stability. Classification of coil mutations based on their locations in the (phi-psi) map improved the correlation significantly, demonstrating the existence of a relationship between stability and strain energy, which indicates that the role of strain energy is very important for the stability of surface mutations. We observed that the inclusion of sequence and structural information raised the correlation, indicating the influence of surrounding residues on the stability of surface mutations. Further, we examined the previously reported "inverse relationship" between stability and hydrophobicity, and observed that the inverse hydrophobic effect was generally applicable only to coil mutations. The present study leads to a simple method for predicting protein stability changes caused by amino acid substitutions, which will be useful for protein engineering in designing novel proteins with increased stability and altered function.

Role of medium- and long-range interactions to the stability of the mutants of T4 lysozyme

Inter-residue interactions play an important role to the folding and stability of protein molecules. In this work, we analyze the role of medium- and long-range interactions to the stability of T4 lysozyme mutants. We found that, in buried mutations, the increase in long-range contacts upon mutations destabilizes the protein, whereas, in surface mutations, the increase in long-range contacts increases the stability, indicating the importance of surrounding polar residues to the stability of surface mutations. Further, the increase in medium-range contacts decreases the stability of buried and surface mutations and a direct relationship is observed between the increase of medium-range contacts and increase in stability for partially buried/exposed mutations. Moreover, the relationship between amino acid properties and stability of T4 lysozyme mutants at positions Ile3, Phe53, and Leu99 showed that the effect of medium- and long-range contacts is less for buried mutations and the inter-residue contacts have significant correlation with the stability of partially buried mutations.

Role of medium--and long-range interactions in discriminating globular and membrane proteins

The analysis of inter-residue interactions in protein structures provides considerable insight to understand their folding and stability. We have previously analyzed the role of medium- and long-range interactions in the folding of globular proteins. In this work, we study the distinct role of such interactions in the three-dimensional structures of membrane proteins. We observed a higher number of long-range contacts in the termini of transmembrane helical (TMH) segments, implying their role in the stabilization of helix-helix interactions. The transmembrane strand (TMS) proteins are having appreciably higher long-range contacts than that in all-beta class of globular proteins, indicating closer packing of the strands in TMS proteins. The residues in membrane spanning segments of TMH proteins have 1.3 times higher medium-range contacts than long-range contacts whereas that of TMS proteins have 14 times higher long-range contacts than medium-range contacts. Residue-wise analysis indicates that in TMH proteins, the residues Cys, Glu, Gly, Pro, Gln, Ser and Tyr have higher long-range contacts than medium-range contacts in contrast with all-alpha class of globular proteins. The charged residue pairs have higher medium-range contacts in all-alpha proteins, whereas hydrophobic residue pairs are dominant in TMH proteins. The information on the preference of residue pairs to form medium-range contacts has been successfully used to discriminate the TMH proteins from all-alpha proteins. The statistical significance of the results obtained from the present study has been verified using randomized structures of TMH and TMS protein templates.

Important inter-residue contacts for enhancing the thermal stability of thermophilic proteins

Proteins from thermophilic organisms exhibit high thermal stability, but have structures that are very similar to their mesophilic homologues. In order to gain insight into the basis of thermostability, we have analyzed the medium- and long-range contacts in mesophilic and thermophilic proteins of 16 different families. We found that the thermophiles prefer to have contacts between residues with hydrogen-bond-forming capability. Apart from hydrophobic contacts, more contacts are observed between polar and non-polar residues in thermophiles than mesophiles. Residue-wise analysis showed that Tyr has good contacts with several other residues, and Cys has considerably higher long-range contacts in thermophiles compared with mesophiles. Furthermore, the residues occurring in the range of 31-34 residues apart in the sequence contribute significant long-range contacts to the stability of thermophilic proteins.

Factors influencing the stability of alpha-helices and beta-strands in thermophilic ribonuclease H

Understanding the influence of structural parameters is crucial to enhance the thermal stability of proteins. In this work, the stability (deltaG) of residues in different secondary structures of Ribonuclease H (RNase H) has been analyzed with 48 amino acid properties. The properties reflecting hydrophobicity show a good correlation with stability. Further, the linear distribution of surrounding hydrophobicity in alpha-helices, obtained from the three dimensional structure of thermophilic RNase H, agrees well with experimental deltaG values. Moreover, the stability parameters correlate better in alpha-helices than those did in beta-strand segments. Multiple regression analysis, incorporating combinations of three properties from among all possible combinations of the 48 properties, increased the correlation coefficient to 0.77.

Distribution of amino acid residues and residue-residue contacts in molecular chaperones

The amino acid distribution and residue-residue contacts in molecular chaperones are different when compared to normal globular proteins. The study of molecular chaperones reveals a different surrounding environment to exist for the residues Cys, Trp, and His which may play an important role in determining the chaperone structures. Unlike globular proteins, it has been observed that a one-to-one correspondence between the amino acid distribution in a sequence and the structures of molecular chaperones. The preference of amino acid residues surrounding all 20 types of residues in secondary structures and their accessible surface areas have been analysed.

Importance of surrounding residues for protein stability of partially buried mutations

For understanding the factors influencing protein stability, we have analyzed the relationship between changes in protein stability caused by partially buried mutations and changes in 48 physico-chemical, energetic and conformational properties of amino acid residues. Multiple regression equations were derived to predict the stability of protein mutants and the efficiency of the method has been verified with both back-check and jack-knife tests. We observed a good agreement between experimental and computed stabilities. Further, we have analyzed the effect of sequence window length from 1 to 12 residues on each side of the mutated residue to include the sequence information for predicting protein stability and we found that the preferred window length for obtaining the highest correlation is different for each secondary structure; the preferred window length for helical, strand and coil mutations are, respectively, 0, 9 and 4 residues on both sides of the mutant residues. However, all the secondary structures have significant correlation for a window length of one residue on each side of the mutant position, implying the role of short-range interactions. Extraction of surrounding residue information for various distances (3 to 20A) around the mutant position showed the highest correlation at 8A, 6A and 7A, respectively, for mutations in helical, strand and coil segments. Overall, the information about the surrounding residues within the sphere of 7 to 8A, may explain better the stability in all subsets of partially buried mutations implying that this distance is sufficient to accommodate the residues influenced by major intramolecular interactions for the stability of protein structures.

Important amino acid properties for enhanced thermostability from mesophilic to thermophilic proteins

Understanding the role of various interactions in enhancing the thermostability of proteins is important not only for clarifying the mechanism of protein stability but also for designing stable proteins. In this work, we have analyzed the thermostability of 16 different families by comparing mesophilic and thermophilic proteins with 48 various physicochemical, energetic and conformational properties. We found that the increase in shape, s (location of branch point in side chain) increases the thermostability, whereas, an opposite trend is observed for Gibbs free energy change of hydration for native proteins, GhN, in 14 families. A good correlation is observed between these two properties and the simultaneous increases of -GhN and s is necessary to enhance the thermostability from mesophile to thermophile. The increase in shape, which tends to increase with increasing number of carbon atoms both for polar and non-polar residues, may generate more packing and compactness, and the position of beta and higher order branches may be important for better packing. On the other hand, the increase in -GhN in thermophilic proteins increases the solubility of the proteins. This tendency counterbalances the increases in insolubility and unfolding heat capacity change due to the increase in the number of carbon atoms. Thus, the present results suggest that the stability of thermophilic proteins may be achieved by a balance between better packing and solubility.

Influence of medium and long range interactions in protein folding

Protein structures are stabilized by both local and long range interactions. In this work, we analyze the residue-residue contacts and the role of medium- and long-range interactions in globular proteins belonging to different structural classes. The results show that while medium range interactions predominate in all-alpha class proteins, long-range interactions predominate in all-beta class. Based on this, we analyze the performance of several structure prediction methods in different structural classes of globular proteins and found that all the methods predict the secondary structures of all-alpha proteins more accurately than other classes. Also, we observed that the residues occurring in the range of 21-30 residues apart contributes more towards long-range contacts and about 85% of residues are involved in long-range contacts. Further, the preference of residue pairs to the folding and stability of globular proteins is discussed.

Role of structural and sequence information in the prediction of protein stability changes: comparison between buried and partially buried mutations

Predicting mutation-induced changes in protein stability is one of the greatest challenges in molecular biology. In this work, we analyzed the correlation between stability changes caused by buried and partially buried mutations and changes in 48 physicochemical, energetic and conformational properties. We found that properties reflecting hydrophobicity strongly correlated with stability of buried mutations, and there was a direct relation between the property values and the number of carbon atoms. Classification of mutations based on their location within helix, strand, turn or coil segments improved the correlation of mutations with stability. Buried mutations within beta-strand segments correlated better than did those in alpha-helical segments, suggesting stronger hydrophobicity of the beta-strands. The stability changes caused by partially buried mutations in ordered structures (helix, strand and turn) correlated most strongly and were mainly governed by hydrophobicity. Due to the disordered nature of coils, the mechanism underlying their stability differed from that of the other secondary structures: the stability changes due to mutations within the coil were mainly influenced by the effects of entropy. Further classification of mutations within coils, based on their hydrogen-bond forming capability, led to much stronger correlations. Hydrophobicity was the major factor in determining the stability of buried mutations, whereas hydrogen bonds, other polar interactions and hydrophobic interactions were all important determinants of the stability of partially buried mutations. Information about local sequence and structural effects were more important for the prediction of stability changes caused by partially buried mutations than for buried mutations; they strengthened correlations by an average of 27% among all data sets.

Relationship between amino acid properties and protein stability: buried mutations

In order to understand the mechanism of protein stability and to develop a simple method for predicting mutation-induced stability changes, we analyzed the relationship between stability changes caused by buried mutations and changes in 48 amino acid properties. As expected from the importance of hydrophobicity, properties reflecting hydrophobicity are strongly correlated with the stability of proteins. We found that subgroup classification based on secondary structure increased correlations significantly, and mutations within beta-strand segments correlated better than did those in alpha-helical segments, which may result from stronger hydrophobicity of the beta-strands. Multiple regression analyses incorporating combinations of three properties from among all possible combinations of the 48 properties increased the correlation coefficient to 0.88 and by an average of 13% for all data sets. Analyzing the stability of tryptophan synthase mutants with Glu49 replaced by all other residues except Arg revealed that combining buriedness, solvent-accessible surface area for denatured protein, and unfolding Gibbs free energy change increased the correlation to 0.95. Consideration of sequence and structural information (neighboring residues in sequence and in space) did not significantly strengthen the correlations in buried mutations, suggesting that nonspecific interactions dominate in the interior of proteins.

Importance of long-range interactions in protein folding

Long-range interactions play an active role in the stability of protein molecules. In this work, we have analyzed the importance of long-range interactions in different structural classes of globular proteins in terms of residue distances. We found that 85% of residues are involved in long-range contacts. The residues occurring in the range of 4-10 residues apart contribute more towards long-range contacts in all-alpha proteins while the range is 11-20 in all-beta proteins. The hydrophobic residues Cys, Ile and Val prefer the 11-20 range and all other residues prefer the 4-10 range. The residues in all-beta proteins have an average of 3-8 long-range contacts whereas the residues in other classes have 1-4 long-range contracts. Furthermore, the preference of residue pairs to the folding and stability will be discussed.

Analysis of hydrophobic and charged patches and influence of medium- and long-range interactions in molecular chaperones

The amino acid composition of the aromatic residues Phe, Tyr and Trp are much less significant in chaperones and the residues Cys, Glu, His, Met and Pro vary significantly in chaperones compared to normal globular proteins. In the present work, we have analysed the hydrophobic and charged patches in molecular chaperones which provide more insight for a better understanding of chaperone folding. Also, we have investigated the role of medium- and long-range contacts in chaperones and the preference of amino acid residues influenced by these interactions. Furthermore, the role of hydrophobic and helix-forming residues and disulfide bonding in these interactions have been discussed.

Importance of long-range interactions in (alpha/beta)8 barrel fold

Protein structures are stabilized by both local and long-range interactions. In this work, we analyzed the importance of long-range interactions in (alpha/beta)8 barrel proteins in terms of residue distances. We found that the residues occurring in the range of 21-30 residues apart contribute more toward long-range contacts. Indeed, about 50% of successive strands in these proteins are found to occur at a sequential distance of 21-30 residues. The aromatic amino acid residues Phe, Trp, and Tyr prefer the 4-10 range and all other residues prefer the 21-30 range. Hydrophobic-hydrophobic residue pairs are the most preferred ones for long-range interactions and they may play a key role in the folding and stabilization of (alpha/beta)8 barrel proteins.

Influence of Medium and Long Range Interactions in (α/β)(8) Barrel Proteins

The residue-residue contacts and the role of medium and long rangeinteractions in 36 (α/β)(8) barrel proteins have beenanalysed. The influence of long range contacts in the formation ofphysico-chemically similar clusters, and the preference of amino acidresidues towards long range contacts have also been studied. Theresults reveal a nearly uniform level of medium and long rangecontacts in most of the proteins. The residues Gln and Ala havehighest medium range contacts and the residue Pro has the lowestmedium range contacts. The residue Cys has the highest long rangecontact followed by other hydrophobic residues namely Val, Ile andLeu. In the physico-chemically similar clusters identified in theseproteins, 25-40 percent residues are influenced by long rangecontacts, and the residues Cys, Ile, Val and Met are the mostpreferred ones.