This thesis describes the tertiary structures and dynamic studies of two protein systems. The first is human γC -crystallin protein, which is present in the nucleus of the human eye lens and the other is the plant viral protein VPg (an intrinsically disordered protein) in its free as well as its protease bound forms. The structural studies described here have been carried out using high-resolution solution NMR spectroscopic methods. Project I: Determination of solution structure and dynamics of Human γC-crystallin (HGC) using NMR spectroscopy The crystallins are the most abundant proteins in the eye lens of vertebrates. These proteins are packed in short-range spatial order to provide the transparency and appropriate refractive index gradient that are required for vision. The crystallins belong to two gene families, which are categorized as the alpha and beta/gamma crystallins respectively. The classification on the basis of molecular size and structure results in the proteins being referred to as alpha, beta and gamma crystallins. Again, each of the crystallins has two or more subtypes. The stoichiometry of the subtypes of α, β and γ crystallins varies with the age of the organism, but the order of abundance remains as β > α > γ irrespective of age. The most abundant crystallins in the nucleus (central region) of eye lens are the γ -crystallins. In the human lens, only three members of the γ− crystallin family are mainly expressed i.e. γS- (HGS), γC - (HGC) and γD - (HGD). HGS is expressed postnatally and thus is present mainly in the cortical region of the lens unlike HGC and HGD crystallins, which are present in the nucleus. It is known that aging and some cataract-associated genetic mutations alter the structure of these proteins. Other point mutations result in minimum structural perturbation but with drastically lowered solubility. Mutation in the human γC -crystallin leads to congenital cataract such as Coppock-like cataract, while structural information is available for HGD & HGS but no structure is available for HGC. However, recently a model structure has been reported for HGC based on a mouse orthologous. Based on this model structure, it was argued that HGC is an insoluble protein and was explained by lower magnitude of dipole moment and fluctuation in N-terminal domain of the model structure. However it is shown that HGC is very soluble protein. Solution structure of human γC-crystallin has been determined from an analysis of multidimensional triple resonance NMR spectroscopy using distance restraints from unambiguously assigned 1H-1H NOE peaks and dihedral angle restraints from HNHA and HNHB spectra. 15N relaxation average T1 and T2 correspond to 0.729 ± 0.02 and 0.060 ± 0.04 second from 15N backbone relaxation study, which gives average rotational correlation time 10.87 ns that shows human γC-crystallin is monomer in solution of molecular weight 21 kDa (173 residues). The ensemble of 20 lowest energy structures shows a root mean square deviation of 0.60 ± 0.12 Å for the backbone atoms, and 1.03 ± 0.09 Å for all heavy atoms. The comparison between the calculated NMR structure with backbone chain atoms C`, Cα and NH, of the x-ray crystal structure of the mouse γC - crystallin shows that the structure determined here of human γC-crystallin is very similar with an RMSD of 1.3 Å, which is not surprising given the 84.5% amino acid sequence identity between the two proteins. More importantly, the NMR structure reported here shows the subtle differences in the orientation of specific residues as well as the domain interface between the human and mouse orthologs. The orientation of the calculated dipole moment for this NMR structure differs from earlier reported for model structure. However it is similar to the other known soluble proteins. The determined solution structure of human γC-crystallin also enables us to estimate the effect of cataract-associative mutations on the structure and properties of the protein. Several such mutations are already known, and the work presented here could likely shed light on the molecular basis of these cataracts. Project II: Solution structural studies of intrinsically disordered protein VPg in free and bound forms from Sesbania mosaic virus Sesbania mosaic virus (SeMV) is a plant virus, which infects the Sesbania grandiflora tree. SeMV belongs to Sobemovirus genus, which is not defined under any family. The length of this viral genome is ~4kb. This viral genome has four open-reading frames (ORF). ORF1 and ORF2 encode movement and coat proteins, respectively. ORF2 is again split into two ORFs i.e. ORF2a and ORF2b by a -1 shift in the reading frame and encode two polypeptide chains. These polypeptide chains generate several functional proteins upon polyprotein processing. Polyprotein processing is a mechanism employed by animal and plant viruses to produce several functional proteins from a single polypeptide chain. The two polyproteins expressed are catalytically cleaved by a serine protease, thus releasing the four proteins: VPg (viral protein genome linked), RdRP (RNA dependent RNA polymerase), P10, and P8. VPg (“Viral Protein genome linked”) as its name suggests, is covalently linked to the 5` end of the viral RNA. VPgs are generally known to be intrinsically disordered proteins and have many interacting partners. Intrinsically Disordered Proteins (IDPs) are not explained by the 3D structure–function dogma. However, they are important for biological functions such as molecular recognition, signal transduction and regulation. It is known that SeMV protease becomes inactive in the absence of the VPg domain at its C-terminal. VPgs of animal viruses are well studied as compared to VPgs of plant virues. The size of VPg varies across the Sobemovirus genus. It is important to know the structure of VPg since it is necessary for protease activity. The studies conducted here focus on the structural analysis of the VPg in its free and bound forms with protease (VPg complex) as well as some aspect of full-length ProVPg. For structural studies, two constructs of VPg as fusion protein with Cytb5 tag, one lacking 23 residues at its C-terminal using the pET21a(+) plasmid vector have been designed. Sub-cloning was also done to add a thrombin recognition site to remove the hexa-His tag from new constructs of full-length ProVPg and protease (PRO). These proteins were highly expressed, isotopically labeled and purified for NMR study. The sample used for structural studies of the ProVPg 23 complex was prepared using selectively protonated Ile, Leu and Val; and isotopically labeled i.e. 2H, 13C, and 15N-VPg 23 protein. VPg in its free form is an intrinsically disordered protein and this has been confirmed by its dynamic nature observed using solution NMR spectroscopy. VPg binds to its partner protease and adopts a 3D-structure, which has been shown here. The tertiary structure has been determined using distance restraints from 1HN-1HN NOEs and methyl 1HN NOEs, and dihedral angle predicted from analysis of chemical shift values. The tertiary structure of ProVPg 23 complex has one β -sheet composed of three antiparallel β-strands and an α-helix. The ensemble of 20 lowest energy structures shows a root mean square deviation of 0.42 ± 0.09 Å for the backbone atoms, and 1.09 ± 0.11 Å for all heavy atoms for residues 15 to 50 that are primarily involved in structure formation. On the other hand RMSD is 2.34 ± 0.72 Å for the backbone and 2.55 ± 0.60 Å for all heavy atoms for all residues including both termini. That the tertiary fold of VPg both in full-length ProVPg and when complexed with protease domain (PRO) are the same has been shown here. The NMR structure reported here provides a structural basis for the origin of resonances in the up-field region of one–dimensional proton spectrum of full length ProVPg. The binding surface based on the structures of ProVPg 23 complex determined here and X-ray structure of PRO; has been determined using HADDOCK. The structural model here of full length ProVPg 23 shows the presence of aromatic interaction between Trp271 of PRO and Trp46 of VPg, which is consistent with the earlier biochemical studies.

The use of desiccant materials is crucial in many applications, such as dehumidification rotors, in OLED screen and as desiccant materials in dish washers, for example. Upsalite® is a novel, anhydrous, micro-mesoporous, and large surface area structure consisting of amorphous magnesium carbonate which has been shown to exhibit a good water sorption capacity. Depending on the heat treatment of Upsalite® after synthesis, the material exhibits different sorption capacity and hydrolytic stability. Calcined Upsalite® has a higher sorption capacity compared to as-synthesized, but crystallizes into nesquehonite when stored in a relative humidity of 100 % for several days. The need to stabilize the material arises and the use of two different aminosilanes as surface stabilizers has been evaluated. Two different deposition techniques from gas phase have been used, atomic layer deposition and vapor phase grafting, which are evaluated and compared.   The results of the functionalization show an increase in decomposition temperature by ~25 °C of the functionalized materials compared to non-functionalized. The initial water sorption capacity of the functionalized material increases by up to 80 %, when stored in a relative humidity of 100 % for 24 h and shows a stabilizing effect after five cycles of repeated exposure to high humidity. The long term stability seems to have decreased due to pore collapse, when the functionalized material is cycled 5 times for one week in a repeated relative humidity of 100 %. The stability of the material when exposed to two liquids of different pH was also evaluated and the functionalized material exhibits a slower increase of the pH in the buffer solution, implying a retardation of Upsalite® dissolution. The conclusion is that a functionalization of the material with aminosilane increases the initial sorption capacity and has a stabilizing effect.

Ces dernières années, les facteurs du complexe d'initiation de la traduction eucaryote ont été identifiés comme des déterminants essentiels dans la sensibilité des plantes aux virus à ARN, y compris les potyvirus, genre le plus important à la fois de par leur nombre et leur importance économique chez des espèces légumières, fruitières et de grandes cultures.En particulier, les allèles récessifs mo11 et mo12 du gène mo1 précédemment identifié comme codant pour le facteur d'initiation de la traduction eIF4E, sont actuellement utilisés pour protéger les cultures de laitue contre le potyvirus de la mosaïque de la laitue (LMV).Partant des résultats obtenus au laboratoire démontrant que les déterminants du LMV impliqués dans le contournement de la résistance mo1 comprennent non seulement le domaine codant pour la VPg mais aussi, en amont, l’extrémité carboxy-terminale de celui codant pour la CI, mon travail de thèse a consisté à (1) confirmer que le LMV code pour deux facteurs de virulence, la CI et la VPg (2) identifier par mutagenèse dirigée et aléatoire des acides aminés clés de la CI impliqués dans le contournement de la résistance contrôlée par eIF4E (3) entamer une caractérisation fonctionnelle des interactions impliquant les trois partenaires eIF4E, CI et VPg.Les résultats obtenus ont montré que l'échange de la VPg d'un isolat virulent (LMV-E) dans un non virulent (LMV-0) est suffisant pour restituer la compatibilité complète avec les variétés de laitue portant l'allèle mo11, mais pas mo12, alors que la région codant pour la portion C-terminale de la CI et la 6K2, suffit pour contourner les deux allèles de mo1. Le mutant ponctuel dans la CI (LMV-0-S621T) obtenu par mutagenèse dirigée est capable de contourner la résistance conférée par mo12 et partiellement celle conférée par mo11 tandis que le mutant réciproque (LMV-E-T621S) perd sa capacité à contourner les deux allèles de résistance. Il s’agit donc là du premier exemple d'un gène de CI de potyvirus, agissant comme un déterminant de contournement de la résistance récessive contrôlée par eIF4E. En effet, la VPg des potyvirus a été identifiée jusque là comme l’unique facteur de virulence vis-à-vis de eIF4E. Il semble donc que le LMV puisse utiliser deux facteurs viraux (CI et VPg) pour le contournement des allèles de résistance mo1.Cette propriété, associée au fait que des isolats de LMV d’origine sauvage ou ornementale soient capables d’évoluer vers le contournement pourraient donc présenter un risque pour la durabilité des résistances mo1. Des travaux préliminaires ont été menés lors de cette thèse afin de mieux comprendre le rôle exact des mutations des facteurs de virulence dans le processus évolutif d’adaptation du LMV aux pressions imposées par les allèles mo1.Enfin, l’implication de la CI dans le contournement de la résistance mo1 laisse supposer que cette protéine pourrait elle aussi interagir (comme la VPg), directement ou non, avec eIF4E. Nous avons montré pour la première fois in vitro et in vivo l’interaction entre la région C-terminale de la CI et la protéine eIF4E de laitue. De plus, la mutation en position 621 de la CI ayant un rôle clé dans le contournement de la résistance mo1 ne semble pas affecter ces interactions in vitro / In recent years, the factors of the eukaryotic translation initiation complex were identified as essential determinants of plant susceptibility to RNA viruses, including potyviruses, the largest and economically the most important of the plant virus groups. Members of this group are responsible for important virus diseases affecting all types of vegetable, fruit, and field crops.In particular, the recessive alleles mo11 and mo12 of mo1 gene, which previously identified as encoding for the translation initiation factor eIF4E, are currently used to protect lettuce crops against lettuce mosaic potyvirus (LMV).Based on the results obtained in the laboratory showing that the LMV determinants involved in the mo1 resistance overcoming include not only the area encoding for the VPg but also upstream, the C-terminal region of that encoding for the CI, my work of thesis consisted in (1) confirm that LMV encodes for two virulence factors, CI and VPg (2) identified by site-directed and random mutagenesis a key amino acids of the CI protein involved in eIF4E-mediated resistance overcoming (3) initiate a functional characterization of interactions involving the three partners eIF4E, VPg and CI.The results obtained showed that the exchange of VPg of a virulent isolate (LMV-E) in a non-virulent (LMV-0) is sufficient to restore full compatibility with lettuce cultivars carrying mo11 allele, but not mo12, whereas the region encoding for the C-terminal portion of the CI and 6K2, is sufficient to overcoming both mo1 alleles. The point mutation in the CI (LMV-0-S621T) obtained by site-directed mutagenesis is able to overcome the resistance conferred by mo12 and partly that conferred by mo11 while the reciprocal mutation (LMV-E-T621S) loses its ability to overcome both resistance alleles.So this is the first example of a potyvirus CI gene acting as a virulence determinant in overcoming eIF4E-mediated resistance. Indeed, the potyvirus VPg was previously identified as the sole virulence determinant vis-a-vis eIF4E. It seems that LMV can use two viral factors (CI and VPg) to overcome the mo1 resistance alleles.This property, combined with the fact that LMV isolates from the wild or ornamental origin are able to evolve towards the overcoming could therefore pose a risk to the durability of the mo1 resistance. Preliminary works were carried on during this thesis to better understand the exact role of mutations affecting virulence factors in the evolutionary process of adaptation of LMV to the pressures imposed by mo1 alleles.Finally, the involvement of the LMV CI in mo1 resistance breaking suggests that this protein could also interact (such as VPg), directly or indirectly with eIF4E. We have shown for the first time in vitro and in vivo interactions between the C-terminal region of the CI protein and the lettuce eIF4E protein. In addition, the mutation at position 621 of the CI which has a key role in mo1 resistance overcoming does not seem to affect these interactions in vitro.

Ces dernières années, les facteurs du complexe d'initiation de la traduction eucaryote ont été identifiés comme des déterminants essentiels dans la sensibilité des plantes aux virus à ARN, y compris les potyvirus, genre le plus important à la fois de par leur nombre et leur importance économique chez des espèces légumières, fruitières et de grandes cultures.En particulier, les allèles récessifs mo11 et mo12 du gène mo1 précédemment identifié comme codant pour le facteur d'initiation de la traduction eIF4E, sont actuellement utilisés pour protéger les cultures de laitue contre le potyvirus de la mosaïque de la laitue (LMV).Partant des résultats obtenus au laboratoire démontrant que les déterminants du LMV impliqués dans le contournement de la résistance mo1 comprennent non seulement le domaine codant pour la VPg mais aussi, en amont, l'extrémité carboxy-terminale de celui codant pour la CI, mon travail de thèse a consisté à (1) confirmer que le LMV code pour deux facteurs de virulence, la CI et la VPg (2) identifier par mutagenèse dirigée et aléatoire des acides aminés clés de la CI impliqués dans le contournement de la résistance contrôlée par eIF4E (3) entamer une caractérisation fonctionnelle des interactions impliquant les trois partenaires eIF4E, CI et VPg.Les résultats obtenus ont montré que l'échange de la VPg d'un isolat virulent (LMV-E) dans un non virulent (LMV-0) est suffisant pour restituer la compatibilité complète avec les variétés de laitue portant l'allèle mo11, mais pas mo12, alors que la région codant pour la portion C-terminale de la CI et la 6K2, suffit pour contourner les deux allèles de mo1. Le mutant ponctuel dans la CI (LMV-0-S621T) obtenu par mutagenèse dirigée est capable de contourner la résistance conférée par mo12 et partiellement celle conférée par mo11 tandis que le mutant réciproque (LMV-E-T621S) perd sa capacité à contourner les deux allèles de résistance. Il s'agit donc là du premier exemple d'un gène de CI de potyvirus, agissant comme un déterminant de contournement de la résistance récessive contrôlée par eIF4E. En effet, la VPg des potyvirus a été identifiée jusque là comme l'unique facteur de virulence vis-à-vis de eIF4E. Il semble donc que le LMV puisse utiliser deux facteurs viraux (CI et VPg) pour le contournement des allèles de résistance mo1.Cette propriété, associée au fait que des isolats de LMV d'origine sauvage ou ornementale soient capables d'évoluer vers le contournement pourraient donc présenter un risque pour la durabilité des résistances mo1. Des travaux préliminaires ont été menés lors de cette thèse afin de mieux comprendre le rôle exact des mutations des facteurs de virulence dans le processus évolutif d'adaptation du LMV aux pressions imposées par les allèles mo1.Enfin, l'implication de la CI dans le contournement de la résistance mo1 laisse supposer que cette protéine pourrait elle aussi interagir (comme la VPg), directement ou non, avec eIF4E. Nous avons montré pour la première fois in vitro et in vivo l'interaction entre la région C-terminale de la CI et la protéine eIF4E de laitue. De plus, la mutation en position 621 de la CI ayant un rôle clé dans le contournement de la résistance mo1 ne semble pas affecter ces interactions in vitro

Acetohydroxyacid synthase is a multisubunit enzyme that catalyses the first committed step in the biosynthesis of the branched chain amino acids viz., valine, leucine and isoleucine. In order to understand the structural basis for the observed allosteric feedback inhibition in AHAS, the regulatory subunit of AHAS isozymes I from E. coli was cloned, expressed, purified and the conditions were optimized for solution NMR spectroscopy. IlvN was found to exist as a dimer both in the presence and absence of the feedback inhibitor. Using high-resolution multidimensional, multinuclear NMR experiments, the structure of the dimeric valine-bound 22 kDa IlvN was determined. The ensemble of twenty low energy structures shows a backbone root mean square deviation of 0.73 ± 0.13 Å and a root mean square deviation of 1.16 ± 0.13 Å for all heavy atoms. Furthermore, greater than 98% of the backbone φ, ψ dihedral angles occupy the allowed and additionally allowed regions of the Ramachandran map. Each protomer exhibits a βαββαβα topology that is a characteristic feature of the ACT domain fold that is observed in regulatory domains of metabolic enzymes. In the free form, IlvN exists as a mixture of conformational states that are in intermediate exchange on the NMR timescale. Important structural properties of the unliganded state were probed by H-D exchange studies by NMR, alkylation studies by mass spectrometry and other biophysical methods. It was observed that the dynamic unliganded IlvN underwent a coil-to-helix transition upon binding the effector molecule and this inherent conformational flexibility was important for activation and valine-binding. A mechanism for allosteric regulation in the AHAS holoenzyme was proposed. Study of the structural and conformational properties of IlvN enabled a better understanding of the mechanism of regulation of branched chain amino acid biosynthesis. Solution structural studies of 32 kDa Protease-VPg (PVPg) from Sesbania mosaic virus (SeMV) Polyprotein processing is a commonly found mechanism in animal and plant viruses, by which more than one functional protein is produced from the same polypeptide chain. In Sesbania Mosaic Virus (SeMV), two polyproteins are expressed that are catalytically cleaved by a serine protease. The VPg protein that is expressed as a part of the polyprotein is an intrinsically disordered protein (by recombinant expression) that binds to various partners to perform several vital functions. The viral protease (Pro), though possessing the necessary catalytic residues and the substrate binding pocket is unable to catalyse the cleavage reactions without the VPg domain fused at the C-terminus. In order to determine the structural basis for the aforementioned activation of protease by VPg I undertook the structural studies of the 32 kDa PVPg domains of SeMV by solution NMR spectroscopy. NMR studies on this protein were a challenge due to the large size and spectral overlap. Using a combination of methods such as deuteration, TROSY-enhanced NMR experiments and selective ‘reverse-labelling’, the sequence specific assignments were completed for ~80% of the backbone and 13C nuclei. NMR studies on mutants such as the C-terminal deletion mutant, I/L/V to A mutants in VPg domain were conducted in order to identify the residues important for aliphatic-aromatic interactions observed in PVPg. Attempts were made to obtain NOE restraints between Pro and VPg domains through ILV labelled samples; however these proved unsuccessful. It was observed that ‘natively unfolded’ VPg possessed both secondary and tertiary structure in PVPg. However, 30 residues at the C-terminus were found to be flexible. Even though atomic-resolution structure could not be determined, the region of interaction between the domains was determined by comparing NMR spectra of Pro and PVPg. The conditions for reconstitution of the Protease-VPg complex by recombinantly expressed Pro and VPg proteins were standardised. These studies lay the foundation for future structural investigations into the Protease-VPg complex.

In the present thesis, two positive sense single-stranded RNA viruses have been used as models to understand the structure and function of viral-encoded proteins. One of them, Pepper Vein Banding Virus (PVBV; genus Potyvirus; family Potyviridae) is a flexuous, rod-shaped virus that encodes for a polyprotein of size ~340 kDa. The polyprotein undergoes proteolytic processing by viral-encoded proteases, of which Nuclear Inclusion-a Protease (NIa-Pro) is the major protease. It is a serine-like cysteine protease which cleaves between a Q/A or Q/S, present in the context of the heptapeptide recognition sequence. The temporal regulation of intermediates and mature proteins released by NIa-Pro cleavage is crucial for a successful infection. In the present study, histidine-tagged NIa-Pro, Viral Protein genome-linked (VPg), and the cleavage site mutant (E191A) VPg-Pro were over-expressed in E. coli and purified. The protease activity of NIa-Pro was monitored using an HPLC-based protease assay developed using a peptide substrate. NIa-Pro protease activity was found to get modulated upon interaction with VPg and upon undergoing phosphorylation. Both these events have been found to involve the face of NIa-Pro which contains the solvent-exposed Trp143. Mutational studies and molecular dynamics analyses provide evidence that this residue is buried upon interaction of NIa-Pro with VPg, and any perturbation of its orientation influences the active site Cys151 via an extensive interaction network. This interaction was found to enhance the velocity of NIa-Pro protease activity, especially if the two domains were present in trans (VPg+Pro). In addition, the main-chain –NH2 group of Trp143 was found to be hydrogen-bonded to the side chain –OH group of Ser129, the residue which was identified to undergo phosphorylation by host plant kinases. Interestingly, when the two domains were present in cis (E191A VPg-Pro), no phosphorylation was observed. Mutations of Ser129 (to phosphorylation-mimic Asp or phosphorylation-deficient Ala residues) which affected this H-bond were found to disturb Trp143 and Cys151 orientation, which drastically reduced the protease activity of NIa-Pro. Within the polyprotein, VPg is present at the N-terminus of NIa-Pro and the cleavage site between them is suboptimal (E/A). In the present study, VPg-Pro was shown to be covalently linked to the genomic RNA present in the virions. Interestingly, during purification, VPg could only be purified from the soluble when it was expressed at the N-terminus of NIa-Pro. A series of bioinformatics and biophysical analysis of VPg showed that PVBV VPg, like other potyviral VPgs, exists as a molten-globule. Moreover, while VPg was shown to harbour the Walker motifs, it was found to exhibit an ATPase activity only when it was present with the NIa-Pro (especially in cis). Lys47 and Asp88:Glu89 were found crucial for optimal activity. Over all the results demonstrated that there is a reciprocal modulation of structure and function of the VPg and NIa-Pro domains. These results can explain the possible significance of an impeded cleavage rate between the two domains of VPg-Pro during PVBV infection. The precursor, VPg-Pro, could offer the advantage of evading the inhibitory phosphorylation of NIa-Pro by the host, as well as drive certain viral processes by virtue of its ATPase activity. And subsequent cleavage of the domains and their trans interaction could offer a higher turnover rate which might assist sufficient CP production required for viral morphogenesis. Another virus, Tobacco Streak Virus (TSV) that belongs to the Ilarvirus genus of the Bromoviridae family is a spherical virus which forms pleiomorphic icosahedral virus particles. It has a tripartite genome and each RNA is encapsidated individually. In the present thesis, TSV was used as a model to understand the properties of its structural protein-the coat protein (CP), with the aim of deciphering TSV assembly process. Thus, the CP gene from TSV RNA 3 was cloned and over-expressed in E. coli. The coat protein thus expressed formed virus-like particles (VLPs), which could be disassembled into dimers using high CaCl2 concentrations. Reassembly of VLPs was possible from dimers even in the absence of any nucleic acid. Mutational analysis of the N-terminal disordered domain showed that 26 amino acid residues from the amino-terminus could be crucial for capsid heterogeneity while, zinc-binding domain was essential for assembly. Overall, the present study shows that the flexible W-C loop of PVBV NIa-Pro, the disordered N-terminal region of PVBV VPg and the disordered N-terminal region of TSV CP harbour residues crucial for regulation of protein function. Such regulatory elements would ultimately allow viruses to maintain a smaller protein number, and thus a smaller genome size.

Approved for public release, distribution is unlimited / This thesis attempts to create a desire for change in DoD's current approach to Network Application Management (NAM). The evolution of NAM into Integrated Network Application Management (INAM) is a crucial component of Network Centric Warfare and achieving Information Superiority and Interoperability. INAM is outlined as three functional requirements, which are Network Awareness, Mission Prioritization linkage to Network Resources, and the Balancing of Service Management. Scenarios play a key role in illustrating the new threats that DoD faces today. These scenarios also identify limitations and challenges to NAM as it exists today. These challenges require significant improvements in flexibility and responsiveness, while providing for wide integration. Trends supporting change are identified in this thesis. Two of the more important trends are the rise of Architectural and Object Oriented Development. Examples such as Training and Testing Enabled Architecture (TENA), Surveillance and Target Acquisition Network (STAN), and Virtual Proving Ground (VPG) are clear examples of these trends. The merging of the Computer Industry's efforts to expand the reach of Operating Systems with the traditional efforts from Network Management is also a trend that is examined. Organizations like Distributed Management Task Force (DMTF) are important to such examinations. Successful change can not be achieved without planning for the transition. This thesis also presents some active transition efforts addressing Network Centric Warfare. TENA, VPG and Naval Postgraduate School's Information Technology Management Master's Program provide three examples of addressing transition in DoD. / Civilian, United States Army Yuma Proving Ground