The Complementary Plot : Now for Protein-Protein Interface :

The Software is available here: SARAMAint (Click to visit the site)





The concept of Complementarity bridges the gap between binding and folding: A brief description (Click to watch the video)

Chronum: A web server to calculate the 'Chromatic number' of a graph : A computational solution to the NP-HARD problem !

প্রোটিন মঙ্গল কাব্য

কাজে লাগতে, ভাঁজে ভাঁজে পেঁচিয়ে পেঁচিয়ে
ধেয়ে এল ওরা, তবু, না ছুঁয়ে এ-ওকে
শ্বাসের নৈকট্য-দোলা খোলা-বুকে নিয়ে
আবেশে আবেশে ছুঁয়ে রইলো চোখে চোখে

এই সে পরিপূরণ ! পূর্ণ আদিপ্রাণে
মাটি-আঁকড়ে বাকি বাড়তি জায়গা ছেড়ে দেওয়া
চকিতে, গতির শীর্ষে পতনে-উত্থানে
পড়শির পড়ন্ত ঝোঁক বুঝে, যুঝে নেওয়া

শুধু কি কাছের খেলা ? হাতের মুঠোর ?
ক্ষেত্রের তরুণ টানে প্রান্ত-দূর থেকে
ফণায় ফণায় ধেয়ে এল এঁকে বেঁকে
দলে দলে সুতাশঙ্খ, বাঁশিতে বিভোর ...

না ছোবলে না চুম্বনে, এমন সে মোহ
শুধু যৌথ দুলুনিতে অধীর আগ্রহ

Proteins are the structural and functional unit of almost all living forms on earth. They govern the entire biochemistry of life either by means of catalysts (classic types) or signal transducers (participation in bio-molecular recognition without breaking or making chemical bonds). It still remains elusive how this giant thread like macro-molecule folds in characteristic time-scale to retain its native three-dimensional and minimum free-energy structure which seemed to be naturally designed in a manner, consistent with its biological function. The extent of complexity in order to decipher this so-called 'second genetic code' is enormous and as it stands out, it still seems far away to resolve this well-posed 'protein folding problem' by mere physico-chemical rules. Protein structures have a certain sense of harmony in their internal architecture and dynamics. The building blocks (amino acid) are so arranged and coordinated that not only they themselves maintain optimum complementarity but also the structure as a whole be able to balance and sustain the local and non-local forces active in the cellular environment. A detail and thorough look into protein structures is reminiscent of a primitive molecular society, active and harmonious, internally optimized and immune to a continuous flow of the external stresses and adversity - a feature which does not seemed to be echoed loud enough to be audible in the upper hierarchy of living society ! 

Native deviations from ideality : Essential for protein structural integrity

Probing the role of native deviations in maintaining protein structural integrity

Native deviations in main-chain geometrical parameters seems crucial for structural integrity of proteins. These deviations are non-random, strategic and context dependent and it seems extremely difficult to predict them given the native main- and side-chain torsion angle profiles of a given structure. In this work, proteins of diverse folds and lengths were gathered spanning the four major protein classes and ranging from ~50 to ~375 residues in chain length and the structures rebuilt by (successive forth atom fixations) reverting all main-chain bond lengths, angles and ω-torsions to their corresponding unimodal ideal values (as tabulated in relevant repositories), while retaining native values for all other dihedral angles (φ, ψ, χ). To much of our surprise, this led to such large-scale distortions in the idealized structures (with respect to the original native model) that often their (C^α) RMSDs exceeded 10 Å (Fig. 1). Although the degree of structural distortions is estimated by the RMSDs, its effect on packing and electrostatics can be conveniently assessed using the CP measures [1, 2]. The distortions were more pronounced for larger polypeptide chains (~100 residues or more in length) due to the accumulation of a higher number of angular idealizations. Also, proteins containing greater β-sheet content had more severe deformations most probably rationalized by the distribution in N-C^α-C (τ) angle with respect to secondary structure. Little or no improvement was observed in the quality of the rebuilt structures by either retaining native ω values or utilizing ideal values (for bond angles) derived from a conformation dependent library (CDL) (Fig. 2) (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2810841/). Energy minimization of these idealized structures did not improve the (C^α) RMSDs (calculated at a one-to-one atomic correspondence subsequent to superposition) between native and idealized coordinates, which in some instances could not even be superposed onto each other (Table 1). Thus, in summary, in no case could the original structure be reconstituted by any form of energy minimization of the idealized coordinates. Calculations using both unimodal and CDL ideal values were repeated on a larger dataset of ultrahigh resolution (≤ 1 Ǻ) structures, which gave a similar pattern of results. Attempts are being carried out to device strategies to predict these deviations in a structure jammed with its native torsion angles. 

Fig. 1. Distortions in the native fold due to the reversal of all main-chain bond lengths, angles and ω-torsions to their corresponding (unimodal) ideal values. (A) the native structure of cyclophilin from L. donovani (2HAQ) and (B) its corresponding idealized structure (C^α-RMSD: 12.86 Ǻ, calculated at one-to-one atomic correspondence). 

Fig. 2. Effect of CDL-idealization probed by CP. Distribution for (A) the native polypeptide chain (1PGS) and (B) its corresponding idealized structure generated utilizing CDL ideal values.

Table 1. Structural distortions due to idealization as reflected in the RMSDs. 

PDB ID	RMSD (Ǻ) a
	Idealized vs. native	Idealized & Energy Minimized vs. native b
1AKO	13.98	-c
1BGF	7.30	6.77
1CEM	16.61	17.35
1CHD	22.42	22.18
1CKA	3.05	3.10
1ERZ	24.44	22.78
1HBQ	22.60	-
1IFC	11.30	11.48
1LMB	4.56	4.56
1MKB	-	-
1MLA	23.33	22.05
1PDO	4.56	5.29
1PGS	-	-
1SFP	-	-
1SRV	13.82	-
1STN	18.02	18.10
1UBI	4.31	4.14
2CPL	12.52	12.58
2END	7.64	7.41
2LIS	9.09	9.11

^a RMSDs calculated between C^α atoms of idealized (all main-chain bond lengths, bond angles and ω) and the native coordinates (calculated at a one-to-one atomic correspondence) subsequent to superposition by Dali server.

^b The same calculation was repeated for energy minimized coordinates subsequent to idealization.

^c ‘-’ stands for non-superposable structures. 

References:  

1. Self-Complementarity within Proteins: Bridging the Gap between Binding and Folding 

Sankar Basu, Dhananjay Bhattacharyya, and Rahul Banerjee*

Biophysical Journal, 2012, 102 (11) : 2605-2614

2. SARAMA: A Standalone Suite of Programs for the Complementarity Plot—

A Graphical Structure Validation Tool for Proteins

3. Applications of the complementarity plot in error detection and structure validation of proteins
Sankar Basu, Dhananjay Bhattacharyya, and Rahul Banerjee*
Indian Journal of Biochemistry and Biophysics, 2014, 51 (June) : 188-200

Sankar Basu*, Dhananjay Bhattacharyya, and Rahul Banerjee*

Journal of Bioinformatics and Intelligent Control, 2013, 2 (4) : 321-323

DNA Melting Thermodynamics : Local Partial melting in Polymeric ds-DNA

polDNAmelt: Local Melting Within Polymeric DNA—An Improved Method and Its Applications

Keywords / Key Attributes : Concentration independent local melting, Formation of interior bubble, Validation of annotated origin of replications / promoter sequences, Local minima of stability.

Local pseudo-unimolecular partial melting in polymeric cellular DNA is very much different from bimolecular comprehensive melting of short oligonucleotides in solutions. Several softwares estimate the melting temperature pretty accurately for the latter case and are used routinely for primer designing in PCR. However, the local partial melting in polymeric DNA involves the formation of a short-lived interior bubble constrained by double helical DNA at both the ends and thus (i) the melting-annealing transition becomes concentration independent and (ii) the fraying effect due to dangling ends are ruled out. Based on these features, the current study appropriately modifies the thermodynamic equations for calculation of local melting within polymeric DNA and incorporates them in a web-server (http://www.saha.ac.in/biop/www/db/local/nsdnamelt.html). Applications of the method in validating annotated promoter sequences and origin of replication have also been surveyed.

Reference : 

polDNAmelt: Local Melting Within Polymeric DNA—An Improved Method and Its Applications

Sankar Basu, Dhananjay Bhattacharyya

Journal of Bioinformatics and Intelligent Control, 2013, 2 (4), 316-320.

Protein Structural Validation: The Complementarity Plot - A Novel Graphical tool, Combined use of shape and electrostatic complementarity of interior residues.

SARAMA: A Standalone Suite of Programs for the Complementarity Plot—A Graphical Structure Validation Tool for Proteins

Keywords / Key Attributes : Detection of packing anomalies and wrong rotamer assignments in obsoleted structures, Signaling unbalanced partial charges in designed protein interiors, Detection of low intensity diffused errors in main-chain geometrical parameters, Applications in Homology modeling.

Structure validation is a crucial component not only in protein crystallography but also in model quality estimation in homology modeling, protein design and de-novo structure prediction. Recent studies have emphasized on the need to improve existing validation tools with the rapid growth of protein crystal structures deposited in the protein data bank. Two key attributes of a correctly determined atomic model are optimal packing between side-chains and absence of destabilizing unbalanced electric fields within the interior of a protein molecule. The complementarity plot (CP) combines them in a single unified measure and is a sensitive indicator of the harmony or disharmony of interior residues of a globular protein with regard to the short and long range forces sustaining the native fold. The plot has previously been demonstrated to be effective in detecting local regions of suboptimal packing or electrostatics [1]. CP has now been compiled into a  user friendly validation  package and made available as a standalone suite of programs in the public domain (http://www.saha.ac.in/biop/www/sarama.html) [2].  A set of  scores have now been included in the methodology which gives an estimate of the probabilities associated with the distribution of points in the plot and the propensities of specific residues to different degrees solvent exposure. These scores have been used to detect a wide variety of local and global structural errors and compared with other standard validation techniques. CP was found to be effective in discriminating between obsolete structures and their corresponding upgraded counterparts, detection of wrong rotamer assignment and in identifying packing anomalies. CP was especially effective in the detection of low-intensity errors diffused over the entire polypeptide chain. A special feature of this validation tool is to signal unbalanced partial charges within protein interiors. Finally, the application of CP in protein homology modeling and design has been surveyed. The current study clearly indicates that over and above the commonly used validation techniques, packing and electrostatics should be included separately in any validation package and thus, CP should be an useful addition in the already existing repertoire of structure validation tools. 

References: 

1.        Self-Complementarity within Proteins: Bridging the Gap between Binding and Folding.
Sankar Basu, Dhananjay Bhattacharyya, and Rahul Banerjee*

Biophysical Journal, 2012, 102 (11) : 2605-2614.

2.        SARAMA: A Standalone Suite of Programs for the Complementarity Plot—
A Graphical Structure Validation Tool for Proteins.

Sankar Basu*, Dhananjay Bhattacharyya, and Rahul Banerjee*

Journal of Bioinformatics and Intelligent Control, 2013, 2 (4) : 321-323. 

Protein Packing and Electrostatics: Estimation of shape and electrostatic complementarity for interior residues, A common conceptual platform to discuss folding and binding.

Self-complementarity within proteins: bridging the gap between binding and folding.

Keywords / Key Attributes : Design of Complementarity scores, Complementarity Plot, Applications in Protein fold recognition, Error detection.

Complementarity, in terms of both shape and electrostatic potential, has been quantitatively estimated at protein-protein interfaces and used extensively to predict the specific geometry of association between interacting proteins. In this work, we attempted to place both binding and folding on a common conceptual platform based on complementarity. To that end, we estimated (for the first time to our knowledge) electrostatic complementarity (Em) for residues buried within proteins. Em measures the correlation of surface electrostatic potential at protein interiors. The results show fairly uniform and significant values for all amino acids. Interestingly, hydrophobic side chains also attain appreciable complementarity primarily due to the trajectory of the main chain. Previous work from our laboratory characterized the surface (or shape) complementarity (Sm) of interior residues, and both of these measures have now been combined to derive two scoring functions to identify the native fold amid a set of decoys. These scoring functions are somewhat similar to functions that discriminate among multiple solutions in a protein-protein docking exercise. The performances of both of these functions on state-of-the-art databases were comparable if not better than most currently available scoring functions. Thus, analogously to interfacial residues of protein chains associated (docked) with specific geometry, amino acids found in the native interior have to satisfy fairly stringent constraints in terms of both Sm and Em. The functions were also found to be useful for correctly identifying the same fold for two sequences with low sequence identity. Finally, inspired by the Ramachandran plot, we developed a plot of Sm versus Em (referred to as the complementarity plot) that identifies residues with suboptimal packing and electrostatics which appear to be correlated to coordinate errors.

Reference: 

Self-Complementarity within Proteins: Bridging the Gap between Binding and Folding. 
Sankar Basu, Dhananjay Bhattacharyya, and Rahul Banerjee*
Biophysical Journal, 2012, 102 (11) : 2605-2614.

Probing Protein Internal Architecture by surface complementarity

Mapping the distribution of packing topologies within protein interiors shows predominant preference for specific packing motifs

Keywords / Key Attributes : Interior Packing, Surface Complementarity, Surface Contact Network, Zigsaw Puzzle Model, Introducing Packing Motifs, Exploring Triplet Cliques, Detection of the native structure situated amid random decoys.

Mapping protein primary sequences to their three dimensional folds referred to as the 'second genetic code' remains an unsolved scientific problem. A crucial part of the problem concerns the geometrical specificity in side chain association leading to densely packed protein cores, a hallmark of correctly folded native structures. Thus, any model of packing within proteins should constitute an indispensable component of protein folding and design. In this study an attempt has been made to find, characterize and classify recurring patterns in the packing of side chain atoms within a protein which sustains its native fold. The interaction of side chain atoms within the protein core has been represented as a contact network based on the surface complementarity and overlap between associating side chain surfaces. Some network topologies definitely appear to be preferred and they have been termed 'packing motifs', analogous to super secondary structures in proteins. Study of the distribution of these motifs reveals the ubiquitous presence of typical smaller graphs, which appear to get linked or coalesce to give larger graphs, reminiscent of the nucleation-condensation model in protein folding. One such frequently occurring motif, also envisaged as the unit of clustering, the three residue clique was invariably found in regions of dense packing. Finally, topological measures based on surface contact networks appeared to be effective in discriminating sequences native to a specific fold amongst a set of decoys.Out of innumerable topological possibilities, only a finite number of specific packing motifs are actually realized in proteins. This small number of motifs could serve as a basis set in the construction of larger networks. Of these, the triplet clique exhibits distinct preference both in terms of composition and geometry.

Reference:

Mapping the distribution of packing topologies within protein interiors shows predominant preference for specific packing motifs
Sankar Basu, Dhananjay Bhattacharyya and Rahul Banerjee*
BMC Bioinformatics, 2011, 12:195