Electrostatic contributions In Interface

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Entropy (−TΔS) and Gibbs free energy (ΔG) values were calculated using the following set of relationships:

Electrostatic potential surface

The electrostatic potential surface was evaluated using the adaptive Poisson-Boltzmann solver (APBS) software (Holst and Saied 1993, 1995; Baker et al. 2001). This software calculates the potential surface by providing a numerical solution to the Poisson-Boltzmann equation using a grid-based approach.

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Electrostatic contributions to binding of individual charged residues on the interface

The electrostatic contribution of an individual residue r to binding, ΔG_elec(r), is calculated as:

ΔG_solv(r) is the loss of favorable solvation interactions of a residue r on complex formation. Δ [Σq(j)(r,j)] is the change, on complex formation, of pairwise electrostatic interactions of residue r with all atoms, j, that do not belong to residue r. q(j) is the charge on atom j, and (r,j) is the electrostatic potential generated by charges on a residue r at the position of a charge j.

Interfac rim core

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Conservation and relative importance of residues across protein-protein interfaces

Mainak Guharoy and Pinak Chakrabarti

The role of hydrophobic residues in protein-protein recognition and the formation of multimeric protein assembly has long been recognized. A quantitative enumeration of the hydrophobic patches on the interface was achieved by dissecting it into core and rim regions, the former containing residues with some atoms fully buried in the interface, whereas the latter only contains atoms that retain partial accessibility. The core possesses more hydrophobic residues and has a composition that is distinct from the rim or the rest of the protein surface. With the division into core and rim residues one can ask the question of whether as two groups these residues have different contributions to binding energy, and consequently have different evolutionary pressure for their conservation. The degree of conservation of each interface residue can be defined in terms of sequence entropy at that position in the polypeptide chain across all of the homologous proteins.

Calculation of Mean Sequence Entropies for the Core and Rim. The amino acid residues comprising the interface were segregated into core and rim based on the solvent accessibility of their constituent atoms in the bound state, the former type of residues having fully buried atoms, whereas the latter contain atoms that remain partially exposed to solvent. 


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Dissecting protein–protein recognition sites

When the interface buries <2000 Å2 of protein surface, the recognition sites usually form a single patch on the surface of each component protein. In contrast, larger interfaces are generally multipatch, with at least one pair of patches that are equivalent in size to a single-patch interface. Each recognition site, or patch within a site, contains a core made of buried interface atoms, surrounded by a rim of atoms that remain accessible to solvent in the complex.

The interface area is the area buried in the interaction, measured as the sum of the solvent accessible surface area (ASA) of the two component proteins, less that of the complex.

Lo Conte et al.12 noted that most of the protein–protein complexes bury a surface area in the range of 1200–2000 Ų and defined their interfaces as “standard size.”



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The atomic structure of protein-protein recognition sites


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core interface, rim interface, and non-interface residues


 

Interface - 整理

Protein–Protein Interfaces: Analysis of Amino Acid Conservation in Homodimers

WilliamS. J. Valdar^1* and Janet M. Thornton^1,2

PROTEINS: Structure, Function, and Genetics 42:108–124 (2001)

The classes are assigned on the basis of solvent accessibility, which is calculated using NACCESS an implementation of the Lee and Richards algorithm, with a

probe sphere of radius 1.4Å. A residue is deemed accessible if its relative accessible surface area (RSA) is < 5%, a cut-off devised and optimized by Miller et al.⁴⁷ If a residue is accessible in the protomer it is in the Surface set, otherwise it is Core. If a residue in the Surface set loses RSA upon complexation it is in the Interface set, otherwise it is Exposed. If a residue in the Interface set is inaccessible (i.e.< 5% RSA) in the multimer complex, it is in the Buried set, else it is Partially Buried.

47. Miller S, Lesk AM, Janin J, Chothia C. The accessible surfacearea

and stability of oligomeric proteins. Nature 1987;328:834–836.

An evolution based classifier for prediction of protein interfaces without using protein structures

I. Reš, I. Mihalek and O. Lichtarge

Vol. 21 no. 10 2005, pages 2496–2501 doi:10.1093/bioinformatics/bti340

Interface residues were defined as surface residues that lost relative surface

accessible areas (RSAs) upon complex formation. Surface residues were

defined as those for which RSA ≥5% (Valdar and Thornton, 2001). The

solvent accessibility was calculated using the program NACCESS (Hubbard

and Thornton, 1993), which implements the Lee and Richards algorithm,

with a probe sphere of radius 1.4 Å (Lee and Richards, 1971). Valdar,V. and Thornton,J.M. (2001) Protein–protein interfaces: analysis of amino acid

conservation in homodimers. Proteins, 42, 108–124.

X-ray crystallographic analysis of the sulfur carrier protein SoxY from Chlorobium limicolaf. thiosulfatophilum reveals a tetrameric structure

JAN STOUT, GONZALEZ VAN DRIESSCHE, SAVVAS N. SAVVIDES, AND JOZEF VAN BEEUMEN

Protein Science (2007), 16:589–601. Published by Cold Spring Harbor Laboratory Press. Copyright _ 2007 The Protein Society

Accessible surface areas (ASA) were calculated with the programs ACCESS and ACCFMT (Lee and Richards 1971). Atoms losing 0.1 Ų in a protein–protein

interaction were identified as interface atoms, and atoms having 0 Ų in a protein–protein interface were classified as buried interface atoms. Surface residues having >5% of their relative accessible surface area (RSA), calculated for each amino acid by Miller et al. (1987), were defined as exposed to the solvent. Fully buried interface residues have a maximum of 5% of their RSA exposed upon oligomerization. Residues having >5% RSA exposed in the interface are partially buried interface residues.

Interface - Fingerprints

Prediction-based fingerprints of protein–protein interactions

Interface definition

The concept of RSA plays an important role in the subsequent definition of an interaction site and novel fingerprints of protein interactions considered here.

RSA of the i-th amino acid residue, RSA_i, is defined as the ratio of the solvent exposed surface area of that residue observed in a given structure, SA_i, and some maximum value of the solvent exposed surface area for this kind of amino acid, MSA_i

• 

Hence, RSA adopts values between 0 and 100%, with 0% corresponding to a fully buried and 100% to a fully accessible residue.37

Unless specified otherwise (which may be relevant for comparison with RSA prediction methods from the literature), the maximum exposed surface areas are taken from,47 and correspond to those observed in an extended conformation of a tripeptide, with the residue of interest as the central residue. The DSSP program48 is used here to compute exposed surface areas. Also, unless specified otherwise, we define surface exposed residues as those that have RSA of 5% and more.

Definition of an Interaction Site

In this work, following in the footsteps of previous studies we define interaction sites based on the RSA change upon complex formation, that is, RSA difference between an unbound and bound (complex) structure of an individual chain.7, 51

For each chain considered here, its coordinates are first extracted from the corresponding complex structure and the DSSP program is used to compute the surface exposure of each amino acid residue in an unbound structure of a single protein chain.

Subsequently, residues that become buried at the interface upon complex formation may be identified by recomputing the level of surface exposure in the whole complex.

Specifically, an amino acid residue is regarded as an interaction site if
 (i) it is surface-exposed when considering the structure of an individual protein chain;
 (ii) the change in its RSA between the isolated chain and the corresponding complex structure is greater than 4% RSA, and the change in its exposed surface area in absolute terms is greater than 5 Ų.

As with other arbitrary thresholds, used in this work, we performed sensitivity analysis to assess the effects of such arbitrary choices and we also followed the literature as much as possible to enable comparison with other methods. In particular, the threshold of 4% RSA for the relative change in surface exposure between an isolated chain and complex structures corresponds to a typical error in RSA prediction for buried residues,35 which are most relevant for the novel fingerprints of protein interaction sites considered here. Moreover, this choice appears to be qualitatively consistent in terms of the resulting interaction interfaces with the work by Jones and Thornton7 and the resulting Protein–Protein Interaction Server for the analysis of protein complexes (http://www.biochem.ucl.ac.uk/bsm/PP/server/), as well as a more recent work by Offman and colleagues.52

Interface - paper NOXclass

NOXclass: prediction of protein-protein interaction types

Definition of interface properties (paper)

In order to characterize the different types of protein-protein interactions, we analyzed the following six interface properties: interface area, ratio of interface area to protein surface area, amino acid composition of the interface, correlation between amino acid compositions of interface and protein surface, gap volume index, and conservation score of the interface. A residue is defined as being part of the interface if its solvent accessible surface area (SASA) decreases by > 1 Ų upon the formation of the complex [13]. A protein-protein interface is defined to be the ensemble of all interface residues from both protomers. Solvent accessible surface areas for residues were calculated using NACCESS [35], with a probe sphere of radius 1.4 Å.

 

Interface area

Interface area is defined as one half of the total decrease of SASA (ΔSASA) of the two protomers upon the formation of the interaction:

where a and b are two protomers in the complex ab; SASA_a, SASA_b and SASA_ab are the SASA values for a, b, and ab, respectively. The native complex may contain additional protomers, but they are not considered.

 

Interface area ratio

Biological interactions that involve a small protomer cannot have large interface areas. This applies to some enzyme-inhibitor complexes, for instance. Therefore, we defined a new feature, in which the interface area is normalized by the SASA of the smaller protomer in the complex:

where SASA_a and SASA_b are the SASA values for protomers a and b, respectively.

 

Amino acid composition of the interface

We calculated both number-based and area-based amino acid composition [9]. The number-based amino acid composition (v_n) is defined as the frequency of each type of the 20 standard amino acids in the protein-protein interface. By weighting each residue with its ΔSASA, the area-based amino acid composition v_a is computed:

where type(r) is the type of the amino acid of residue r.

The Δν distance between two vectors ν and ν' of amino acid composition, number or area-based, is defined as [9,14]:

     

Interface Properties (web)

To discriminate the three types of interactions, we utilize the following interface properties.

• interface area
  Interface area is defined as one half of the total decrease of solvent accessible surface area (SASA) of the two protomers upon the formation of the interaction. NACCESS [2] has been used to calculate the SASA for proteins.
  
  
• interface area ratio
  Biological interactions in which a small protomer is involved, cannot have large interface areas. This applies to some enzyme-inhibitor complexes, for instance. Therefore, we defined a new feature, interface area ratio, in which the interface area is normalized by the SASA of the smaller protomer in the complex.
  
  
• area-based amino acid composition of protein-protein interface
  To calculate area-based amino acid composition for protein-protein interface, we first obtain number-based amino acid composition, which is defined as the frequency of each type of the 20 standard amino acids in the protein-protein interface. The area-based amino acid composition is then computed by weighting each residue with its decrease of SASA upon the formation of the interaction.
  
  
• correlation between area-based amino acid compositions of interface and the rest of protein surface
  The amino acid composition of the biological interface was shown to be significantly different from that of the rest of the protein surface [3]. It is reasonable to expect the amino acid composition of the crystal packing interface to be similar to that of the rest of the protein surface. To measure this effect, the Pearson's correlation coefficient between the amino acid compositions of interface and surface were calculated. These correlations were calculated for both number-based and area-based amino acid compositions.
  
  
• gap volume index
  Gap volume between two protomers is calculated using SURFNET [4]. The gap volume value is then normalized using interface area to produce a gap volume index [5].
  
  
• conservation score of protein-protein interface
  We calculated the conservation scores for residues in the interface as determined by the ConSurf method [6]. In a similar way to the area-based amino acid composition, we weighted the conservation score for each residue by its decrease of SASA upon the formation of the interaction. The average of these weighted residue conservation scores was used as the area-based conservation score of the interface.

thermophilic interface detail

Structural adaptation of the subunit interface of oligomeric thermophilic and hyperthermophilic enzymes

2.3. Identification of interface residues

Interface residues were defined as those residues that show a change in solvent accessibility area upon monomer association. Those residues for which the change was more than 90% were defined as composing the core interface (Bahadur et al., 2003). Solvent accessibility computation was performed with the program NACCESS (Hubbard and Thornton, 1993). The change in solvent accessibility area for each residue in the monomeric state and in the oligomeric state was calculated using a Perl script.

The structural similarity of the subunit interfaces within each protein family was evaluated on the basis of the multiple structure alignment. To ensure that the interface was structurally conserved within each family and the selected structural data comparable, the interface C_α carbons of each mesophilic member were superimposed to the equivalent atoms from the thermophilic homolog. 

Only interfaces showing RMSD ≤ 1.3 Å were considered similar. This threshold is within the expected structural variation corresponding to the range of sequence similarities of the multiple structure alignments (Chothia and Lesk, 1986). Indeed, the expected value of RMSD for a pair of homologous proteins whose sequence identity is 30% is equal to 1.42 Å. RMSDs were calculated using DeepView-Swiss-PdbViewer “iterative magic fit” tool (Guex and Peitsch, 1997) and the InsightII package (version 2005; Accelrys, San Diego, CA 92121, USA).

thermophilic interface papers

2009 Subunit interfaces of oligomeric hyperthermophilic enzymes display enhanced compactness

2008 Cavities and Atomic Packing in Protein Structures and Interfaces


利用 VOIDOO 軟體去 probe the cavity in the interface or intra-protein for further analysis !

Naccess

Hubbard S, Thornton J:
NACCESS Computer Program, Department of Biochemistry and Molecular Biology. 

[http://www.bioinf.manchester.ac.uk/naccess/]

Accessible surface area (ASA) analysis        Link

The ASA is the area of the protein surface which can be in contact with the solvent. The total apolar (and the complementary polar) component of the entire accessible surface area of each protein in its quaternary form was calculated with the server GETAREA http://curie.utmb.edu/getarea.html webcite with default settings [44]. The contribution of different atomic types to the polar area, namely oxygens, side-chain oxygens, nitrogens and side-chain nitrogens was also investigated. To compare the different surface areas of halophilic and non-halophilic proteins, they were normalized by division by the total accessible surface area of the corresponding protein.

The differences between the fraction of apolar accessible surface area in the unfolded and folded form of each protein considered (ΔApA_U-F) were calculated through the web server http://roselab.jhu.edu/utils/unfolded.html webcite[28]. The differences between the ΔApA_U-F in each halophilic protein and in its corresponding homolog (ΔΔApA_U-F) were calculated and statistically tested. 

 

HotSpot

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HotSprint database can be accessed through a web interface where users can search for computational hot spots in protein interfaces.

The evolutionarily conserved residues are found by Rate4Site algorithm (20). Rate4Site makes use of topology and branch lengths of the phylogenetic trees constructed from multiple sequence alignments (MSA) of proteins and estimates conservation rates of amino acids based on the empirical Bayesian rule. MSAs of proteins constituting interfaces are taken from HSSP (Homology-Derived Secondary Structure of Proteins) (23) database as of 14 January 2006. All MSAs obtained from HSSP are converted to FASTA format to be used in Rate4Site step.

In addition, some residues are more frequently observed to be hot spots, so each of the 20 amino acids has a different propensity to be a hot spot. Hot spot propensities are used to rescale the conservation scores. Further, hot spots prefer to reside in protein cavities (24), therefore surface area accessibility of interface residues are incorporated into our hot spot scoring formula.



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Definition of interface residues

ASA (Solvent-accessible surface area) of a residue was calculated using the program NACCESS. [25] A residue with an interface area (ΔASA) > 1Ų is defined as an interface residue and ΔASA is the change in ASA of the residue upon protein dimer formation from monomer state.