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Article ; Online: Effect of Lithium Drug on Binding Affinities of Glycogen Synthase Kinase-3 β to Its Network Partners: A New Computational Approach.

Rouhani, Maryam / Hadi-Alijanvand, Hamid

Journal of chemical information and modeling

2021 Volume 61, Issue 10, Page(s) 5280–5292

Abstract: Finding new methods to study the effect of small molecules on protein interaction networks provides us with invaluable tools in the fields of pharmacodynamics and drug design. Lithium is an antimanic drug that has been used for the treatment of bipolar ... ...

Abstract	Finding new methods to study the effect of small molecules on protein interaction networks provides us with invaluable tools in the fields of pharmacodynamics and drug design. Lithium is an antimanic drug that has been used for the treatment of bipolar disorder for more than 60 years. Here, we utilized a new approach to study the effect of lithium as a drug on the protein interaction network of GSK-3β as a hub protein and computed the affinities of GSK-3β to its partners in the presence of lithium or sodium ions. For this purpose, ensembles of GSK-3β protein structures were created in the presence of either lithium or sodium ions using adaptive tempering molecular dynamics simulations. The protein binding patches of GSK-3β for its partners were determined, and finally, the affinity of each binding patch to the related partner was computed for structures of ensembles using a monomer-based approach. Besides, by comparing structural dynamics of GSK-3β during MD simulations in the presence of LiCl and NaCl, we suggested a new mechanism for the inhibitory effect of lithium on GSK-3β.
MeSH term(s)	Antimanic Agents/therapeutic use ; Bipolar Disorder/drug therapy ; Glycogen Synthase Kinase 3 beta ; Humans ; Lithium ; Pharmaceutical Preparations
Chemical Substances	Antimanic Agents ; Pharmaceutical Preparations ; Lithium (9FN79X2M3F) ; Glycogen Synthase Kinase 3 beta (EC 2.7.11.1)
Language	English
Publishing date	2021-09-17
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	190019-5
ISSN	1549-960X ; 0095-2338
ISSN (online)	1549-960X
ISSN	0095-2338
DOI	10.1021/acs.jcim.1c00952
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Article ; Online: Complex Stability is Encoded in Binding Patch Softness: a Monomer-Based Approach to Predict Inter-Subunit Affinity of Protein Dimers.

Hadi-Alijanvand, Hamid

Journal of proteome research

2019 Volume 19, Issue 1, Page(s) 409–423

Abstract: Knowledge about the structure and stability of protein-protein interactions is vital to decipher the behavior of protein systems. Prediction of protein complexes' stability is an interesting topic in the field of structural biology. There are some ... ...

Abstract	Knowledge about the structure and stability of protein-protein interactions is vital to decipher the behavior of protein systems. Prediction of protein complexes' stability is an interesting topic in the field of structural biology. There are some promising published computational approaches that predict the affinity between subunits of protein dimers using 3D structures of both subunits. In the current study, we classify protein complexes with experimentally measured affinities into distinct classes with different mean affinities. By predicting the mechanical stiffness of the protein binding patch (PBP) region on a single subunit, we successfully predict the assigned affinity class of the PBP in the classification step. Now to predict the experimentally measured affinity between protein monomers in solution, we just need the 3D structure of the suggested PBP on one subunit of the proposed dimer. We designed the SEPAS software and have made the software freely available for academic non-commercial research purposes at " http://biophysics.ir/affinity ". SEPAS predicts the stability of the intended dimer in a classwise manner by utilizing the computed mechanical stiffness of the introduced binding site on one subunit with the minimum accuracy of 0.72.
MeSH term(s)	Binding Sites ; Computational Biology/methods ; Databases, Protein ; Elastic Modulus ; Humans ; Multiprotein Complexes/chemistry ; Multiprotein Complexes/metabolism ; Presenilins/chemistry ; Presenilins/metabolism ; Protein Binding ; Protein Multimerization ; Protein Stability ; Proteins/chemistry ; Proteins/metabolism ; Software
Chemical Substances	Multiprotein Complexes ; Presenilins ; Proteins
Language	English
Publishing date	2019-12-20
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/acs.jproteome.9b00594
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Article ; Online: Soft regions of protein surface are potent for stable dimer formation.

Hadi-Alijanvand, Hamid

Journal of biomolecular structure & dynamics

2019 Volume 38, Issue 12, Page(s) 3587–3598

Abstract: By having knowledge about the characteristics of protein interaction interfaces, we will be able to manipulate protein complexes for therapies. Dimer state is considered as the primary alphabet of the most proteins' quaternary structure. The properties ... ...

Abstract	By having knowledge about the characteristics of protein interaction interfaces, we will be able to manipulate protein complexes for therapies. Dimer state is considered as the primary alphabet of the most proteins' quaternary structure. The properties of binding interface between subunits and of noninterface region define the specificity and stability of the intended protein complex. Considering some topological properties and amino acids' affinity for binding in interfaces of protein dimers, we construct the interface-specific recurrence plots. The data obtained from recurrence quantitative analysis, and accessibility-related metrics help us to classify the protein dimers into four distinct classes. Some mechanical properties of binding interfaces are computed for each predefined class of the dimers. The computed mechanical characteristics of binding patch region are compared with those of nonbinding region of proteins. Our observations indicate that the mechanical properties of protein binding sites have a decisive impact on determining the dimer stability. We introduce a new concept in analyzing protein structure by considering mechanical properties of protein structure. We conclude that the interface region between subunits of stable dimers is usually mechanically softer than the interface of unstable protein dimers. AbbreviationsAABaverage affinity for bindingANManisotropic network modelAPCaffinity propagation clusteringASAaccessible surface areaCCDinter residues distanceCSCcomplex stability codeDMdistance matrixΔG
MeSH term(s)	Amino Acids ; Binding Sites ; Membrane Proteins ; Protein Binding ; Protein Conformation
Chemical Substances	Amino Acids ; Membrane Proteins
Language	English
Publishing date	2019-09-12
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2019.1662328
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Article ; Online: Studying the Effects of ACE2 Mutations on the Stability, Dynamics, and Dissociation Process of SARS-CoV-2 S1/hACE2 Complexes.

Hadi-Alijanvand, Hamid / Rouhani, Maryam

Journal of proteome research

2020 Volume 19, Issue 11, Page(s) 4609–4623

Abstract: A highly infectious coronavirus, SARS-CoV-2, has spread in many countries. This virus recognizes its receptor, angiotensin-converting enzyme 2 (ACE2), using the receptor binding domain of its spike protein subunit S1. Many missense mutations are reported ...

Abstract	A highly infectious coronavirus, SARS-CoV-2, has spread in many countries. This virus recognizes its receptor, angiotensin-converting enzyme 2 (ACE2), using the receptor binding domain of its spike protein subunit S1. Many missense mutations are reported in various human populations for the ACE2 gene. In the current study, we predict the affinity of many ACE2 variants for binding to S1 protein using different computational approaches. The dissociation process of S1 from some variants of ACE2 is studied in the current work by molecular dynamics approaches. We study the relation between structural dynamics of ACE2 in closed and open states and its affinity for S1 protein of SARS-CoV-2.
MeSH term(s)	Angiotensin-Converting Enzyme 2 ; Betacoronavirus ; COVID-19 ; Coronavirus Infections ; Humans ; Iran ; Molecular Dynamics Simulation ; Mutation, Missense/genetics ; Mutation, Missense/physiology ; Pandemics ; Peptidyl-Dipeptidase A/chemistry ; Peptidyl-Dipeptidase A/genetics ; Peptidyl-Dipeptidase A/metabolism ; Pneumonia, Viral ; Protein Binding ; SARS-CoV-2 ; Spike Glycoprotein, Coronavirus/chemistry ; Spike Glycoprotein, Coronavirus/metabolism ; Thermodynamics
Chemical Substances	Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; Peptidyl-Dipeptidase A (EC 3.4.15.1) ; ACE2 protein, human (EC 3.4.17.23) ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23)
Keywords	covid19
Language	English
Publishing date	2020-08-18
Publishing country	United States
Document type	Journal Article
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/acs.jproteome.0c00348
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Article ; Online: Partner-Specific Prediction of Protein-Dimer Stability from Unbound Structure of Monomer.

Hadi-Alijanvand, Hamid / Rouhani, Maryam

Journal of chemical information and modeling

2018 Volume 58, Issue 3, Page(s) 733–745

Abstract: Protein complexes play deterministic roles in live entities in sensing, compiling, controlling, and responding to external and internal stimuli. Thermodynamic stability is an important property of protein complexes; having knowledge about complex ... ...

Abstract	Protein complexes play deterministic roles in live entities in sensing, compiling, controlling, and responding to external and internal stimuli. Thermodynamic stability is an important property of protein complexes; having knowledge about complex stability helps us to understand the basics of protein assembly-related diseases and the mechanism of protein assembly clearly. Enormous protein-protein interactions, detected by high-throughput methods, necessitate finding fast methods for predicting the stability of protein assemblies in a quantitative and qualitative manner. The existing methods of predicting complex stability need knowledge about the three-dimensional (3D) structure of the intended protein complex. Here, we introduce a new method for predicting dissociation free energy of subunits by analyzing the structural and topological properties of a protein binding patch on a single subunit of the desired protein complex. The method needs the 3D structure of just one subunit and the information about the position of the intended binding site on the surface of that subunit to predict dimer stability in a classwise manner. The patterns of structural and topological properties of a protein binding patch are decoded by recurrence quantification analysis. Nonparametric discrimination is then utilized to predict the stability class of the intended dimer with accuracy greater than 85%.
MeSH term(s)	Algorithms ; Animals ; Binding Sites ; Computer Simulation ; Databases, Protein ; Humans ; Models, Biological ; Protein Conformation ; Protein Multimerization ; Protein Stability ; Protein Subunits/chemistry ; Proteins/chemistry ; Thermodynamics
Chemical Substances	Protein Subunits ; Proteins
Language	English
Publishing date	2018-02-26
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	190019-5
ISSN	1549-960X ; 0095-2338
ISSN (online)	1549-960X
ISSN	0095-2338
DOI	10.1021/acs.jcim.7b00606
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Article ; Online: Studying the Effects of ACE2 Mutations on the Stability, Dynamics, and Dissociation Process of SARS-CoV-2 S1/hACE2 Complexes

Hadi-Alijanvand, Hamid / Rouhani, Maryam

Journal of Proteome Research

2020 Volume 19, Issue 11, Page(s) 4609–4623

Keywords	Biochemistry ; General Chemistry ; covid19
Language	English
Publisher	American Chemical Society (ACS)
Publishing country	us
Document type	Article ; Online
ZDB-ID	2078618-9
ISSN	1535-3893
ISSN	1535-3893
DOI	10.1021/acs.jproteome.0c00348
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Studying the Effects of ACE2 Mutations on the Stability, Dynamics, and Dissociation Process of SARS-CoV-2 S1/hACE2 Complexes

Hadi-Alijanvand, Hamid / Rouhani, Maryam

J Proteome Res

Abstract	A highly infectious coronavirus, SARS-CoV-2, has spread in many countries. This virus recognizes its receptor, angiotensin-converting enzyme 2 (ACE2), using the receptor binding domain of its spike protein subunit S1. Many missense mutations are reported in various human populations for the ACE2 gene. In the current study, we predict the affinity of many ACE2 variants for binding to S1 protein using different computational approaches. The dissociation process of S1 from some variants of ACE2 is studied in the current work by molecular dynamics approaches. We study the relation between structural dynamics of ACE2 in closed and open states and its affinity for S1 protein of SARS-CoV-2.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #695776
Database	COVID19

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Article ; Online: Application of OmpF nanochannel forming protein in polynucleotide sequence recognition.

Hadi-Alijanvand, Saeid / Mobasheri, Hamid / Hadi-Alijanvand, Hamid

Journal of molecular recognition : JMR

2014 Volume 27, Issue 10, Page(s) 575–587

Abstract: Recognition of the sequence of human genome sequence is vital to address malfunctions occurring at molecular, cellular and tissue levels and requires a great deal of time, cost and efforts. Thus, various synthetic and natural pores were considered to ... ...

Abstract	Recognition of the sequence of human genome sequence is vital to address malfunctions occurring at molecular, cellular and tissue levels and requires a great deal of time, cost and efforts. Thus, various synthetic and natural pores were considered to fabricate high-throughput systems capable to fulfill the task in an efficient manner. Here, voltage gating OmpF nanochannel, whose structure is known at an atomic level, was used to recognize and differentiate between polynucleotide primers through voltage clamp technique. Our results showed that poly(T) occasionally blocked the channel at both polarities, while poly(C) and poly(G) obstructed it only at positive polarity. The channel was blocked at potential differences of as low as 80 mV in the presence of poly(T). The conductance of channel decreased in the presence of poly(C) and poly(G) by 61 and 5% respectively. Analysis of the number of events showed that poly(T) caused more closing events at higher voltages, while poly(G) and poly(C) induced it at lower voltages. Application of the hazard function as a statistical parameter and analysis of event closing times in various voltages demonstrated the most efficient differentiation at 60 mV. The results of practical and theoretical approaches presented here show that OmpF porin channel possesses the structural and dynamic characteristics required to be considered as a biosensor capable for continuous polynucleotide sequencing.
MeSH term(s)	Genome, Human ; Humans ; Models, Molecular ; Patch-Clamp Techniques ; Poly C/chemistry ; Poly G/chemistry ; Poly T/chemistry ; Polynucleotides/chemistry ; Porins/chemistry ; Sequence Analysis, DNA/methods
Chemical Substances	OmpF protein ; Polynucleotides ; Porins ; Poly T (25086-81-1) ; Poly G (25191-14-4) ; Poly C (30811-80-4)
Language	English
Publishing date	2014-10
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1015084-5
ISSN	1099-1352 ; 0952-3499
ISSN (online)	1099-1352
ISSN	0952-3499
DOI	10.1002/jmr.2381
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Article ; Online: Biophysical Insight into the SARS-CoV2 Spike-ACE2 Interaction and Its Modulation by Hepcidin through a Multifaceted Computational Approach.

Hadi-Alijanvand, Hamid / Di Paola, Luisa / Hu, Guang / Leitner, David M / Verkhivker, Gennady M / Sun, Peixin / Poudel, Humanath / Giuliani, Alessandro

ACS omega

2022 Volume 7, Issue 20, Page(s) 17024–17042

Abstract: At the center of the SARS-CoV2 infection, the spike protein and its interaction with the human receptor ACE2 play a central role in the molecular machinery of SARS-CoV2 infection of human cells. Vaccine therapies are a valuable barrier to the worst ... ...

Abstract	At the center of the SARS-CoV2 infection, the spike protein and its interaction with the human receptor ACE2 play a central role in the molecular machinery of SARS-CoV2 infection of human cells. Vaccine therapies are a valuable barrier to the worst effects of the virus and to its diffusion, but the need of purposed drugs is emerging as a core target of the fight against COVID19. In this respect, the repurposing of drugs has already led to discovery of drugs thought to reduce the effects of the cytokine storm, but still a drug targeting the spike protein, in the infection stage, is missing. In this work, we present a multifaceted computational approach strongly grounded on a biophysical modeling of biological systems, so to disclose the interaction of the SARS-CoV2 spike protein with ACE2 with a special focus to an allosteric regulation of the spike-ACE2 interaction. Our approach includes the following methodologies: Protein Contact Networks and Network Clustering, Targeted Molecular Dynamics, Elastic Network Modeling, Perturbation Response Scanning, and a computational analysis of energy flow and SEPAS as a protein-softness and monomer-based affinity predictor. We applied this approach to free (closed and open) states of spike protein and spike-ACE2 complexes. Eventually, we analyzed the interactions of free and bound forms of spike with hepcidin (HPC), the major hormone in iron regulation, recently addressed as a central player in the COVID19 pathogenesis, with a special emphasis to the most severe outcomes. Our results demonstrate that, compared with closed and open states, the spike protein in the ACE2-bound state shows higher allosteric potential. The correspondence between hinge sites and the Allosteric Modulation Region (AMR) in the S-ACE complex suggests a molecular basis for hepcidin involvement in COVID19 pathogenesis. We verify the importance of AMR in different states of spike and then study its interactions with HPC and the consequence of the HPC-AMR interaction on spike dynamics and its affinity for ACE2. We propose two complementary mechanisms for HPC effects on spike of SARS-CoV-2; (a) HPC acts as a competitive inhibitor when spike is in a preinfection state (open and with no ACE2), (b) the HPC-AMR interaction pushes the spike structure into the safer closed state. These findings need clear molecular in vivo verification beside clinical observations.
Language	English
Publishing date	2022-05-10
Publishing country	United States
Document type	Journal Article
ISSN	2470-1343
ISSN (online)	2470-1343
DOI	10.1021/acsomega.2c00154
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Article ; Online: Journey of poly-nucleotides through OmpF porin.

Hadi-Alijanvand, Hamid / Rouhani, Maryam

The journal of physical chemistry. B

2015 Volume 119, Issue 20, Page(s) 6113–6128

Abstract: OmpF is an abundant porin in many bacteria which attracts attention as a promising biological nanopore for DNA sequencing. We study the interactions of OmpF with pentameric poly-nucleotides (poly-Ns) in silico. The poly-N molecule is forced to ... ...

Abstract	OmpF is an abundant porin in many bacteria which attracts attention as a promising biological nanopore for DNA sequencing. We study the interactions of OmpF with pentameric poly-nucleotides (poly-Ns) in silico. The poly-N molecule is forced to translocate through the lumen of OmpF. Subsequently, the structural and dynamical effects of translocation steps on protein and poly-N molecules are explored in detail. The external loops of OmpF are introduced as the main region for discrimination of poly-Ns based on their organic bases. Structural network analyses of OmpF in the presence or absence of poly-Ns characterize special residues in the structural network of porin. These residues pave the way for engineering OmpF protein. The poly-N-specific pattern of OmpF's local conductance is detected in the current study. Computing the potential of mean force for translocation steps, we define the energetic barrier ahead of poly-N to move through OmpF's lumen. We suggest that fast translocation of the examined poly-N molecules through OmpF seems unattainable by small external driving forces. Our computational results suggest some abilities for OmpF porin like OmpF's potential for being used in poly-N sequencing.
MeSH term(s)	Escherichia coli/chemistry ; Escherichia coli/metabolism ; Molecular Dynamics Simulation ; Nucleotides/chemistry ; Nucleotides/metabolism ; Porins/chemistry ; Porins/metabolism ; Protein Conformation ; Thermodynamics
Chemical Substances	Nucleotides ; OmpF protein ; Porins
Language	English
Publishing date	2015-05-21
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1520-5207
ISSN (online)	1520-5207
DOI	10.1021/acs.jpcb.5b00763
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