scholarly journals Simulating the function of sodium/proton antiporters

2015 ◽  
Vol 112 (40) ◽  
pp. 12378-12383 ◽  
Author(s):  
Raphael Alhadeff ◽  
Arieh Warshel
Keyword(s):  
Conformational Changes ◽  
Molecular Basis ◽  
Molecular Level ◽  
Structural Information ◽  
Coarse Grained ◽  
Charged State ◽  
Transport Models ◽  
Coarse Grained Model ◽  
Effective Transport ◽  
Molecular Origin

The molecular basis of the function of transporters is a problem of significant importance, and the emerging structural information has not yet been converted to a full understanding of the corresponding function. This work explores the molecular origin of the function of the bacterial Na+/H+ antiporter NhaA by evaluating the energetics of the Na+ and H+ movement and then using the resulting landscape in Monte Carlo simulations that examine two transport models and explore which model can reproduce the relevant experimental results. The simulations reproduce the observed transport features by a relatively simple model that relates the protein structure to its transporting function. Focusing on the two key aspartic acid residues of NhaA, D163 and D164, shows that the fully charged state acts as an Na+ trap and that the fully protonated one poses an energetic barrier that blocks the transport of Na+. By alternating between the former and latter states, mediated by the partially protonated protein, protons, and Na+ can be exchanged across the membrane at 2:1 stoichiometry. Our study provides a numerical validation of the need of large conformational changes for effective transport. Furthermore, we also yield a reasonable explanation for the observation that some mammalian transporters have 1:1 stoichiometry. The present coarse-grained model can provide a general way for exploring the function of transporters on a molecular level.

scholarly journals Molecular determinants of the interactions between proteins and ssDNA

2015 ◽  
Vol 112 (16) ◽  
pp. 5033-5038 ◽  
Author(s):  
Garima Mishra ◽  
Yaakov Levy
Keyword(s):  
Conformational Changes ◽  
Protein Interactions ◽  
Binding Pocket ◽  
Dna Bases ◽  
Coarse Grained ◽  
Binding Modes ◽  
Ssdna Binding ◽  
Coarse Grained Model ◽  
Molecular Determinants ◽  
Ssdna Binding Proteins

ssDNA binding proteins (SSBs) protect ssDNA from chemical and enzymatic assault that can derail DNA processing machinery. Complexes between SSBs and ssDNA are often highly stable, but predicting their structures is challenging, mostly because of the inherent flexibility of ssDNA and the geometric and energetic complexity of the interfaces that it forms. Here, we report a newly developed coarse-grained model to predict the structure of SSB–ssDNA complexes. The model is successfully applied to predict the binding modes of six SSBs with ssDNA strands of lengths of 6–65 nt. In addition to charge–charge interactions (which are often central to governing protein interactions with nucleic acids by means of electrostatic complementarity), an essential energetic term to predict SSB–ssDNA complexes is the interactions between aromatic residues and DNA bases. For some systems, flexibility is required from not only the ssDNA but also, the SSB to allow it to undergo conformational changes and the penetration of the ssDNA into its binding pocket. The association mechanisms can be quite varied, and in several cases, they involve the ssDNA sliding along the protein surface. The binding mechanism suggests that coarse-grained models are appropriate to study the motion of SSBs along ssDNA, which is expected to be central to the function carried out by the SSBs.

scholarly journals The P1 and P2 helices of the Guanidinium-II riboswitch interact in a ligand-dependent manner

2021 ◽  
Author(s):  
Christin Fuks ◽  
Sebastian Falkner ◽  
Nadine Schwierz ◽  
Martin Hengesbach
Keyword(s):  
Single Molecule ◽  
Conformational Changes ◽  
Environmental Conditions ◽  
Structural Information ◽  
Coarse Grained ◽  
Regulation Mechanism ◽  
Dependent Manner ◽  
Loop Formation ◽  
Coarse Grained Simulations ◽  
Kissing Loop

ABSTRACTRiboswitch RNAs regulate gene expression by conformational changes induced by environmental conditions and specific ligand binding. The guanidine-II riboswitch is proposed to bind the small molecule guanidinium and to subsequently form a kissing loop interaction between the P1 and P2 hairpins. While an interaction was shown for isolated hairpins in crystallization and EPR experiments, an intrastrand kissing loop formation has not been demonstrated. Here, we report the first evidence of this interaction in cis in a ligand and Mg2+ dependent manner. Using single-molecule FRET spectroscopy and detailed structural information from coarse-grained simulations, we observe and characterize three interconvertible states representing an open and kissing loop conformation as well as a novel Mg2+ dependent state for the guanidine-II riboswitch from E. coli. The results further substantiate the proposed switching mechanism and provide detailed insight into the regulation mechanism for the guanidine-II riboswitch class. Combining single molecule experiments and coarse-grained simulations therefore provides a promising perspective in resolving the conformational changes induced by environmental conditions and to yield molecular insights into RNA regulation.

scholarly journals Coarse-grained molecular simulations of the binding of the SARS-CoV-2 spike protein RBD to the ACE2 receptor

2020 ◽  
Author(s):  
David De Sancho ◽  
José A. Gavira ◽  
Raul Pérez-Jiménez
Keyword(s):  
Bound States ◽  
Dynamic Behaviour ◽  
Molecular Level ◽  
Molecular Simulations ◽  
Bound State ◽  
Spike Protein ◽  
Coarse Grained ◽  
Receptor Binding Domain ◽  
Coarse Grained Model ◽  
Dynamic Description

AbstractSince it was first observed, the COVID-19 pandemic has created a global emergency for national health systems due to millions of confirmed cases and hundreds of thousands of deaths. At a molecular level, the bottleneck for the infection is the binding of the receptor binding domain (RBD) of the viral spike protein to ACE2, an enzyme exposed on human cell membranes. Several experimental structures of the ACE2:RBD complex have been made available, however they offer only a static description of the arrangements of the molecules in either the free or bound states. In order to gain a dynamic description of the binding process that is key to infection, we use molecular simulations with a coarse grained model of the RBD and ACE2. We find that binding occurs in an all-or-none way, without intermediates, and that even in the bound state, the RBD exhibits a considerably dynamic behaviour. From short equilibrium simulations started in the unbound state we provide snapshots that result in a tentative mechanism of binding. Our findings may be important for the development of drug discovery strategies that target the RBD.

scholarly journals Analyzing the electrogenicity of cytochrome c oxidase

2016 ◽  
Vol 113 (28) ◽  
pp. 7810-7815 ◽  
Author(s):  
Ilsoo Kim ◽  
Arieh Warshel
Keyword(s):  
Molecular Mechanisms ◽  
Molecular Level ◽  
Theoretical Models ◽  
Proton Pumping ◽  
Coarse Grained ◽  
Transfer Reactions ◽  
Coarse Grained Model ◽  
Fundamental Information ◽  
Wide Range ◽  
Charge Transfer Reactions

Measurements of voltage changes in response to charge separation within membrane proteins can offer fundamental information on spectroscopically “invisible” steps. For example, results from studies of voltage changes associated with electron and proton transfer in cytochrome c oxidase could, in principle, be used to discriminate between different theoretical models describing the molecular mechanism of proton pumping. Earlier analyses of data from these measurements have been based on macroscopic considerations that may not allow for exploring the actual molecular mechanisms. Here, we have used a coarse-grained model describing the relation between observed voltage changes and specific charge-transfer reactions, which includes an explicit description of the membrane, the electrolytes, and the electrodes. The results from these calculations offer mechanistic insights at the molecular level. Our main conclusion is that previously assumed mechanistic evidence that was based on electrogenic measurements is not unique. However, the ability of our calculations to obtain reliable voltage changes means that we have a tool that can be used to describe a wide range of electrogenic charge transfers in channels and transporters, by combining voltage measurements with other experiments and simulations to analyze new mechanistic proposals.

scholarly journals Dynamics of Allosteric Transitions in Dynein

2018 ◽  
Author(s):  
Yonathan Goldtzvik ◽  
Mauro L. Mugnai ◽  
D. Thirumalai
Keyword(s):  
Conformational Changes ◽  
Cytoplasmic Dynein ◽  
Motor Domain ◽  
Coarse Grained ◽  
Power Stroke ◽  
Coarse Grained Model ◽  
Multiple Routes ◽  
Adp Release ◽  
Mechanical Element ◽  
Allosteric Transitions

1SummaryCytoplasmic Dynein, a motor with an unusual architecture made up of a motor domain belonging to the AAA+ family, walks on microtubule towards the minus end. Prompted by the availability of structures in different nucleotide states, we performed simulations based on a new coarse-grained model to illustrate the molecular details of the dynamics of allosteric transitions in the motor. The simulations show that binding of ATP results in the closure of the cleft between the AAA1 and AAA2, which in turn triggers conformational changes in the rest of the motor domain, thus poising dynein in the pre-power stroke state. Interactions with the microtubule, which are modeled implicitly, substantially enhances the rate of ADP release, and formation of the post-power stroke state. The dynamics associated with the key mechanical element, the linker (LN) domain, which changes from a straight to a bent state and vice versa, are highly heterogeneous suggestive of multiple routes in the pre power stroke to post power stroke transition. We show that persistent interactions between the LN and the insert loops in the AAA2 domain prevent the formation of pre-power stroke state when ATP is bound to AAA3, thus locking dynein in a non-functional repressed state. Motility in such a state may be rescued by applying mechanical force to the LN domain. Taken together, these results show how the intricate signaling dynamics within the motor domain facilitate the stepping of dynein.

scholarly journals A coarse-grained model of the expansion of the human rhinovirus 2 capsid reveals insights in genome release

2019 ◽  
Vol 16 (157) ◽  
pp. 20190044 ◽  
Author(s):  
Giuliana Indelicato ◽  
Paolo Cermelli ◽  
Reidun Twarock
Keyword(s):  
Conformational Changes ◽  
Minimum Energy ◽  
Human Rhinovirus ◽  
Coarse Grained ◽  
Coarse Grained Model ◽  
Transition Pathways ◽  
Causative Agents ◽  
The Common ◽  
Minimum Energy Paths

Human rhinoviruses are causative agents of the common cold. In order to release their RNA genome into the host during a viral infection, these small viruses must undergo conformational changes in their capsids, whose detailed mechanism is strictly related to the process of RNA extrusion, which has been only partially elucidated. We study here a mathematical model for the structural transition between the native particle of human rhinovirus type 2 and its expanded form, viewing the process as an energy cascade, i.e. a sequence of metastable states with decreasing energy connected by minimum energy paths. We explore several transition pathways and discuss their implications for the RNA exit process.

Crystal structures of Magnaporthe oryzae trehalose-6-phosphate synthase (MoTps1) suggest a model for catalytic process of Tps1

2019 ◽  
Vol 476 (21) ◽  
pp. 3227-3240 ◽  
Author(s):  
Shanshan Wang ◽  
Yanxiang Zhao ◽  
Long Yi ◽  
Minghe Shen ◽  
Chao Wang ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Conformational Changes ◽  
Magnaporthe Oryzae ◽  
Structural Information ◽  
Complex Structure ◽  
Critical Role ◽  
Catalytic Process ◽  
Structural Basis ◽  
Salt Bridges ◽  
Terminal Domain

Trehalose-6-phosphate (T6P) synthase (Tps1) catalyzes the formation of T6P from UDP-glucose (UDPG) (or GDPG, etc.) and glucose-6-phosphate (G6P), and structural basis of this process has not been well studied. MoTps1 (Magnaporthe oryzae Tps1) plays a critical role in carbon and nitrogen metabolism, but its structural information is unknown. Here we present the crystal structures of MoTps1 apo, binary (with UDPG) and ternary (with UDPG/G6P or UDP/T6P) complexes. MoTps1 consists of two modified Rossmann-fold domains and a catalytic center in-between. Unlike Escherichia coli OtsA (EcOtsA, the Tps1 of E. coli), MoTps1 exists as a mixture of monomer, dimer, and oligomer in solution. Inter-chain salt bridges, which are not fully conserved in EcOtsA, play primary roles in MoTps1 oligomerization. Binding of UDPG by MoTps1 C-terminal domain modifies the substrate pocket of MoTps1. In the MoTps1 ternary complex structure, UDP and T6P, the products of UDPG and G6P, are detected, and substantial conformational rearrangements of N-terminal domain, including structural reshuffling (β3–β4 loop to α0 helix) and movement of a ‘shift region' towards the catalytic centre, are observed. These conformational changes render MoTps1 to a ‘closed' state compared with its ‘open' state in apo or UDPG complex structures. By solving the EcOtsA apo structure, we confirmed that similar ligand binding induced conformational changes also exist in EcOtsA, although no structural reshuffling involved. Based on our research and previous studies, we present a model for the catalytic process of Tps1. Our research provides novel information on MoTps1, Tps1 family, and structure-based antifungal drug design.

scholarly journals Recent Advances in the Chemical Biology of N-Glycans

Molecules ◽  
2021 ◽  
Vol 26 (4) ◽  
pp. 1040
Author(s):  
Asuka Shirakawa ◽  
Yoshiyuki Manabe ◽  
Koichi Fukase
Keyword(s):  
Nuclear Magnetic Resonance ◽  
Magnetic Resonance ◽  
Molecular Basis ◽  
Chemical Biology ◽  
Molecular Level ◽  
Chemoenzymatic Synthesis ◽  
Complex Structures ◽  
Recent Advances ◽  
Protein Functions ◽  
Potential Applications

Asparagine-linked N-glycans on proteins have diverse structures, and their functions vary according to their structures. In recent years, it has become possible to obtain high quantities of N-glycans via isolation and chemical/enzymatic/chemoenzymatic synthesis. This has allowed for progress in the elucidation of N-glycan functions at the molecular level. Interaction analyses with lectins by glycan arrays or nuclear magnetic resonance (NMR) using various N-glycans have revealed the molecular basis for the recognition of complex structures of N-glycans. Preparation of proteins modified with homogeneous N-glycans revealed the influence of N-glycan modifications on protein functions. Furthermore, N-glycans have potential applications in drug development. This review discusses recent advances in the chemical biology of N-glycans.

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