Structure-activity correlationship and folding of recombinant Escherichia coli dihydro folate reductase (DHFR) enzyme through biochemical and biophysical approaches

The design of any antagonist or inhibitor for any enzyme requires the knowledge of structure- function relationship of the protein and the optimum conformational states for maximum and minimum activities. Furthermore, designing of the inhibitors or drugs against an enzyme becomes easier if there is information available about various well characterized intermediate conformation of the molecule. In vivo folding pathway of any recombinant protein is an important parameter for understanding its ability to fold by itself inside the cell, which always dictates the downstream processing for the purification. In the present manuscript we have discussed about the in vivo and in vitro folding, and structure-function relationship of Dihydrofolate reductase enzyme. This is an important enzyme involved in the cell growth and hence inhibition or inactivation of the enzyme may reduce the cell growth. It was observed that the equilibrium unfolding transition of DHFR proceeds through the formation of intermediates having higher exposed surface hydrophobicity, unchanged enzymatic activity and minimum changes in the secondary structural elements. Because of enhanced surface hydrophobicity, and unchanged enzymatic activity, these intermediates could be a nice target for designing drugs against DHFR.

Wideband spectrum sensing using step-sampling based on the multipath nyquist folding receiver

Wideband spectrum sensing with a high-speed analog-digital converter(ADC) presents a challenge for practical systems.The Nyquist folding receiver(NYFR) is a promising scheme for achieving cost-effective real-time spectrum sensing,which is subject to the complexity of processing the modulated outputs.In this case,a multipath NYFR architecture with a step-sampling rate for the different paths is proposed.The different numbers of digital channels for each path are designed based on the Chinese remainder theorem(CRT).Then,the detectable frequency range is divided into multiple frequency grids,and the Nyquist zone(NZ) of the input can be obtained by sensing these grids.Thus,high-precision parameter estimation is performed by utilizing the NYFR characteristics.Compared with the existing methods,the scheme proposed in this paper overcomes the challenge of NZ estimation,information damage,many computations,low accuracy,and high false alarm probability.Comparative simulation experiments verify the effectiveness of the proposed architecture in this paper.

Guided Folding of Life’s Proteins in Integrate Cells with Holographic Memory and GM-Biophysical Steering

The current geometric and thermodynamic approaches in protein folding studies do not provide a definite solution to understanding mechanisms of folding of biological proteins. A major problem is that the protein is first synthesized as a linear molecule that subsequently must reach its native configuration in an extremely short time. Hydrophobicity-hydrophilicity models and random search mechanism cannot explain folding to the 3-D functional form in less than 1 second, as it occurs in the intact cell. We propose an integral approach, based on the embedding of proteins in the whole cellular context under the postulate: a life protein is never alone. In this concept the protein molecule is influenced by various long and short distance force fields of nature such as coherent electromagnetic waves and zero-point energy. In particular, the role of solitons is reviewed in relation to a novel GM-scale biophysical principle, revealed by us. This recent finding of a set of discrete EM frequency bands, that either promote or endanger life conditions, could be a key in further studies directed at the morphogenetic aspects of protein folding in a biological evolutionary context. In addition, an alternative hypothesis is presented in which each individual cell may store integral 3-D information holographically at the virtual border of a 4-D hypersphere that surrounds each living cell, providing a field receptive memory structure that is instrumental in guiding the folding process towards coherently oscillating protein networks that are crucial for cell survival.

Conformational dynamics as an intrinsic determinant of prion protein misfolding and neurotoxicity

The prion protein(PrP) is the key molecular and pathological mediator of prion diseases,a heterogeneous group of brain disorders with fatal outcomes.Prion diseases are rare but deserve special attention because of their unique familial,sporadic,and transmissible etiologies,all caused by a single agent:misfolded conformations of PrP.

MAUN:Memory-Augmented Deep Unfolding Network for Hyperspectral Image Reconstruction

Spectral compressive imaging has emerged as a powerful technique to collect the 3D spectral information as 2D measurements.The algorithm for restoring the original 3D hyperspectral images(HSIs)from compressive measurements is pivotal in the imaging process.Early approaches painstakingly designed networks to directly map compressive measurements to HSIs,resulting in the lack of interpretability without exploiting the imaging priors.While some recent works have introduced the deep unfolding framework for explainable reconstruction,the performance of these methods is still limited by the weak information transmission between iterative stages.In this paper,we propose a Memory-Augmented deep Unfolding Network,termed MAUN,for explainable and accurate HSI reconstruction.Specifically,MAUN implements a novel CNN scheme to facilitate a better extrapolation step of the fast iterative shrinkage-thresholding algorithm,introducing an extra momentum incorporation step for each iteration to alleviate the information loss.Moreover,to exploit the high correlation of intermediate images from neighboring iterations,we customize a cross-stage transformer(CSFormer)as the deep denoiser to simultaneously capture self-similarity from both in-stage and cross-stage features,which is the first attempt to model the long-distance dependencies between iteration stages.Extensive experiments demonstrate that the proposed MAUN is superior to other state-of-the-art methods both visually and metrically.Our code is publicly available at https://github.com/HuQ1an/MAUN.

Mutation in a non-force-bearing region of protein L influences force-dependent unfolding behavior

Single-molecule magnetic tweezers(MTs) have revealed multiple transition barriers along the unfolding pathway of several two-state proteins, such as GB1 and Csp. In this study, we utilized MTs to measure the force-dependent folding and unfolding rates of both protein L(PLWT) and its Y47W mutant(PLY47W) where the mutation point is not at the force-bearing β-strands. The measurements were conducted within a force range of 3–120 pN. Notably, the unfolding rates of both PLWT and PWY47W exhibit distinct force sensitivities below 50 pN and above 60 pN, implying a two-barrier free energy landscape. Both PLWT and PLY47W share the same force-dependent folding rate and the same transition barriers,but the unfolding rate of PLY47W is faster than that of PLWT. Our finding demonstrates that the residue outside of the force-bearing region will also affect the force-induced unfolding dynamics.

Elaboration of Simplest Folding Structures in 2-Dimensional Lattice with Delta-Hemolysin and Its Variants in HP Model

Although the advanced 3-dimensional structure measurements provide more and more detailed structures in Protein Data Bank, the simplest 2-dimensional lattice model still looks meaningful because 2-dimensional structures play a complementary role with respect to 3-dimensional structures. In this study, the folding structures of delta-hemolysin and its six variants were studied at 2-dimensional lattice, and their amino acid contacts in folding structures were considered according to HP model with the aid of normalized amino acid hydrophobicity index. The results showed that: 1) either delta-hemolysin or each of its variants could find any of its folding structure in one eighth of 1,129,718,145,924 folding structures because of symmetry, which reduces the time required for folding, 2) the impact of pH on folding structures is varying and associated directly with the amino acid sequence itself, 3) the changes in folding structures of variants appeared different case by case, and 4) the assigning of hydrophobicity index to each amino acid was a way to distinguish folding structures at the same native state. This study can help to understand the structure of delta-hemolysin, and such an analysis can shed lights on NP-problem listed in millennium prize because the HP folding in lattice belongs to a sub-problem of NP-problem.

Deep learning-based LPI radar signals analysis and identification using a Nyquist Folding Receiver architecture

Nyquist Folding Receiver(NYFR)is a perceptron structure that realizes a low probability of intercept(LPI)signal analog to information.Aiming at the problem of LPI radar signal receiving,the time domain,frequency domain,and time-frequency domain problems of signals intercepted by NYFR structure are studied.Combined with the time-frequency analysis(TFA)method,a radar recognition scheme based on deep learning(DL)is introduced,which can reliably classify common LPI radar signals.First,the structure of NYFR and its characteristics in the time domain,frequency domain,and time and frequency domain are analyzed.Then,the received signal is then converted into a time-frequency image(TFI).Finally,four kinds of DL algorithms are used to classify LPI radar signals.Simulation results demonstrate the correctness of the NYFR structure,and the effectiveness of the proposed recognition method is verified by comparison experiments.

2-Dimensional HP Foldings of Dermaseptin-J2

Although the hydrophobic-polar (HP) model is a simple model to study protein folding, it is an approximation to the real-life case. Dermaseptin is a subfamily of frog skin active peptide family, which has various antimicrobial activities, and dermaseptin-J2 is a newly found peptide composed of 26 amino acids. In this study, the 2-dimensional HP model was used to analyze the foldings of dermaseptin-J2 and its nine mutants, which were converted to different HP sequences according to the normalized amino acid hydrophobicity index with respect to pH levels and the conversion of glycine as hydrophobic or polar, and each has 847,288,609,443 possible foldings. The results show that the foldings with minimal energy have different native states, which are chiral and can be numerically distinguished and ranked according to the normalized amino acid hydrophobicity index. The nine mutants of dermaseptin-J2 do not affect the minimal energy but affect their native states at pH 7. The results demonstrate that two pH levels and conversion of glycine as hydrophobic or polar affect the native state and minimal energy, suggesting these are two ways to modify dermaseptin-J2.

Geomechanical Modeling of Stress and Fracture Distribution during Contractional Fault-Related Folding

Understanding and predicting the distribution of fractures in the deep tight sandstone reservoir are important for both gas exploration and exploitation activities in Kuqa Depression. We analyzed the characteristics of regional structural evolution and paleotectonic stress setting based on acoustic emission tests and structural feature analysis. Several suites of geomechanical models and experiments were developed to analyze how the geological factors influenced and controlled the development and distribution of fractures during folding. The multilayer model used elasto-plastic finite element method to capture the stress variations and slip along bedding surfaces, and allowed large deformation. The simulated results demonstrate that this novel Quasi-Binary Method coupling composite failure criterion and geomechanical model can effectively quantitatively predict the developed area of fracture parameters in fault-related folds. High-density regions of fractures are mainly located in the fold limbs during initial folding stage, then gradually migrate from forelimb to backlimb, from limbs to hinge, from deep to shallow along with the fold uplift. Among these factors, the fold uplift and slip displacement along fault have the most important influence on distributions of fractures and stress field, meanwhile the lithology and distance to fault have also has certain influences. When the uplift height exceeds approximately 55 percent of the total height of fold the facture density reaches a peak, which conforms to typical top-graben fold type with large amplitude and high-density factures in the top. The overall simulated results match well with core observation and FMI results both in the whole geometry and fracture distribution.

Strategies to stabilize compact folding and minimize aggregation of antibody-based fragments

Monoclonal antibodies (mAbs) have proven to be useful for development of new therapeutic drugs and diagnostic techniques. To overcome the difficulties posed by their complex structure and folding, reduce undesired immunogenicity, and improve pharmacoki- netic properties, a plethora of different Ab fragments have been developed. These include recombinant Fab and Fv segments that can display improved properties over those of the original mAbs upon which they are based. Antibody (Ab) fragments such as Fabs, scFvs, diabodies, and nanobodies, all contain the variable Ig domains responsible for binding to specific antigenic epitopes, allowing for specific targeting of pathological cells and/or molecules. These fragments can be easier to produce, purify and refold than a full Ab, and due to their smaller size they can be well absorbed and distributed into target tissues. However, the physicochemical and structural properties of the immunoglobulin (Ig) domain, upon which the folding and conformation of all these Ab fragments is based, can limit the stability of Ab-based drugs. The Ig domain is fairly sensitive to unfolding and aggregation when produced out of the structural context of an intact Ab molecule. When unfolded, Ab fragments may lose their specificity as well as establish non-native interactions leading to protein aggregation. Aggregated antibody fragments display altered pharmacokinetic and immunogenic properties that can augment their toxicity. Therefore, much effort has been placed in understanding the factors impacting the stability of Ig folding at two different levels: 1) intrinsically, by studying the effects of the amino acid sequence on Ig folding;2) extrinsically, by determining the environmental conditions that may influence the stability of Ig folding. In this review we will describe the structure of the Ig domain, and the factors that impact its stability, to set the context for the different approaches currently used to achieve stable recombinant Ig domains when pursuing the development of Ab fragment-based biotechnologies.

Prediction of protein folding rates from primary sequence by fusing multiple sequential features

We have developed a web-server for predicting the folding rate of a protein based on its amino acid sequence information alone. The web- server is called Pred-PFR (Predicting Protein Folding Rate). Pred-PFR is featured by fusing multiple individual predictors, each of which is established based on one special feature derived from the protein sequence. The ensemble pre-dictor thus formed is superior to the individual ones, as demonstrated by achieving higher correlation coefficient and lower root mean square deviation between the predicted and observed results when examined by the jack-knife cross-validation on a benchmark dataset constructed recently. As a user-friendly web- server, Pred-PFR is freely accessible to the public at www.csbio.sjtu.edu.cn/bioinf/Folding Rate/.

The M3Y Double Folding Dissipative Model in Agreement with Precise Fusion Cross Sections

Large numbers of precision fusion excitation functions were fitted in the literature using the nucleus-nucleus interaction potential having the Woods-Saxon shape. The diffuseness of this potential fusion ranges from 0.75 to 1.5 fm. This is much larger than the value of 0.65 fm required by the elastic scattering data. Trying to resolve this contradiction we develop the dissipative trajectory model based on the density-dependent M3Y NN-forces folded with the nuclear matter distribution. Resulting potential possesses the normal diffuseness about 0.65 fm. With this potential we reach the agreement with the data for 16O+208Pb, 28Si+208Pb, 32S+208Pb reactions within 5%.

The Unique Folding Style in the Zagros Simply Folded Belt, the Kuh-e Qazi Anticline, South Iran

The study area is located in the Zagros Simply Folded Belt of Iran and in the interior Fars sub-basin (175 km from Persian Gulf). The Zagros fold-thrust belt is home to one of the largest petroleum producing reservoirs in the world. Structures in this area have complications and the study anticline has unique structures in the Fars region. In the study area, the Kuh-e Qazi anticline due to special fold style and rotation toward Northeast is the unique structure between anticlines of the Zagros belt. This anticline is fault bend fold and plunge of the anticline in eastern part rotated toward Northeast along with the Nezamabad fault trend. In this area, the Kuh-e Qazi anticline has asymmetric structures and some faults such as the Nezamabad and the Sarvestan strike slip fault effect on this anticline. The geometry of anticlines in the Zagros fold-thrust belt is affected by the type of deformation and mechanical behavior of stratigraphic units specially detachment units. The purpose of this research is to determine of folding pattern of the Kuh-e Qazi anticline and define structural features affected on them in the study area. This paper presents a part of the results of a regional study of the Fars province in the Zagros Simply Folded Belt, based on original fieldwork, satellite images, structural sections, geological maps and well data. Also, we use some software as Global Mapper and Tectonics FP for preparing some data.?Based on the research, which have been done, the boundary between ductile and frictional substrates causes rotation as a result of lateral, along-strike migration of the ductile substrate. The ductile or viscose layer in the study area is Hormuz Series. Due to lack or thinning of Hormuz salt over the Gavbandi basement high and in the eastern side of the Nezamabad basement fault, causes translation of strain and anticlockwise rotation in Southeast of the Kuh-e Qazi anticline toward Northwest unlike foreland basin due to the Nezamabad fault activity. This style between all of the anticlines in the study area is unique that rotates unlike foreland basin. In addition, influence on anticlockwise rotation, extensional stress has been created and then salt dome cropping out in Southeast of the Kuh-Qazi anticline. One of the best evidence for effect of extensional stress is triangular facets in this part of the study anticline. Based on folding analysis (geometry of axial plane and fold orientation), it is clearly confirmed that the translation of strain and anticlockwise rotation in Southeast of the Kuh-e Qazi anticline toward Northwest has been formed by basement fault activity as the Nezamabad fault in the boundary between ductile and frictional substrates of the study area.

Folding rate prediction using complex network analysis for proteins with two- and three-state folding kinetics

It is a challenging task to investigate the different in- fluence of long-range and short-range interactions on two-state and three-state folding kinetics of protein. The networks of the 30 two-state proteins and 15 three-state proteins were constructed by complex networks analysis at three length scales: Protein Contact Networks, Long-range Interaction Networks and Short-range Interaction Networks. To uncover the relationship between structural properties and folding kinetics of the proteins, the correlations of protein network parameters with protein folding rate and topology parameters contact order were analyzed. The results show that Protein Contact Networks and Short-range Interaction Networks (for both two-state and three-state proteins) exhibit the “small-world” property and Long-range Interaction networks indicate “scale-free” behavior. Our results further indicate that all Protein Contact Networks and Short- range Interaction networks are assortative type. While some of Long-range Interaction Networks are of assortative type, the others are of disassortative type. For two-state proteins, the clustering coefficients of Short-range Interaction Networks show prominent correlation with folding rate and contact order. The assortativity coefficients of Short-range Interaction Networks also show remarkable correlation with folding rate and contact order. Similar correlations exist in Protein Contact Networks of three-state proteins. For two-state proteins, the correlation between contact order and folding rate is determined by the numbers of local contacts. Short- range interactions play a key role in determining the connecting trend among amino acids and they impact the folding rate of two-state proteins directly. For three-state proteins, the folding rate is determined by short-range and long-range interactions among residues together.

Improvement of Artificial Foldable Wing Models by Mimicking the Unfolding/Folding Mechanism of a Beetle Hind Wing

In an attempt to realize a flapping wing micro-air vehicle with morphing wings, we report on improvements to our previousfoldable artificial hind wing.Multiple hinges, which were implemented to mimic the bending zone of a beetle hind wing, weremade of small composite hinge plates and tiny aluminum rivets.The buck-tails of rivets were flared after the hinge plates wereassembled with the rivets so that the folding/unfolding motions could be completed in less time, and the straight shape of theartificial hind wing could be maintained after fabrication.Folding and unfolding actions were triggered by electrically-activatedShape Memory Alloy (SMA) wires.For wing folding, the actuation characteristics of the SMA wire actuator were modifiedthrough heat treatment.Through a series of flapping tests, we confirmed that the artificial wings did not fold back and arbitrarilyfluctuate during the flapping motion.

Protein Folding Mediated by an Intramolecular Chaperone: Energy Landscape for Unimolecular Pro-Subtilisin E Maturation

Efficient and precise assembly of polypeptides into native functional states is critical for normal cellular processes. Understanding how a specific structure is encoded in the polypeptide sequence and what drives the structural progression to the native state is essential to deciphering the folding problem. Several prokaryotic and eukaryotic proteins require their propeptide-domains to function as dedicated intramolecular chaperones (IMCs). In this manuscript, we investigate the elementary steps in the IMC mediated maturation of Subtilisin E, a bacterial serine protease, and a prototype for the eukaryotic proprotein convertases (PCs). Through detailed analyses, we have attempted to define the unimolecular folding energy landscape for SbtE to understand how the stabilization of folding intermediates influences the maturation process, an aspect that is difficult to study in eukaryotic PCs. Our studies demonstrate that a rapid hydrophobic collapse precedes acquisition of tertiary structure during the folding of Pro-SbtE and results in formation of a molten-globule like intermediate. Induction of structure within the IMC stabilizes both the molten globule-like folding intermediate and the native state, and appears to expedite initial stages of folding, purely through thermodynamic stabilization of the folded state. While the induced structure does not affect the activation energies in the unimolecular folding reaction, it is detrimental to the autoproteolytic cleavage of the precursor and subsequent release and degradation of the inhibitory IMC-domain since both these stages require some degree of unfolding. Completion of Pro-SbtE maturation results in the formation of a kinetically trapped and extremely stable native state. Hence, our results suggest that the SbtE IMC appears to have evolved to be intrinsically unstructured and to bind with its cognate protease with a specific affinity that is critical for biological regulation.

Thermodynamic Principle Revisited: Theory of Protein Folding

Anfinsen’s thermodynamic hypothesis is reviewed and misunderstandings are clarified. It really should be called the thermodynamic principle of protein folding. Energy landscape is really just the mathematical graph of the Gibbs free energy function G(X;U ,EN), a very high dimensional hyper surface. Without knowing it any picture of the Gibbs free energy landscape has no theoretical base, including the funnel shape claims. New insight given by newly obtained analytic Gibbs free energy function G(X;U ,EN) of protein folding derived via quantum statistical mechanics are discussed. Disputes such as target-based or cause-based;what is the folding force, hydrophobic effect or hydrophilic force? Single molecule or ensemble of molecules to be used for the statistical physics study of protein folding, are discussed. Classical observations of 1970’s and 1980’s about global geometric characteristics of native structures of globular proteins turn out to have grabbed the essence of protein folding, but unfortunately have been largely forgotten.

Folding Style of the Kuh-e Siah Anticline in the Sarvestan Area, Interior Fars, Zagros, Iran

The Kuh-e Siah anticline is located in the Sarvestan area of the Fars province (186 km to Persian Gulf) and Interior Fars sub basin. This anticline is a fault bend fold and is located in the Sarvestan fault zone with Northwest-Southeast trend. The Sarvestan fault zone has caused main deformation by dextral strike slip activity in southern part of the Zagros fold-thrust belt. The main aim of this paper is to determine of fold style elements and folding pattern of the Kuh-e Siah anticline. This paper presents part of the results of a regional study of the Fars province in the Zagros Simply folded belt, based on original fieldwork, satellite images, structural sections, geological maps and well data. In addition, we used some software as Global Mapper and Tectonics FP for prepared some data. Folds, which are close sideways, are neutral and these require special attention. It is remarkable that, in all sections of the Kuh-e Siah anticline, fold type is close and in the middle part of the anticline, fold type is different with other parts. In the middle part, fold type is upright-moderately gently plunging. On the other hand, in northwestern and southeastern parts fold type is similar together. These results maybe show that fold style follow that fold sigmoidal shape that created with two-fault segment of the Sarvestan fault zone in the study area. Therefore, it seems that the Kuh-e Siah anticline has suffered high deformation in the Sarvestan fault zone and this fault zone has created shear zone.