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Kumar V, Sood A, Munshi A, Gautam T, Kulharia M. Geometrical and electro-static determinants of protein-protein interactions. Bioinformation 2021; 17:851-860. [PMID: 35574504 PMCID: PMC9070632 DOI: 10.6026/97320630017851] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/12/2021] [Accepted: 10/12/2021] [Indexed: 11/23/2022] Open
Abstract
Protein-protein interactions (PPI) are pivotal to the numerous processes in the cell. Therefore, it is of interest to document the analysis of these interactions in terms of binding sites, topology of the interacting structures and physiochemical properties of interacting interfaces and the of forces interactions. The interaction interface of obligatory protein-protein complexes differs from that of the transient interactions. We have created a large database of protein-protein interactions containing over100 thousand interfaces. The structural redundancy was eliminated to obtain a non-redundant database of over 2,265 interaction interfaces. Therefore, it is of interest to document the analysis of these interactions in terms of binding sites, topology of the interacting structures and physiochemical properties of interacting interfaces and the offorces interactions. The residue interaction propensity and all of the rest of the parametric scores converged to a statistical indistinguishable common sub-range and followed the similar distribution trends for all three classes of sequence-based classifications PPInS. This indicates that the principles of molecular recognition are dependent on the preciseness of the fit in the interaction interfaces. Thus, it reinforces the importance of geometrical and electrostatic complementarity as the main determinants for PPIs.
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Affiliation(s)
- Vicky Kumar
- Department of Computational Sciences, School of Basic and Applied Sciences, CentralUniversity of Punjab, Bathinda, India, 151001
| | - Ashita Sood
- Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, Kangra, India, 176206
| | - Anjana Munshi
- Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India, 151001
| | - Tarkeshwar Gautam
- Department of Zoology, Kalindi College, University of Delhi , Delhi, India
| | - Mahesh Kulharia
- Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, Kangra, India, 176206
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2
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Jin R, Grasso M, Zhou M, Marmorstein R, Baumgart T. Unfolding Mechanisms and Conformational Stability of the Dimeric Endophilin N-BAR Domain. ACS OMEGA 2021; 6:20790-20803. [PMID: 34423187 PMCID: PMC8374900 DOI: 10.1021/acsomega.1c01905] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 07/13/2021] [Indexed: 06/13/2023]
Abstract
Endophilin, which is a member of the Bin-amphiphysin-Rvs (BAR) domain protein superfamily, contains a homodimeric N-BAR domain of a characteristic crescent shape. The N-BAR domain comprises a six-helix bundle and is known to sense and generate membrane curvature. Here, we characterize aspects of the unfolding mechanism of the endophilin A1 N-BAR domain during thermal denaturation and examine factors that influence the thermal stability of this domain. Far-UV circular dichroism (CD) spectroscopy was applied to monitor changes in the secondary structure above room temperature. The protein's conformational changes were further characterized through Foerster resonance energy transfer and cross-linking experiments at varying temperatures. Our results indicate that thermal unfolding of the endophilin N-BAR is (minimally) a two-step process, with a dimeric intermediate that displays partial helicity loss. Furthermore, a thermal shift assay and temperature-dependent CD were applied to compare the unfolding processes of several truncated versions of endophilin. The melting temperature of the N-BAR domain decreased when we deleted either the N-terminal H0 helix or the unstructured linker of endophilin. This result suggests that these intrinsically disordered domains may play a role in structurally stabilizing the functional N-BAR domain in vivo. Finally, we show that single-site mutations can also compromise endophilin's thermal stability.
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Affiliation(s)
- Rui Jin
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Michael Grasso
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Department
of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Mingyang Zhou
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Abramson
Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Ronen Marmorstein
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Department
of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Abramson
Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Tobias Baumgart
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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Kangueane P. From Anna University to America and to Agriculture. Bioinformation 2021; 17:29-36. [PMID: 34393415 PMCID: PMC8340703 DOI: 10.6026/97320630017029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 11/06/2020] [Indexed: 11/23/2022] Open
Abstract
Anna University (AU) is an awesome alma mater for attracting the attention of the invincible through awareness from education. It is a place with a plan for preparing a palace in a person's life. It is an avenue for America through adequate cGPA and Advanced GRE (AGRE) with good TOEFL score. The views,visions, modes and models of several faculty members shaped many technocrats, teachers, entrepreneurs, journalists, editors and even farmers. Technology is engineering with science. The foundation and facilities at AU is priceless. AU created the framework for Industrial Biotechnology, a truly inter disciplinary curriculum with an optimal blend of Engineering and Science (Biology especially Agriculture and Healthcare through Organic chemistry) in 1992 almost 28 years back. The place was positioned just perfect in the world for wonders to come true. The Raman auditorium (in reverence to the Nobel Laureate Sir CV Raman) reassured rational research with reasonable respect in many minds at the ACTECH (Alagappa College of Technology) under the administration of AU. The admiration, acknowledgement and accountability for the alma mater, the AU will always remain precious.
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Nilofer C, Sukhwal A, Mohanapriya A, Sakharkar MK, Kangueane P. Small protein-protein interfaces rich in electrostatic are often linked to regulatory function. J Biomol Struct Dyn 2019; 38:3260-3279. [PMID: 31495333 DOI: 10.1080/07391102.2019.1657040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Protein-protein interaction (PPI) is critical for several biological functions in living cells through the formation of an interface. Therefore, it is of interest to characterize protein-protein interfaces using an updated non-redundant structural dataset of 2557 homo (identical subunits) and 393 hetero (different subunits) dimer protein complexes determined by X-ray crystallography. We analyzed the interfaces using van der Waals (vdW), hydrogen bonding and electrostatic energies. Results show that on average homo and hetero interfaces are similar. Hence, we further grouped the 2950 interfaces based on percentage vdW to total energies into dominant (≥60%) and sub-dominant (<60%) vdW interfaces. Majority (92%) of interfaces have dominant vdW energy with large interface size (146 ± 87 (homo) and 137 ± 76 (hetero) residues) and interface area (1622 ± 1135 Å2 (homo) and 1579 ± 1060 Å2 (hetero)). However, a proportion (8%) of interfaces have sub-dominant vdW energy with small interface size (85 ± 46 (homo) and 88 ± 36 (hetero) residues) and interface area (823 ± 538 Å2 (homo) and 881 ± 377 Å2 (hetero)). It is found that large interfaces have two-fold more interface area and interface size than small interfaces with increasing hydrogen bonding energy to interface size. However, small interfaces have three-fold more electrostatics energy than large interfaces with increasing electrostatics to interface size. Thus, 8% of complexes having small interfaces with limited interface area and sub-dominant vdW energy are rich in electrostatics. It is interesting to observe that complexes having small interfaces are often associated with regulatory function. Hence, the observed structural features with known molecular function provide insights for the better understanding of PPI.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Christina Nilofer
- Biomedical Informatics (P) Ltd., Pondicherry, India.,School of Biosciences & Technology, VIT University, Vellore, Tamil Nadu, India
| | - Anshul Sukhwal
- National Centre for Biological Sciences (NCBS), Bangalore, India
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Suresh A, Karthikraja V, Lulu S, Kangueane U, Kangueane P. A decision tree model for the prediction of homodimer folding mechanism. Bioinformation 2009; 4:197-205. [PMID: 20461159 PMCID: PMC2859576 DOI: 10.6026/97320630004197] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2009] [Accepted: 11/09/2009] [Indexed: 11/25/2022] Open
Abstract
The formation of protein homodimer complexes for molecular catalysis and regulation is fascinating. The homodimer formation through 2S (2 state), 3SMI (3 state with monomer intermediate) and 3SDI (3 state with dimer intermediate) folding mechanism is known for 47 homodimer structures. Our dataset of forty-seven homodimers consists of twenty-eight 2S, twelve 3SMI and seven 3SDI. The dataset is characterized using monomer length, interface area and interface/total (I/T) residue ratio. It is found that 2S are often small in size with large I/T ratio and 3SDI are frequently large in size with small I/T ratio. Nonetheless, 3SMI have a mixture of these features. Hence, we used these parameters to develop a decision tree model. The decision tree model produced positive predictive values (PPV) of 72% for 2S, 58% for 3SMI and 57% for 3SDI in cross validation. Thus, the method finds application in assigning homodimers with folding mechanism.
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Affiliation(s)
- Abishek Suresh
- Biomedical Informatics, Pondicherry 607402
- AIMST University, Semeling 08100, Malaysia
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Karthikraja V, Suresh A, Lulu S, Kangueane U, Kangueane P. Types of interfaces for homodimer folding and binding. Bioinformation 2009; 4:101-11. [PMID: 20198182 PMCID: PMC2828894 DOI: 10.6026/97320630007101] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2009] [Revised: 09/03/2009] [Accepted: 09/05/2009] [Indexed: 11/23/2022] Open
Abstract
Homodimers have a role in catalysis and regulation through the formation of stable interfaces. These interfaces are formed through different folding mechanisms such as 2-state without stable intermediate (2S), 3-state with monomer intermediate (3SMI) and 3-state with dimer intermediate (3SDI). Therefore, it is of interest to understand folding mechanism using structural features at the interfaces. Several studies have documented the significance of structural features for the understanding of homodimer folding mechanisms. However, the known features provide limited information for understanding homodimer folding mechanisms. Hence, we created an extended dataset of 47 homodimers (twenty eight 2S, twelve 3SMI and seven 3SDI) to examine the types of interfaces in protein homodimers. 2S are usually small sized, 3SMI are often medium sized and 3SDI often exist as large sized proteins. The ratio of interface to total (I/T) residue is large in 2S and small in 3SMI and 3SDI. Hence, we used I/T measure to group 2S, 3SMI and 3SDI into categories with large I/T (>> 50%), moderate I/T (50 - 25%) and small I/T (<< 25%) interfaces. The grouping is further sub-grouped based on the type of physical interaction visualized at the interface using representations in two dimensions (2D). 2D representation of the interface shows eight different forms of interactions in these homodimers. 2S homodimers frequently have large I/T and thus, utilize the entire protein structure in the formation of the interface where the individual subunits are heavily inter communicated with each other. This is not true in the case of 3SMI and 3SDI. 3SMI subunits usually interact with each other at the interface with a gentle touch-like contact and hence, they have low I/T ratio. 3SDI are often quite different in interaction compared to 3SMI and their subunits do deeply interact at the interface with only one part of the surface and hence also having low I/T ratio.
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Affiliation(s)
| | - Abishek Suresh
- Biomedical Informatics, Pondicherry 607402, India
- AIMST SDN BHD, Kedha 08100, Malaysia
| | - Sajitha Lulu
- Biomedical Informatics, Pondicherry 607402, India
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Lulu S, Suresh A, Karthikraja V, Arumugam M, Kayathri R, Kangueane P. Structural features for homodimer folding mechanism. J Mol Graph Model 2009; 28:88-94. [PMID: 19442545 DOI: 10.1016/j.jmgm.2009.04.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2008] [Revised: 03/30/2009] [Accepted: 04/11/2009] [Indexed: 10/20/2022]
Abstract
The homodimers have essential role in catalysis and regulation. The homodimer folding mechanism through 2-state without stable intermediate (2S), 3-state with monomer intermediate (3SMI) and 3-state with dimer intermediate (3SDI) is fascinating. 23MI and 3SDI constitute 3-state (3S). Hence, it is important to differentiate 2S, 3SMI and 3SDI homodimers using structural features. We used the dataset of Li et al. [L. Li, K. Gunasekaran, J.G. Gan, C. Zhanhua, P. Shapshak, M.K. Sakharkar, P. Kangueane, Structural features differentiate the mechanisms between 2S and 3S folding of homodimers, Bioinformation 1 (2005) 42-49] consisting of twenty-five 2S, ten 3SMI and six 3SDI homodimer structures for the study. Interface to total (I/T) residues ratio is large for 2S than 3SMI and 3SDI. Interface to total residues ratio is similar for 3SMI (mean monomer length (ML)=208) and 3SDI (mean monomer length (ML)=404) despite difference in mean monomer size. Interface residues correlate with monomer size in 2S (Pearson's correlation coefficient (r); r(2)=0.41) and 3SMI (r(2)=0.52). This is not true for 3SDI with interface residues and monomer length (r(2)=0.17). Interface area (B/2) does not correlate with interface residues (r(2)<0.001) and monomer size (r(2)=0.023) in 2S. This is despite a relationship with interface residues and monomer size (r(2)=0.41) in 2S. However, this is not true for 3SMI (r(2)=0.61 with interface residues and r(2)=0.25 with monomer size). In 3SDI, a different relationship is seen (r(2)=0.28 with interface residues and r(2)=0.09 with size). The mean hydrophobicity factor (H(f)) is 3-fold less in 3S than 2S. H(f) does not correlate with interface area in 2S (r(2)=0.03) and 3SDI (r(2)=0.0). However, a weak causal relation is seen in 3SMI (r(2)=0.23). Hydrophilic amino acid residues (E, R, K, S and Q) are prominent in 2S than 3S. Charged negative amino acid residues (D, E) are more than positive amino acid residues (R, K, H) in 2S and charged positive amino acid residues (R, K, H) are more than negative amino acid residues (D, E) in 3S. These features help to distinguish 2S, 3SMI and 3SDI providing insights to homodimer folding and binding.
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Affiliation(s)
- Sajitha Lulu
- School of Biotechnology, Chemical and Biomedical Engineering, VIT University, Vellore 632014, Tamil Nadu, India
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Rumfeldt JAO, Galvagnion C, Vassall KA, Meiering EM. Conformational stability and folding mechanisms of dimeric proteins. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2008; 98:61-84. [PMID: 18602415 DOI: 10.1016/j.pbiomolbio.2008.05.004] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The folding of multisubunit proteins is of tremendous biological significance since the large majority of proteins exist as protein-protein complexes. Extensive experimental and computational studies have provided fundamental insights into the principles of folding of small monomeric proteins. Recently, important advances have been made in extending folding studies to multisubunit proteins, in particular homodimeric proteins. This review summarizes the equilibrium and kinetic theory and models underlying the quantitative analysis of dimeric protein folding using chemical denaturation, as well as the experimental results that have been obtained. Although various principles identified for monomer folding also apply to the folding of dimeric proteins, the effects of subunit association can manifest in complex ways, and are frequently overlooked. Changes in molecularity typically give rise to very different overall folding behaviour than is observed for monomeric proteins. The results obtained for dimers have provided key insights pertinent to understanding biological assembly and regulation of multisubunit proteins. These advances have set the stage for future advances in folding involving protein-protein interactions for natural multisubunit proteins and unnatural assemblies involved in disease.
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Affiliation(s)
- Jessica A O Rumfeldt
- Guelph-Waterloo Centre for Graduate Work in Chemistry and Biochemistry, Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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